# define source subdirectories
SUBDIRS = $(SRC_DIR)/api \
$(SRC_DIR)/utils \
- $(SRC_DIR)/toolkit
+ $(SRC_DIR)/third_party \
+ $(SRC_DIR)/toolkit
all:
@echo "Building BamTools:"
@echo "Version: $$BAMTOOLS_VERSION"
@echo "========================================================="
-
- mkdir -p $(BIN_DIR)
- mkdir -p $(OBJ_DIR)
-
+ @echo ""
+ @echo "- Creating target directories"
+ @mkdir -p $(BIN_DIR)
+ @mkdir -p $(OBJ_DIR)
+ @echo ""
@for dir in $(SUBDIRS); do \
echo "- Building in $$dir"; \
$(MAKE) --no-print-directory -C $$dir; \
BamTools: a C++ API & toolkit for reading/writing/manipulating BAM files.
-I. Introduction
- a. The API
- b. The Toolkit
+I. Introduction
+ a. The API
+ b. The Toolkit
-II. Usage
- a. The API
- b. The Toolkit
+II. Usage
+ a. The API
+ b. The Toolkit
-III. Contact
+III. License
+
+IV. Acknowledgements
+
+V. Contact
------------------------------------------------------------
I. Introduction:
+
BamTools provides both a programmer's API and an end-user's toolkit for handling
BAM files.
-Ia. The API
+
+Ia. The API:
+
The API consists of 2 main modules - BamReader and BamWriter. As you would expect,
-BamReader provides read-access to BAM files, while BamWriter does the writing of BAM
-files. BamReader provides an interface for random-access (jumping) in a BAM file,
+BamReader provides read-access to BAM files, while BamWriter handles writing data to
+BAM files. BamReader provides an interface for random-access (jumping) in a BAM file,
as well as generating BAM index files.
BamMultiReader is an extra module that allows you to manage multiple open BAM file
for reading. It provides some validation & bookkeeping under the hood to keep all
-files sync'ed for
-
-An additional file, BamAux.h, is included as well.
-This file contains the common data structures and typedefs used throught the API.
+files sync'ed up for you.
-BGZF.h & BGZF.cpp contain our implementation of the Broad Institute's
-BGZF compression format.
+Additional files used by the API:
+ - BamAux.h : contains the common data structures and typedefs used throught the API.
+ - BamIndex.* : implements both the standard BAM format index (".bai") as well as a
+ new BamTools-specific index (".bti").
+ - BGZF.* : contains our implementation of the Broad Institute's BGZF compression format.
-Ib. The Toolkit
-If you've been using BamTools since the early days, you'll notice that our 'toy' API
-examples (BamConversion, BamDump, and BamTrim) are now gone. In their place is a set
-of features we hope you find useful.
+Ib. The Toolkit:
-** More explanation here **
+If you've been using the BamTools since the early days, you'll notice that our 'toy' API
+examples (BamConversion, BamDump, BamTrim,...) are now gone. We dumped these in favor of
+a suite of small utilities that we hope both developers and end-users find useful:
usage: bamtools [--help] COMMAND [ARGS]
Available bamtools commands:
convert Converts between BAM and a number of other formats
- count Prints number of alignments in BAM file
+ count Prints number of alignments in BAM file(s)
coverage Prints coverage statistics from the input BAM file
filter Filters BAM file(s) by user-specified criteria
header Prints BAM header information
index Generates index for BAM file
merge Merge multiple BAM files into single file
- sam Prints the BAM file in SAM (text) format
+ random Select random alignments from existing BAM file(s)
sort Sorts the BAM file according to some criteria
- stats Prints some basic statistics from the input BAM file
+ stats Prints some basic statistics from input BAM file(s)
See 'bamtools help COMMAND' for more information on a specific command.
To use this API, you simply need to do 3 things:
- 1 - Drop the BamTools files somewhere the compiler can find them.
- (i.e. in your source tree, or somewhere else in your include path)
+ 1 - Drop the BamTools API files somewhere the compiler can find them.
+ (i.e. in your project's source tree, or somewhere else in your include path)
2 - Import BamTools API with the following lines of code
- #include "BamReader.h" // as needed
+ #include "BamReader.h" // or "BamMultiReader.h", as needed
#include "BamWriter.h" // as needed
using namespace BamTools;
3 - Compile with '-lz' ('l' as in Lima) to access ZLIB compression library
- (For VS users, I can provide you zlib headers - just contact me).
+ (For MSVC users, I can provide you modified zlib headers - just contact me).
See any included programs and Makefile for more specific compiling/usage examples.
See comments in the header files for more detailed API documentation.
------------------------------------------------------------
-III. Contact :
+III. License :
+
+Both the BamTools API and toolkit are released under the MIT License.
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
+See file LICENSE for details.
+
+------------------------------------------------------------
+
+IV. Acknowledgements :
+
+ * Aaron Quinlan for several key feature ideas and bug fix contributions
+ * Baptiste Lepilleur for the public-domain JSON parser (JsonCPP)
+ * Heng Li, author of SAMtools - the original C-language BAM API/toolkit.
+
+------------------------------------------------------------
+
+V. Contact :
Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
- Derek Barnett
Email: barnetde@bc.edu
Project Websites: http://github.com/pezmaster31/bamtools (ACTIVE SUPPORT)
http://sourceforge.net/projects/bamtools (major updates only)
+
// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 27 July 2010 (DB)\r
+// Last modified: 3 September 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Provides the basic constants, data structures, etc. for using BAM files\r
// ***************************************************************************\r
\r
// C++ includes\r
#include <exception>\r
+#include <fstream>\r
+#include <iostream>\r
#include <map>\r
#include <string>\r
#include <utility>\r
SwapEndian_64(value);\r
}\r
\r
+inline bool FileExists(const std::string& filename) {\r
+ std::ifstream f(filename.c_str(), std::ifstream::in);\r
+ return !f.fail();\r
+}\r
+\r
// ----------------------------------------------------------------\r
// BamAlignment member methods\r
\r
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 17 August 2010 (DB)
+// Last modified: 3 September 2010 (DB)
// ---------------------------------------------------------------------------
// Provides index functionality - both for the default (standardized) BAM
// index format (.bai) as well as a BamTools-specific (nonstandard) index
#include <cstdio>
#include <cstdlib>
#include <algorithm>
-// #include <iostream>
#include <map>
#include "BamIndex.h"
#include "BamReader.h"
// #########################################################################################
// -------------------------------
-// BamDefaultIndex structs & typedefs
+// BamStandardIndex structs & typedefs
namespace BamTools {
// --------------------------------------------------
-// BamDefaultIndex data structures & typedefs
+// BamStandardIndex data structures & typedefs
struct Chunk {
// data members
{ }
};
-typedef vector<ReferenceIndex> BamDefaultIndexData;
+typedef vector<ReferenceIndex> BamStandardIndexData;
} // namespace BamTools
// -------------------------------
-// BamDefaultIndex implementation
+// BamStandardIndex implementation
-struct BamDefaultIndex::BamDefaultIndexPrivate {
+struct BamStandardIndex::BamStandardIndexPrivate {
// -------------------------
// data members
- BamDefaultIndexData m_indexData;
- BamDefaultIndex* m_parent;
+ BamStandardIndexData m_indexData;
+ BamStandardIndex* m_parent;
// -------------------------
// ctor & dtor
- BamDefaultIndexPrivate(BamDefaultIndex* parent) : m_parent(parent) { }
- ~BamDefaultIndexPrivate(void) { }
+ BamStandardIndexPrivate(BamStandardIndex* parent) : m_parent(parent) { }
+ ~BamStandardIndexPrivate(void) { m_indexData.clear(); }
// -------------------------
// internal methods
};
-BamDefaultIndex::BamDefaultIndex(BgzfData* bgzf, BamReader* reader, bool isBigEndian)
+BamStandardIndex::BamStandardIndex(BgzfData* bgzf, BamReader* reader, bool isBigEndian)
: BamIndex(bgzf, reader, isBigEndian)
{
- d = new BamDefaultIndexPrivate(this);
+ d = new BamStandardIndexPrivate(this);
}
-BamDefaultIndex::~BamDefaultIndex(void) {
- d->m_indexData.clear();
+BamStandardIndex::~BamStandardIndex(void) {
delete d;
d = 0;
}
// calculate bins that overlap region
-int BamDefaultIndex::BamDefaultIndexPrivate::BinsFromRegion(const BamRegion& region, const bool isRightBoundSpecified, uint16_t bins[MAX_BIN]) {
+int BamStandardIndex::BamStandardIndexPrivate::BinsFromRegion(const BamRegion& region, const bool isRightBoundSpecified, uint16_t bins[MAX_BIN]) {
// get region boundaries
uint32_t begin = (unsigned int)region.LeftPosition;
return i;
}
-bool BamDefaultIndex::Build(void) {
+bool BamStandardIndex::Build(void) {
// be sure reader & BGZF file are valid & open for reading
if ( m_reader == 0 || m_BGZF == 0 || !m_BGZF->IsOpen )
// update saveRefID
saveRefID = bAlignment.RefID;
- // if invalid RefID, break out (why?)
- if ( saveRefID < 0 ) { break; }
+ // if invalid RefID, break out
+ if ( saveRefID < 0 ) break;
}
// make sure that current file pointer is beyond lastOffset
// iterate through references in index
// store whether reference has data &
// sort offsets in linear offset vector
- BamDefaultIndexData::iterator indexIter = d->m_indexData.begin();
- BamDefaultIndexData::iterator indexEnd = d->m_indexData.end();
+ BamStandardIndexData::iterator indexIter = d->m_indexData.begin();
+ BamStandardIndexData::iterator indexEnd = d->m_indexData.end();
for ( int i = 0; indexIter != indexEnd; ++indexIter, ++i ) {
// get reference index data
return m_reader->Rewind();
}
-bool BamDefaultIndex::GetOffsets(const BamRegion& region, const bool isRightBoundSpecified, vector<int64_t>& offsets) {
+bool BamStandardIndex::GetOffsets(const BamRegion& region, const bool isRightBoundSpecified, vector<int64_t>& offsets) {
// calculate which bins overlap this region
uint16_t* bins = (uint16_t*)calloc(MAX_BIN, 2);
map<uint32_t, ChunkVector>::const_iterator binIter = binMap.find(binKey);
if ( (binIter != binMap.end()) && ((*binIter).first == binKey) ) {
+ // iterate over chunks
const ChunkVector& chunks = (*binIter).second;
std::vector<Chunk>::const_iterator chunksIter = chunks.begin();
std::vector<Chunk>::const_iterator chunksEnd = chunks.end();
}
// saves BAM bin entry for index
-void BamDefaultIndex::BamDefaultIndexPrivate::InsertBinEntry(BamBinMap& binMap,
+void BamStandardIndex::BamStandardIndexPrivate::InsertBinEntry(BamBinMap& binMap,
const uint32_t& saveBin,
const uint64_t& saveOffset,
const uint64_t& lastOffset)
}
// saves linear offset entry for index
-void BamDefaultIndex::BamDefaultIndexPrivate::InsertLinearOffset(LinearOffsetVector& offsets,
+void BamStandardIndex::BamStandardIndexPrivate::InsertLinearOffset(LinearOffsetVector& offsets,
const BamAlignment& bAlignment,
const uint64_t& lastOffset)
{
}
}
-bool BamDefaultIndex::Load(const string& filename) {
+bool BamStandardIndex::Load(const string& filename) {
// open index file, abort on error
FILE* indexStream = fopen(filename.c_str(), "rb");
// get number of reference sequences
uint32_t numRefSeqs;
elementsRead = fread(&numRefSeqs, 4, 1, indexStream);
- if ( m_isBigEndian ) { SwapEndian_32(numRefSeqs); }
+ if ( m_isBigEndian ) SwapEndian_32(numRefSeqs);
- // intialize space for BamDefaultIndexData data structure
+ // intialize space for BamStandardIndexData data structure
d->m_indexData.reserve(numRefSeqs);
// iterate over reference sequences
// get number of bins for this reference sequence
int32_t numBins;
elementsRead = fread(&numBins, 4, 1, indexStream);
- if ( m_isBigEndian ) { SwapEndian_32(numBins); }
+ if ( m_isBigEndian ) SwapEndian_32(numBins);
if ( numBins > 0 ) {
RefData& refEntry = m_references[i];
binMap.insert( pair<uint32_t, ChunkVector>(binID, regionChunks) );
}
+ // -----------------------------------------------------
// load linear index for this reference sequence
// get number of linear offsets
int32_t numLinearOffsets;
elementsRead = fread(&numLinearOffsets, 4, 1, indexStream);
- if ( m_isBigEndian ) { SwapEndian_32(numLinearOffsets); }
+ if ( m_isBigEndian ) SwapEndian_32(numLinearOffsets);
// intialize LinearOffsetVector
LinearOffsetVector offsets;
for ( int j = 0; j < numLinearOffsets; ++j ) {
// read a linear offset & store
elementsRead = fread(&linearOffset, 8, 1, indexStream);
- if ( m_isBigEndian ) { SwapEndian_64(linearOffset); }
+ if ( m_isBigEndian ) SwapEndian_64(linearOffset);
offsets.push_back(linearOffset);
}
}
// merges 'alignment chunks' in BAM bin (used for index building)
-void BamDefaultIndex::BamDefaultIndexPrivate::MergeChunks(void) {
+void BamStandardIndex::BamStandardIndexPrivate::MergeChunks(void) {
// iterate over reference enties
- BamDefaultIndexData::iterator indexIter = m_indexData.begin();
- BamDefaultIndexData::iterator indexEnd = m_indexData.end();
+ BamStandardIndexData::iterator indexIter = m_indexData.begin();
+ BamStandardIndexData::iterator indexEnd = m_indexData.end();
for ( ; indexIter != indexEnd; ++indexIter ) {
// get BAM bin map for this reference
// get chunk vector for this bin
ChunkVector& binChunks = (*binIter).second;
- if ( binChunks.size() == 0 ) { continue; }
+ if ( binChunks.size() == 0 ) continue;
ChunkVector mergedChunks;
mergedChunks.push_back( binChunks[0] );
// writes in-memory index data out to file
// N.B. - (this is the original BAM filename, method will modify it to use applicable extension)
-bool BamDefaultIndex::Write(const std::string& bamFilename) {
+bool BamStandardIndex::Write(const std::string& bamFilename) {
string indexFilename = bamFilename + ".bai";
FILE* indexStream = fopen(indexFilename.c_str(), "wb");
// write number of reference sequences
int32_t numReferenceSeqs = d->m_indexData.size();
- if ( m_isBigEndian ) { SwapEndian_32(numReferenceSeqs); }
+ if ( m_isBigEndian ) SwapEndian_32(numReferenceSeqs);
fwrite(&numReferenceSeqs, 4, 1, indexStream);
// iterate over reference sequences
- BamDefaultIndexData::const_iterator indexIter = d->m_indexData.begin();
- BamDefaultIndexData::const_iterator indexEnd = d->m_indexData.end();
+ BamStandardIndexData::const_iterator indexIter = d->m_indexData.begin();
+ BamStandardIndexData::const_iterator indexEnd = d->m_indexData.end();
for ( ; indexIter != indexEnd; ++ indexIter ) {
// get reference index data
// write number of bins
int32_t binCount = binMap.size();
- if ( m_isBigEndian ) { SwapEndian_32(binCount); }
+ if ( m_isBigEndian ) SwapEndian_32(binCount);
fwrite(&binCount, 4, 1, indexStream);
// iterate over bins
const ChunkVector& binChunks = (*binIter).second;
// save BAM bin key
- if ( m_isBigEndian ) { SwapEndian_32(binKey); }
+ if ( m_isBigEndian ) SwapEndian_32(binKey);
fwrite(&binKey, 4, 1, indexStream);
// save chunk count
int32_t chunkCount = binChunks.size();
- if ( m_isBigEndian ) { SwapEndian_32(chunkCount); }
+ if ( m_isBigEndian ) SwapEndian_32(chunkCount);
fwrite(&chunkCount, 4, 1, indexStream);
// iterate over chunks
// write linear offsets size
int32_t offsetSize = offsets.size();
- if ( m_isBigEndian ) { SwapEndian_32(offsetSize); }
+ if ( m_isBigEndian ) SwapEndian_32(offsetSize);
fwrite(&offsetSize, 4, 1, indexStream);
// iterate over linear offsets
// write linear offset value
uint64_t linearOffset = (*offsetIter);
- if ( m_isBigEndian ) { SwapEndian_64(linearOffset); }
+ if ( m_isBigEndian ) SwapEndian_64(linearOffset);
fwrite(&linearOffset, 8, 1, indexStream);
}
}
// if block is full, get offset for next block, reset currentBlockCount
if ( currentBlockCount == d->m_blockSize ) {
-
d->m_indexData.push_back( BamToolsIndexEntry(blockStartOffset, blockStartId, blockStartPosition) );
blockStartOffset = m_BGZF->Tell();
currentBlockCount = 0;
}
// no index was found
- if ( previousOffset == -1 )
- return false;
+ if ( previousOffset == -1 ) return false;
// store offset & return success
offsets.push_back(previousOffset);
// read in block size
elementsRead = fread(&d->m_blockSize, sizeof(d->m_blockSize), 1, indexStream);
- if ( m_isBigEndian ) { SwapEndian_32(d->m_blockSize); }
+ if ( m_isBigEndian ) SwapEndian_32(d->m_blockSize);
// read in number of offsets
uint32_t numOffsets;
elementsRead = fread(&numOffsets, sizeof(numOffsets), 1, indexStream);
- if ( m_isBigEndian ) { SwapEndian_32(numOffsets); }
+ if ( m_isBigEndian ) SwapEndian_32(numOffsets);
// reserve space for index data
d->m_indexData.reserve(numOffsets);
// write block size
int32_t blockSize = d->m_blockSize;
- if ( m_isBigEndian ) { SwapEndian_32(blockSize); }
+ if ( m_isBigEndian ) SwapEndian_32(blockSize);
fwrite(&blockSize, sizeof(blockSize), 1, indexStream);
// write number of offset entries
uint32_t numOffsets = d->m_indexData.size();
- if ( m_isBigEndian ) { SwapEndian_32(numOffsets); }
+ if ( m_isBigEndian ) SwapEndian_32(numOffsets);
fwrite(&numOffsets, sizeof(numOffsets), 1, indexStream);
// iterate over offset entries
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 17 August 2010 (DB)
+// Last modified: 3 September 2010 (DB)
// ---------------------------------------------------------------------------
-// Provides index functionality - both for the default (standardized) BAM
-// index format (.bai) as well as a BamTools-specific (nonstandard) index
-// format (.bti).
+// Provides index functionality - both for the standardized BAM index format
+// (".bai") as well as a BamTools-specific (nonstandard) index format (".bti").
// ***************************************************************************
#ifndef BAM_INDEX_H
#define BAM_INDEX_H
+#include <iostream>
#include <string>
#include <vector>
#include "BamAux.h"
// BamIndex base class
class BamIndex {
+ // ctor & dtor
public:
- BamIndex(BamTools::BgzfData* bgzf,
- BamTools::BamReader* reader,
- bool isBigEndian);
+ BamIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* reader, bool isBigEndian);
virtual ~BamIndex(void) { }
+ // index interface
public:
// creates index data (in-memory) from current reader data
virtual bool Build(void) =0;
+ // returns supported file extension
+ virtual const std::string Extension(void) const =0;
// calculates offset(s) for a given region
virtual bool GetOffsets(const BamTools::BamRegion& region, const bool isRightBoundSpecified, std::vector<int64_t>& offsets) =0;
- // loads existing data from file into memory
- virtual bool Load(const std::string& filename) =0;
// returns whether reference has alignments or no
virtual bool HasAlignments(const int& referenceID);
+ // loads existing data from file into memory
+ virtual bool Load(const std::string& filename) =0;
// writes in-memory index data out to file
// N.B. - (this is the original BAM filename, method will modify it to use applicable extension)
virtual bool Write(const std::string& bamFilename) =0;
+ // factory methods for returning proper BamIndex-derived type based on available index files
+ public:
+
+ // returns index based on BAM filename 'stub'
+ // checks first for preferred type, returns that type if found
+ // (if not found, attmempts to load other type(s), returns 0 if NONE found)
+ //
+ // ** default preferred type is BamToolsIndex ** use this anytime it exists
+ enum PreferredIndexType { BAMTOOLS = 0, STANDARD };
+ static BamIndex* FromBamFilename(const std::string& bamFilename,
+ BamTools::BgzfData* bgzf,
+ BamTools::BamReader* reader,
+ bool isBigEndian,
+ const BamIndex::PreferredIndexType& type = BamIndex::BAMTOOLS);
+
+ // returns index based on explicitly named index file (or 0 if not found)
+ static BamIndex* FromIndexFilename(const std::string& indexFilename,
+ BamTools::BgzfData* bgzf,
+ BamTools::BamReader* reader,
+ bool isBigEndian);
+
+ // data members
protected:
BamTools::BgzfData* m_BGZF;
BamTools::BamReader* m_reader;
};
// --------------------------------------------------
-// BamDefaultIndex class
+// BamStandardIndex class
//
-// implements default (per SAM/BAM spec) index file ops
-class BamDefaultIndex : public BamIndex {
+// implements standardized (per SAM/BAM spec) index file ops
+class BamStandardIndex : public BamIndex {
// ctor & dtor
public:
- BamDefaultIndex(BamTools::BgzfData* bgzf,
+ BamStandardIndex(BamTools::BgzfData* bgzf,
BamTools::BamReader* reader,
bool isBigEndian);
- ~BamDefaultIndex(void);
+ ~BamStandardIndex(void);
// interface (implements BamIndex virtual methods)
public:
// creates index data (in-memory) from current reader data
bool Build(void);
+ // returns supported file extension
+ const std::string Extension(void) const { return std::string(".bai"); }
// calculates offset(s) for a given region
bool GetOffsets(const BamTools::BamRegion& region, const bool isRightBoundSpecified, std::vector<int64_t>& offsets);
// loads existing data from file into memory
// internal implementation
private:
- struct BamDefaultIndexPrivate;
- BamDefaultIndexPrivate* d;
+ struct BamStandardIndexPrivate;
+ BamStandardIndexPrivate* d;
};
// --------------------------------------------------
public:
// creates index data (in-memory) from current reader data
bool Build(void);
+ // returns supported file extension
+ const std::string Extension(void) const { return std::string(".bti"); }
// calculates offset(s) for a given region
bool GetOffsets(const BamTools::BamRegion& region, const bool isRightBoundSpecified, std::vector<int64_t>& offsets);
// loads existing data from file into memory
BamToolsIndexPrivate* d;
};
+// --------------------------------------------------
+// BamIndex factory methods
+//
+// return proper BamIndex-derived type based on available index files
+
+inline
+BamIndex* BamIndex::FromBamFilename(const std::string& bamFilename,
+ BamTools::BgzfData* bgzf,
+ BamTools::BamReader* reader,
+ bool isBigEndian,
+ const BamIndex::PreferredIndexType& type)
+{
+ // ---------------------------------------------------
+ // attempt to load preferred type first
+
+ const std::string bamtoolsIndexFilename = bamFilename + ".bti";
+ const bool bamtoolsIndexExists = BamTools::FileExists(bamtoolsIndexFilename);
+ if ( (type == BamIndex::BAMTOOLS) && bamtoolsIndexExists )
+ return new BamToolsIndex(bgzf, reader, isBigEndian);
+
+ const std::string standardIndexFilename = bamFilename + ".bai";
+ const bool standardIndexExists = BamTools::FileExists(standardIndexFilename);
+ if ( (type == BamIndex::STANDARD) && standardIndexExists )
+ return new BamStandardIndex(bgzf, reader, isBigEndian);
+
+ // ----------------------------------------------------
+ // preferred type could not be found, try other (non-preferred) types
+ // if none found, return 0
+
+ if ( bamtoolsIndexExists ) return new BamToolsIndex(bgzf, reader, isBigEndian);
+ if ( standardIndexExists ) return new BamStandardIndex(bgzf, reader, isBigEndian);
+ return 0;
+}
+
+inline
+BamIndex* BamIndex::FromIndexFilename(const std::string& indexFilename,
+ BamTools::BgzfData* bgzf,
+ BamTools::BamReader* reader,
+ bool isBigEndian)
+{
+ // see if specified file exists
+ const bool indexExists = BamTools::FileExists(indexFilename);
+ if ( !indexExists ) return 0;
+
+ const std::string bamtoolsIndexExtension(".bti");
+ const std::string standardIndexExtension(".bai");
+
+ // if has bamtoolsIndexExtension
+ if ( indexFilename.find(bamtoolsIndexExtension) == (indexFilename.length() - bamtoolsIndexExtension.length()) )
+ return new BamToolsIndex(bgzf, reader, isBigEndian);
+
+ // if has standardIndexExtension
+ if ( indexFilename.find(standardIndexExtension) == (indexFilename.length() - standardIndexExtension.length()) )
+ return new BamStandardIndex(bgzf, reader, isBigEndian);
+
+ // otherwise, unsupported file type
+ return 0;
+}
+
} // namespace BamTools
-#endif // BAM_INDEX_H
\ No newline at end of file
+#endif // BAM_INDEX_H
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 20 July 2010 (DB)
+// Last modified: 3 September 2010 (DB)
// ---------------------------------------------------------------------------
// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
// Institute.
// C++ includes
#include <algorithm>
+#include <fstream>
+#include <iostream>
#include <iterator>
+#include <sstream>
#include <string>
#include <vector>
-#include <iostream>
-#include <sstream>
// BamTools includes
#include "BGZF.h"
// destructor
BamMultiReader::~BamMultiReader(void) {
- Close(); // close the bam files
- // clean up reader objects
- for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
- delete it->first;
- delete it->second;
- }
+ Close();
}
// close the BAM files
void BamMultiReader::Close(void) {
+
+ // close all BAM readers and clean up pointers
+ vector<pair<BamReader*, BamAlignment*> >::iterator readerIter = readers.begin();
+ vector<pair<BamReader*, BamAlignment*> >::iterator readerEnd = readers.end();
+ for ( ; readerIter != readerEnd; ++readerIter) {
+
+ BamReader* reader = (*readerIter).first;
+ BamAlignment* alignment = (*readerIter).second;
+
+ // close the reader
+ if ( reader) reader->Close();
+
+ // delete reader pointer
+ delete reader;
+ reader = 0;
+
+ // delete alignment pointer
+ delete alignment;
+ alignment = 0;
+ }
+
+ // clear out the container
+ readers.clear();
+}
+
+// saves index data to BAM index files (".bai"/".bti") where necessary, returns success/fail
+bool BamMultiReader::CreateIndexes(bool useDefaultIndex) {
+ bool result = true;
for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
BamReader* reader = it->first;
- reader->Close(); // close the reader
+ result &= reader->CreateIndex(useDefaultIndex);
}
+ return result;
}
-// updates the reference id stored in the BamMultiReader
-// to reflect the current state of the readers
-void BamMultiReader::UpdateReferenceID(void) {
- // the alignments are sorted by position, so the first alignment will always have the lowest reference ID
- if (alignments.begin()->second.second->RefID != CurrentRefID) {
- // get the next reference id
- // while there aren't any readers at the next ref id
- // increment the ref id
- int nextRefID = CurrentRefID;
- while (alignments.begin()->second.second->RefID != nextRefID) {
- ++nextRefID;
- }
- //cerr << "updating reference id from " << CurrentRefID << " to " << nextRefID << endl;
- CurrentRefID = nextRefID;
+// for debugging
+void BamMultiReader::DumpAlignmentIndex(void) {
+ for (AlignmentIndex::const_iterator it = alignments.begin(); it != alignments.end(); ++it) {
+ cerr << it->first.first << ":" << it->first.second << " " << it->second.first->GetFilename() << endl;
}
}
-// checks if any readers still have alignments
-bool BamMultiReader::HasOpenReaders() {
- return alignments.size() > 0;
+// makes a virtual, unified header for all the bam files in the multireader
+const string BamMultiReader::GetHeaderText(void) const {
+
+ string mergedHeader = "";
+ map<string, bool> readGroups;
+
+ // foreach extraction entry (each BAM file)
+ for (vector<pair<BamReader*, BamAlignment*> >::const_iterator rs = readers.begin(); rs != readers.end(); ++rs) {
+
+ map<string, bool> currentFileReadGroups;
+
+ BamReader* reader = rs->first;
+
+ stringstream header(reader->GetHeaderText());
+ vector<string> lines;
+ string item;
+ while (getline(header, item))
+ lines.push_back(item);
+
+ for (vector<string>::const_iterator it = lines.begin(); it != lines.end(); ++it) {
+
+ // get next line from header, skip if empty
+ string headerLine = *it;
+ if ( headerLine.empty() ) { continue; }
+
+ // if first file, save HD & SQ entries
+ if ( rs == readers.begin() ) {
+ if ( headerLine.find("@HD") == 0 || headerLine.find("@SQ") == 0) {
+ mergedHeader.append(headerLine.c_str());
+ mergedHeader.append(1, '\n');
+ }
+ }
+
+ // (for all files) append RG entries if they are unique
+ if ( headerLine.find("@RG") == 0 ) {
+ stringstream headerLineSs(headerLine);
+ string part, readGroupPart, readGroup;
+ while(std::getline(headerLineSs, part, '\t')) {
+ stringstream partSs(part);
+ string subtag;
+ std::getline(partSs, subtag, ':');
+ if (subtag == "ID") {
+ std::getline(partSs, readGroup, ':');
+ break;
+ }
+ }
+ if (readGroups.find(readGroup) == readGroups.end()) { // prevents duplicate @RG entries
+ mergedHeader.append(headerLine.c_str() );
+ mergedHeader.append(1, '\n');
+ readGroups[readGroup] = true;
+ currentFileReadGroups[readGroup] = true;
+ } else {
+ // warn iff we are reading one file and discover duplicated @RG tags in the header
+ // otherwise, we emit no warning, as we might be merging multiple BAM files with identical @RG tags
+ if (currentFileReadGroups.find(readGroup) != currentFileReadGroups.end()) {
+ cerr << "WARNING: duplicate @RG tag " << readGroup
+ << " entry in header of " << reader->GetFilename() << endl;
+ }
+ }
+ }
+ }
+ }
+
+ // return merged header text
+ return mergedHeader;
}
// get next alignment among all files
}
+// ---------------------------------------------------------------------------------------
+//
+// NB: The following GetReferenceX() functions assume that we have identical
+// references for all BAM files. We enforce this by invoking the above
+// validation function (ValidateReaders) to verify that our reference data
+// is the same across all files on Open, so we will not encounter a situation
+// in which there is a mismatch and we are still live.
+//
+// ---------------------------------------------------------------------------------------
+
+// returns the number of reference sequences
+const int BamMultiReader::GetReferenceCount(void) const {
+ return readers.front().first->GetReferenceCount();
+}
+
+// returns vector of reference objects
+const BamTools::RefVector BamMultiReader::GetReferenceData(void) const {
+ return readers.front().first->GetReferenceData();
+}
+
+// returns refID from reference name
+const int BamMultiReader::GetReferenceID(const string& refName) const {
+ return readers.front().first->GetReferenceID(refName);
+}
+
+// ---------------------------------------------------------------------------------------
+
+// checks if any readers still have alignments
+bool BamMultiReader::HasOpenReaders() {
+ return alignments.size() > 0;
+}
+
+// returns whether underlying BAM readers ALL have an index loaded
+// this is useful to indicate whether Jump() or SetRegion() are possible
+bool BamMultiReader::IsIndexLoaded(void) const {
+ bool ok = true;
+ vector<pair<BamReader*, BamAlignment*> >::const_iterator readerIter = readers.begin();
+ vector<pair<BamReader*, BamAlignment*> >::const_iterator readerEnd = readers.end();
+ for ( ; readerIter != readerEnd; ++readerIter ) {
+ const BamReader* reader = (*readerIter).first;
+ if ( reader ) ok &= reader->IsIndexLoaded();
+ }
+ return ok;
+}
+
// jumps to specified region(refID, leftBound) in BAM files, returns success/fail
bool BamMultiReader::Jump(int refID, int position) {
return result;
}
-bool BamMultiReader::SetRegion(const int& leftRefID, const int& leftPosition, const int& rightRefID, const int& rightPosition) {
-
- BamRegion region(leftRefID, leftPosition, rightRefID, rightPosition);
-
- return SetRegion(region);
-
-}
-
-bool BamMultiReader::SetRegion(const BamRegion& region) {
-
- Region = region;
-
- // NB: While it may make sense to track readers in which we can
- // successfully SetRegion, In practice a failure of SetRegion means "no
- // alignments here." It makes sense to simply accept the failure,
- // UpdateAlignments(), and continue.
-
- for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
- it->first->SetRegion(region);
- }
-
- UpdateAlignments();
-
- return true;
-
-}
-
-void BamMultiReader::UpdateAlignments(void) {
- // Update Alignments
- alignments.clear();
- for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
- BamReader* br = it->first;
- BamAlignment* ba = it->second;
- if (br->GetNextAlignment(*ba)) {
- alignments.insert(make_pair(make_pair(ba->RefID, ba->Position),
- make_pair(br, ba)));
- } else {
- // assume BamReader end of region / EOF
- }
- }
-}
-
// opens BAM files
bool BamMultiReader::Open(const vector<string> filenames, bool openIndexes, bool coreMode, bool useDefaultIndex) {
// for filename in filenames
fileNames = filenames; // save filenames in our multireader
for (vector<string>::const_iterator it = filenames.begin(); it != filenames.end(); ++it) {
- string filename = *it;
+
+ const string filename = *it;
BamReader* reader = new BamReader;
bool openedOK = true;
if (openIndexes) {
- if (useDefaultIndex)
- openedOK = reader->Open(filename, filename + ".bai");
- else
- openedOK = reader->Open(filename, filename + ".bti");
- } else {
- openedOK = reader->Open(filename); // for merging, jumping is disallowed
- }
+
+ // leave index filename empty
+ // this allows BamReader & BamIndex to search for any available
+ // useDefaultIndex gives hint to prefer BAI over BTI
+ openedOK = reader->Open(filename, "", true, useDefaultIndex);
+ }
+
+ // ignoring index file(s)
+ else openedOK = reader->Open(filename);
// if file opened ok, check that it can be read
if ( openedOK ) {
bool fileOK = true;
BamAlignment* alignment = new BamAlignment;
- if (coreMode) {
- fileOK &= reader->GetNextAlignmentCore(*alignment);
- } else {
- fileOK &= reader->GetNextAlignment(*alignment);
- }
+ fileOK &= ( coreMode ? reader->GetNextAlignmentCore(*alignment) : reader->GetNextAlignment(*alignment) );
if (fileOK) {
readers.push_back(make_pair(reader, alignment)); // store pointers to our readers for cleanup
// if only file available & could not be read, return failure
if ( filenames.size() == 1 ) return false;
}
-
}
- // TODO; any more error handling on openedOK ??
+ // TODO; any further error handling when openedOK is false ??
else
return false;
}
}
}
-// for debugging
-void BamMultiReader::DumpAlignmentIndex(void) {
- for (AlignmentIndex::const_iterator it = alignments.begin(); it != alignments.end(); ++it) {
- cerr << it->first.first << ":" << it->first.second << " " << it->second.first->GetFilename() << endl;
- }
-}
-
// returns BAM file pointers to beginning of alignment data
bool BamMultiReader::Rewind(void) {
bool result = true;
return result;
}
-// saves index data to BAM index files (".bai"/".bti") where necessary, returns success/fail
-bool BamMultiReader::CreateIndexes(bool useDefaultIndex) {
- bool result = true;
- for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
- BamReader* reader = it->first;
- result &= reader->CreateIndex(useDefaultIndex);
- }
- return result;
+bool BamMultiReader::SetRegion(const int& leftRefID, const int& leftPosition, const int& rightRefID, const int& rightPosition) {
+ BamRegion region(leftRefID, leftPosition, rightRefID, rightPosition);
+ return SetRegion(region);
}
-// makes a virtual, unified header for all the bam files in the multireader
-const string BamMultiReader::GetHeaderText(void) const {
-
- string mergedHeader = "";
- map<string, bool> readGroups;
-
- // foreach extraction entry (each BAM file)
- for (vector<pair<BamReader*, BamAlignment*> >::const_iterator rs = readers.begin(); rs != readers.end(); ++rs) {
-
- map<string, bool> currentFileReadGroups;
-
- BamReader* reader = rs->first;
+bool BamMultiReader::SetRegion(const BamRegion& region) {
- stringstream header(reader->GetHeaderText());
- vector<string> lines;
- string item;
- while (getline(header, item))
- lines.push_back(item);
+ Region = region;
- for (vector<string>::const_iterator it = lines.begin(); it != lines.end(); ++it) {
+ // NB: While it may make sense to track readers in which we can
+ // successfully SetRegion, In practice a failure of SetRegion means "no
+ // alignments here." It makes sense to simply accept the failure,
+ // UpdateAlignments(), and continue.
- // get next line from header, skip if empty
- string headerLine = *it;
- if ( headerLine.empty() ) { continue; }
+ for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
+ it->first->SetRegion(region);
+ }
- // if first file, save HD & SQ entries
- if ( rs == readers.begin() ) {
- if ( headerLine.find("@HD") == 0 || headerLine.find("@SQ") == 0) {
- mergedHeader.append(headerLine.c_str());
- mergedHeader.append(1, '\n');
- }
- }
+ UpdateAlignments();
+ return true;
+}
- // (for all files) append RG entries if they are unique
- if ( headerLine.find("@RG") == 0 ) {
- stringstream headerLineSs(headerLine);
- string part, readGroupPart, readGroup;
- while(std::getline(headerLineSs, part, '\t')) {
- stringstream partSs(part);
- string subtag;
- std::getline(partSs, subtag, ':');
- if (subtag == "ID") {
- std::getline(partSs, readGroup, ':');
- break;
- }
- }
- if (readGroups.find(readGroup) == readGroups.end()) { // prevents duplicate @RG entries
- mergedHeader.append(headerLine.c_str() );
- mergedHeader.append(1, '\n');
- readGroups[readGroup] = true;
- currentFileReadGroups[readGroup] = true;
- } else {
- // warn iff we are reading one file and discover duplicated @RG tags in the header
- // otherwise, we emit no warning, as we might be merging multiple BAM files with identical @RG tags
- if (currentFileReadGroups.find(readGroup) != currentFileReadGroups.end()) {
- cerr << "WARNING: duplicate @RG tag " << readGroup
- << " entry in header of " << reader->GetFilename() << endl;
- }
- }
- }
+void BamMultiReader::UpdateAlignments(void) {
+ // Update Alignments
+ alignments.clear();
+ for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {
+ BamReader* br = it->first;
+ BamAlignment* ba = it->second;
+ if (br->GetNextAlignment(*ba)) {
+ alignments.insert(make_pair(make_pair(ba->RefID, ba->Position),
+ make_pair(br, ba)));
+ } else {
+ // assume BamReader end of region / EOF
}
}
+}
- // return merged header text
- return mergedHeader;
+// updates the reference id stored in the BamMultiReader
+// to reflect the current state of the readers
+void BamMultiReader::UpdateReferenceID(void) {
+ // the alignments are sorted by position, so the first alignment will always have the lowest reference ID
+ if (alignments.begin()->second.second->RefID != CurrentRefID) {
+ // get the next reference id
+ // while there aren't any readers at the next ref id
+ // increment the ref id
+ int nextRefID = CurrentRefID;
+ while (alignments.begin()->second.second->RefID != nextRefID) {
+ ++nextRefID;
+ }
+ //cerr << "updating reference id from " << CurrentRefID << " to " << nextRefID << endl;
+ CurrentRefID = nextRefID;
+ }
}
// ValidateReaders checks that all the readers point to BAM files representing
}
}
}
-
-// NB: The following functions assume that we have identical references for all
-// BAM files. We enforce this by invoking the above validation function
-// (ValidateReaders) to verify that our reference data is the same across all
-// files on Open, so we will not encounter a situation in which there is a
-// mismatch and we are still live.
-
-// returns the number of reference sequences
-const int BamMultiReader::GetReferenceCount(void) const {
- return readers.front().first->GetReferenceCount();
-}
-
-// returns vector of reference objects
-const BamTools::RefVector BamMultiReader::GetReferenceData(void) const {
- return readers.front().first->GetReferenceData();
-}
-
-const int BamMultiReader::GetReferenceID(const string& refName) const {
- return readers.front().first->GetReferenceID(refName);
-}
// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 20 July 2010 (DB)\r
+// Last modified: 3 September 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Functionality for simultaneously reading multiple BAM files\r
// ***************************************************************************\r
// indexes.\r
// @coreMode - setup our first alignments using GetNextAlignmentCore();\r
// also useful for merging\r
- bool Open(const vector<string> filenames, bool openIndexes = true, bool coreMode = false, bool useDefaultIndex = true);\r
-\r
+ // @preferStandardIndex - look for standard BAM index ".bai" first. If false, \r
+ // will look for BamTools index ".bti". \r
+ bool Open(const vector<string> filenames, bool openIndexes = true, bool coreMode = false, bool preferStandardIndex = true);\r
+\r
+ // returns whether underlying BAM readers ALL have an index loaded\r
+ // this is useful to indicate whether Jump() or SetRegion() are possible\r
+ bool IsIndexLoaded(void) const;\r
+ \r
// performs random-access jump to reference, position\r
bool Jump(int refID, int position = 0);\r
\r
// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 15 July 2010 (DB)\r
+// Last modified: 7 September 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
// Institute.\r
\r
// file operations\r
void Close(void);\r
- bool Jump(int refID, int position = 0);\r
- bool Open(const string& filename, const string& indexFilename = "");\r
+ bool Jump(int refID, int position);\r
+ bool Open(const std::string& filename, \r
+ const std::string& indexFilename, \r
+ const bool lookForIndex, \r
+ const bool preferStandardIndex);\r
bool Rewind(void);\r
bool SetRegion(const BamRegion& region);\r
\r
int GetReferenceID(const string& refName) const;\r
\r
// index operations\r
- bool CreateIndex(bool useDefaultIndex);\r
+ bool CreateIndex(bool useStandardIndex);\r
\r
// -------------------------------\r
// internal methods\r
// clear out inernal index data structure\r
void ClearIndex(void);\r
// loads index from BAM index file\r
- bool LoadIndex(void);\r
+ bool LoadIndex(const bool lookForIndex, const bool preferStandardIndex);\r
};\r
\r
// -----------------------------------------------------\r
\r
// file operations\r
void BamReader::Close(void) { d->Close(); }\r
+bool BamReader::IsIndexLoaded(void) const { return d->IsIndexLoaded; }\r
bool BamReader::IsOpen(void) const { return d->mBGZF.IsOpen; }\r
-bool BamReader::Jump(int refID, int position) { \r
+bool BamReader::Jump(int refID, int position) \r
+{ \r
d->Region.LeftRefID = refID;\r
d->Region.LeftPosition = position;\r
d->IsLeftBoundSpecified = true;\r
d->IsRightBoundSpecified = false;\r
return d->Jump(refID, position); \r
}\r
-bool BamReader::Open(const string& filename, const string& indexFilename) { return d->Open(filename, indexFilename); }\r
+bool BamReader::Open(const std::string& filename, \r
+ const std::string& indexFilename, \r
+ const bool lookForIndex, \r
+ const bool preferStandardIndex) \r
+{ \r
+ return d->Open(filename, indexFilename, lookForIndex, preferStandardIndex); \r
+}\r
bool BamReader::Rewind(void) { return d->Rewind(); }\r
bool BamReader::SetRegion(const BamRegion& region) { return d->SetRegion(region); }\r
bool BamReader::SetRegion(const int& leftRefID, const int& leftBound, const int& rightRefID, const int& rightBound) {\r
const std::string BamReader::GetFilename(void) const { return d->Filename; }\r
\r
// index operations\r
-bool BamReader::CreateIndex(bool useDefaultIndex) { return d->CreateIndex(useDefaultIndex); }\r
+bool BamReader::CreateIndex(bool useStandardIndex) { return d->CreateIndex(useStandardIndex); }\r
\r
// -----------------------------------------------------\r
// BamReaderPrivate implementation\r
\r
// calculate character lengths/offsets\r
const unsigned int dataLength = bAlignment.SupportData.BlockLength - BAM_CORE_SIZE;\r
- const unsigned int cigarDataOffset = bAlignment.SupportData.QueryNameLength;\r
const unsigned int seqDataOffset = bAlignment.SupportData.QueryNameLength + (bAlignment.SupportData.NumCigarOperations * 4);\r
const unsigned int qualDataOffset = seqDataOffset + (bAlignment.SupportData.QuerySequenceLength+1)/2;\r
const unsigned int tagDataOffset = qualDataOffset + bAlignment.SupportData.QuerySequenceLength;\r
\r
// set up char buffers\r
const char* allCharData = bAlignment.SupportData.AllCharData.data();\r
- uint32_t* cigarData = (uint32_t*)(allCharData + cigarDataOffset);\r
const char* seqData = ((const char*)allCharData) + seqDataOffset;\r
const char* qualData = ((const char*)allCharData) + qualDataOffset;\r
char* tagData = ((char*)allCharData) + tagDataOffset;\r
\r
- // store alignment name (depends on null char as terminator)\r
+ // store alignment name (relies on null char in name as terminator)\r
bAlignment.Name.assign((const char*)(allCharData)); \r
- \r
- // save CigarOps \r
- CigarOp op;\r
- bAlignment.CigarData.clear();\r
- bAlignment.CigarData.reserve(bAlignment.SupportData.NumCigarOperations);\r
- for (unsigned int i = 0; i < bAlignment.SupportData.NumCigarOperations; ++i) {\r
-\r
- // swap if necessary\r
- if ( IsBigEndian ) { SwapEndian_32(cigarData[i]); }\r
- \r
- // build CigarOp structure\r
- op.Length = (cigarData[i] >> BAM_CIGAR_SHIFT);\r
- op.Type = CIGAR_LOOKUP[ (cigarData[i] & BAM_CIGAR_MASK) ];\r
\r
- // save CigarOp\r
- bAlignment.CigarData.push_back(op);\r
- }\r
- \r
- \r
// save query sequence\r
bAlignment.QueryBases.clear();\r
bAlignment.QueryBases.reserve(bAlignment.SupportData.QuerySequenceLength);\r
void BamReader::BamReaderPrivate::ClearIndex(void) {\r
delete NewIndex;\r
NewIndex = 0;\r
+ IsIndexLoaded = false;\r
}\r
\r
// closes the BAM file\r
IsRegionSpecified = false;\r
}\r
\r
-// create BAM index from BAM file (keep structure in memory) and write to default index output file\r
-bool BamReader::BamReaderPrivate::CreateIndex(bool useDefaultIndex) {\r
+// creates index for BAM file, saves to file\r
+// default behavior is to create the BAM standard index (".bai")\r
+// set flag to false to create the BamTools-specific index (".bti")\r
+bool BamReader::BamReaderPrivate::CreateIndex(bool useStandardIndex) {\r
\r
// clear out prior index data\r
ClearIndex();\r
\r
- // create default index\r
- if ( useDefaultIndex )\r
- NewIndex = new BamDefaultIndex(&mBGZF, Parent, IsBigEndian);\r
+ // create index based on type requested\r
+ if ( useStandardIndex ) \r
+ NewIndex = new BamStandardIndex(&mBGZF, Parent, IsBigEndian);\r
// create BamTools 'custom' index\r
else\r
NewIndex = new BamToolsIndex(&mBGZF, Parent, IsBigEndian);\r
\r
+ // build new index\r
bool ok = true;\r
ok &= NewIndex->Build();\r
+ IsIndexLoaded = ok;\r
+ \r
+ // attempt to save index data to file\r
ok &= NewIndex->Write(Filename); \r
\r
- // return success/fail\r
+ // return success/fail of both building & writing index\r
return ok;\r
}\r
\r
BamReader::BamReaderPrivate::RegionState state = IsOverlap(bAlignment);\r
\r
// if alignment lies after region, return false\r
- if ( state == AFTER_REGION ) \r
- return false;\r
+ if ( state == AFTER_REGION ) return false;\r
\r
while ( state != WITHIN_REGION ) {\r
// if no valid alignment available (likely EOF) return failure\r
if ( !LoadNextAlignment(bAlignment) ) return false;\r
// if alignment lies after region, return false (no available read within region)\r
state = IsOverlap(bAlignment);\r
- if ( state == AFTER_REGION) return false;\r
- \r
+ if ( state == AFTER_REGION ) return false;\r
}\r
\r
// return success (alignment found that overlaps region)\r
vector<string> refNames;\r
RefVector::const_iterator refIter = References.begin();\r
RefVector::const_iterator refEnd = References.end();\r
- for ( ; refIter != refEnd; ++refIter) {\r
+ for ( ; refIter != refEnd; ++refIter) \r
refNames.push_back( (*refIter).RefName );\r
- }\r
\r
// return 'index-of' refName ( if not found, returns refNames.size() )\r
return distance(refNames.begin(), find(refNames.begin(), refNames.end(), refName));\r
\r
// -----------------------------------------------------------------------\r
// check for existing index \r
- if ( NewIndex == 0 ) return false; \r
+ if ( !IsIndexLoaded || NewIndex == 0 ) return false; \r
// see if reference has alignments\r
if ( !NewIndex->HasAlignments(refID) ) return false; \r
// make sure position is valid\r
// get BAM header text length\r
mBGZF.Read(buffer, 4);\r
unsigned int headerTextLength = BgzfData::UnpackUnsignedInt(buffer);\r
- if ( IsBigEndian ) { SwapEndian_32(headerTextLength); }\r
+ if ( IsBigEndian ) SwapEndian_32(headerTextLength); \r
\r
// get BAM header text\r
char* headerText = (char*)calloc(headerTextLength + 1, 1);\r
free(headerText);\r
}\r
\r
-// load existing index data from BAM index file (".bai"), return success/fail\r
-bool BamReader::BamReaderPrivate::LoadIndex(void) {\r
+// load existing index data from BAM index file (".bti" OR ".bai"), return success/fail\r
+bool BamReader::BamReaderPrivate::LoadIndex(const bool lookForIndex, const bool preferStandardIndex) {\r
\r
// clear out any existing index data\r
ClearIndex();\r
\r
- // skip if index file empty\r
- if ( IndexFilename.empty() )\r
- return false;\r
-\r
- // check supplied filename for index type\r
- size_t defaultExtensionFound = IndexFilename.find(".bai");\r
- size_t customExtensionFound = IndexFilename.find(".bti");\r
- \r
- // if SAM/BAM default (".bai")\r
- if ( defaultExtensionFound != string::npos )\r
- NewIndex = new BamDefaultIndex(&mBGZF, Parent, IsBigEndian);\r
- \r
- // if BamTools custom index (".bti")\r
- else if ( customExtensionFound != string::npos )\r
- NewIndex = new BamToolsIndex(&mBGZF, Parent, IsBigEndian);\r
+ // if no index filename provided, so we need to look for available index files\r
+ if ( IndexFilename.empty() ) {\r
+ \r
+ // attempt to load BamIndex based on current Filename provided & preferStandardIndex flag\r
+ const BamIndex::PreferredIndexType type = (preferStandardIndex ? BamIndex::STANDARD : BamIndex::BAMTOOLS);\r
+ NewIndex = BamIndex::FromBamFilename(Filename, &mBGZF, Parent, IsBigEndian, type);\r
+ \r
+ // if null, return failure\r
+ if ( NewIndex == 0 ) return false;\r
+ \r
+ // generate proper IndexFilename based on type of index created\r
+ IndexFilename = Filename + NewIndex->Extension();\r
+ }\r
\r
- // else unknown\r
else {\r
- fprintf(stderr, "ERROR: Unknown index file extension.\n");\r
- return false;\r
+ // attempt to load BamIndex based on IndexFilename provided by client\r
+ NewIndex = BamIndex::FromIndexFilename(IndexFilename, &mBGZF, Parent, IsBigEndian);\r
+ \r
+ // if null, return failure\r
+ if ( NewIndex == 0 ) return false; \r
}\r
\r
- // return success of loading index data\r
- return NewIndex->Load(IndexFilename);\r
+ // an index file was found\r
+ // return success of loading the index data from file\r
+ IsIndexLoaded = NewIndex->Load(IndexFilename);\r
+ return IsIndexLoaded;\r
}\r
\r
// populates BamAlignment with alignment data under file pointer, returns success/fail\r
mBGZF.Read(buffer, 4);\r
bAlignment.SupportData.BlockLength = BgzfData::UnpackUnsignedInt(buffer);\r
if ( IsBigEndian ) { SwapEndian_32(bAlignment.SupportData.BlockLength); }\r
- if ( bAlignment.SupportData.BlockLength == 0 ) { return false; }\r
+ if ( bAlignment.SupportData.BlockLength == 0 ) return false;\r
\r
// read in core alignment data, make sure the right size of data was read\r
char x[BAM_CORE_SIZE];\r
- if ( mBGZF.Read(x, BAM_CORE_SIZE) != BAM_CORE_SIZE ) { return false; }\r
+ if ( mBGZF.Read(x, BAM_CORE_SIZE) != BAM_CORE_SIZE ) return false; \r
\r
if ( IsBigEndian ) {\r
- for ( int i = 0; i < BAM_CORE_SIZE; i+=sizeof(uint32_t) ) { \r
- SwapEndian_32p(&x[i]); \r
- }\r
+ for ( int i = 0; i < BAM_CORE_SIZE; i+=sizeof(uint32_t) ) \r
+ SwapEndian_32p(&x[i]); \r
}\r
\r
// set BamAlignment 'core' and 'support' data\r
\r
// set success flag\r
readCharDataOK = true;\r
+ \r
+ // save CIGAR ops \r
+ // need to calculate this here so that BamAlignment::GetEndPosition() performs correctly, \r
+ // even when BamReader::GetNextAlignmentCore() is called \r
+ const unsigned int cigarDataOffset = bAlignment.SupportData.QueryNameLength;\r
+ uint32_t* cigarData = (uint32_t*)(allCharData + cigarDataOffset);\r
+ CigarOp op;\r
+ bAlignment.CigarData.clear();\r
+ bAlignment.CigarData.reserve(bAlignment.SupportData.NumCigarOperations);\r
+ for (unsigned int i = 0; i < bAlignment.SupportData.NumCigarOperations; ++i) {\r
+\r
+ // swap if necessary\r
+ if ( IsBigEndian ) SwapEndian_32(cigarData[i]);\r
+ \r
+ // build CigarOp structure\r
+ op.Length = (cigarData[i] >> BAM_CIGAR_SHIFT);\r
+ op.Type = CIGAR_LOOKUP[ (cigarData[i] & BAM_CIGAR_MASK) ];\r
+\r
+ // save CigarOp\r
+ bAlignment.CigarData.push_back(op);\r
+ }\r
}\r
\r
free(allCharData);\r
char buffer[4];\r
mBGZF.Read(buffer, 4);\r
unsigned int numberRefSeqs = BgzfData::UnpackUnsignedInt(buffer);\r
- if ( IsBigEndian ) { SwapEndian_32(numberRefSeqs); }\r
- if (numberRefSeqs == 0) { return; }\r
+ if ( IsBigEndian ) SwapEndian_32(numberRefSeqs);\r
+ if ( numberRefSeqs == 0 ) return;\r
References.reserve((int)numberRefSeqs);\r
\r
// iterate over all references in header\r
// get length of reference name\r
mBGZF.Read(buffer, 4);\r
unsigned int refNameLength = BgzfData::UnpackUnsignedInt(buffer);\r
- if ( IsBigEndian ) { SwapEndian_32(refNameLength); }\r
+ if ( IsBigEndian ) SwapEndian_32(refNameLength);\r
char* refName = (char*)calloc(refNameLength, 1);\r
\r
// get reference name and reference sequence length\r
mBGZF.Read(refName, refNameLength);\r
mBGZF.Read(buffer, 4);\r
int refLength = BgzfData::UnpackSignedInt(buffer);\r
- if ( IsBigEndian ) { SwapEndian_32(refLength); }\r
+ if ( IsBigEndian ) SwapEndian_32(refLength); \r
\r
// store data for reference\r
RefData aReference;\r
}\r
\r
// opens BAM file (and index)\r
-bool BamReader::BamReaderPrivate::Open(const string& filename, const string& indexFilename) {\r
+bool BamReader::BamReaderPrivate::Open(const string& filename, const string& indexFilename, const bool lookForIndex, const bool preferStandardIndex) {\r
\r
+ // store filenames\r
Filename = filename;\r
IndexFilename = indexFilename;\r
\r
// open the BGZF file for reading, return false on failure\r
- if ( !mBGZF.Open(filename, "rb") ) \r
- return false;\r
+ if ( !mBGZF.Open(filename, "rb") ) return false; \r
\r
// retrieve header text & reference data\r
LoadHeaderData();\r
// store file offset of first alignment\r
AlignmentsBeginOffset = mBGZF.Tell();\r
\r
- // open index file & load index data (if exists)\r
- if ( !IndexFilename.empty() )\r
- LoadIndex();\r
+ // if no index filename provided \r
+ if ( IndexFilename.empty() ) {\r
+ \r
+ // client did not specify that index SHOULD be found\r
+ // useful for cases where sequential access is all that is required\r
+ if ( !lookForIndex ) return true; \r
+ \r
+ // otherwise, look for index file, return success/fail\r
+ return LoadIndex(lookForIndex, preferStandardIndex) ;\r
+ }\r
\r
- // return success\r
- return true;\r
+ // client supplied an index filename\r
+ // attempt to load index data, return success/fail\r
+ return LoadIndex(lookForIndex, preferStandardIndex); \r
}\r
\r
// returns BAM file pointer to beginning of alignment data\r
Region = region;\r
\r
// set flags\r
- if ( region.LeftRefID >= 0 && region.LeftPosition >= 0 ) \r
- IsLeftBoundSpecified = true;\r
- if ( region.RightRefID >= 0 && region.RightPosition >= 0 ) \r
- IsRightBoundSpecified = true;\r
+ if ( region.LeftRefID >= 0 && region.LeftPosition >= 0 ) IsLeftBoundSpecified = true;\r
+ if ( region.RightRefID >= 0 && region.RightPosition >= 0 ) IsRightBoundSpecified = true;\r
\r
// attempt jump to beginning of region, return success/fail of Jump()\r
return Jump( Region.LeftRefID, Region.LeftPosition );\r
// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 9 July 2010 (DB)\r
+// Last modified: 3 September 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
// Institute.\r
\r
// close BAM file\r
void Close(void);\r
+ // returns whether index data is loaded (i.e. reader is able to Jump() or not)\r
+ bool IsIndexLoaded(void) const;\r
// returns whether reader is open for reading or not\r
bool IsOpen(void) const;\r
// performs random-access jump to reference, position\r
bool Jump(int refID, int position = 0);\r
// opens BAM file (and optional BAM index file, if provided)\r
- bool Open(const std::string& filename, const std::string& indexFilename = "");\r
+ // @lookForIndex - if no indexFilename provided, look for an existing index file\r
+ // @preferStandardIndex - if true, give priority in index file searching to standard BAM index\r
+ bool Open(const std::string& filename, \r
+ const std::string& indexFilename = "", \r
+ const bool lookForIndex = false, \r
+ const bool preferStandardIndex = false);\r
// returns file pointer to beginning of alignments\r
bool Rewind(void);\r
// sets a region of interest (with left & right bound reference/position)\r
// BAM index operations\r
// ----------------------\r
\r
- // creates index for BAM file, saves to file (default = bamFilename + ".bai")\r
- bool CreateIndex(bool useDefaultIndex = true);\r
+ // creates index for BAM file, saves to file\r
+ // default behavior is to create the BAM standard index (".bai")\r
+ // set flag to false to create the BamTools-specific index (".bti")\r
+ bool CreateIndex(bool useStandardIndex = true);\r
\r
// private implementation\r
private:\r
--- /dev/null
+# ==========================
+# BamTools Makefile
+# (c) 2010 Derek Barnett
+#
+# src/third_party
+# ==========================
+
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
+SRC_DIR =
+
+# define source subdirectories
+SUBDIRS = jsoncpp
+
+all:
+ @for dir in $(SUBDIRS); do \
+ echo "- Building in $$dir"; \
+ $(MAKE) --no-print-directory -C $$dir; \
+ echo ""; \
+ done
+
+.PHONY: all
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+.PHONY: clean
--- /dev/null
+The JsonCpp library's source code, including accompanying documentation,
+tests and demonstration applications, are licensed under the following
+conditions...
+
+The author (Baptiste Lepilleur) explicitly disclaims copyright in all
+jurisdictions which recognize such a disclaimer. In such jurisdictions,
+this software is released into the Public Domain.
+
+In jurisdictions which do not recognize Public Domain property (e.g. Germany as of
+2010), this software is Copyright (c) 2007-2010 by Baptiste Lepilleur, and is
+released under the terms of the MIT License (see below).
+
+In jurisdictions which recognize Public Domain property, the user of this
+software may choose to accept it either as 1) Public Domain, 2) under the
+conditions of the MIT License (see below), or 3) under the terms of dual
+Public Domain/MIT License conditions described here, as they choose.
+
+The MIT License is about as close to Public Domain as a license can get, and is
+described in clear, concise terms at:
+
+ http://en.wikipedia.org/wiki/MIT_License
+
+The full text of the MIT License follows:
+
+========================================================================
+Copyright (c) 2007-2010 Baptiste Lepilleur
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use, copy,
+modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+========================================================================
+(END LICENSE TEXT)
+
+The MIT license is compatible with both the GPL and commercial
+software, affording one all of the rights of Public Domain with the
+minor nuisance of being required to keep the above copyright notice
+and license text in the source code. Note also that by accepting the
+Public Domain "license" you can re-license your copy using whatever
+license you like.
--- /dev/null
+# ==========================
+# BamTools Makefile
+# (c) 2010 Derek Barnett
+#
+# src/third_party/jsoncpp
+# ==========================
+
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES = json_reader.cpp \
+ json_value.cpp \
+ json_writer.cpp
+OBJECTS= $(SOURCES:.cpp=.o)
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+
+all: $(BUILT_OBJECTS)
+
+$(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+ @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+.PHONY: all
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+.PHONY: clean
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#ifndef JSON_JSON_H_INCLUDED
+# define JSON_JSON_H_INCLUDED
+
+//# include "autolink.h"
+# include "json_value.h"
+# include "json_reader.h"
+# include "json_writer.h"
+# include "json_features.h"
+
+#endif // JSON_JSON_H_INCLUDED
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#ifndef JSONCPP_BATCHALLOCATOR_H_INCLUDED
+# define JSONCPP_BATCHALLOCATOR_H_INCLUDED
+
+# include <stdlib.h>
+# include <assert.h>
+
+# ifndef JSONCPP_DOC_EXCLUDE_IMPLEMENTATION
+
+namespace Json {
+
+/* Fast memory allocator.
+ *
+ * This memory allocator allocates memory for a batch of object (specified by
+ * the page size, the number of object in each page).
+ *
+ * It does not allow the destruction of a single object. All the allocated objects
+ * can be destroyed at once. The memory can be either released or reused for future
+ * allocation.
+ *
+ * The in-place new operator must be used to construct the object using the pointer
+ * returned by allocate.
+ */
+template<typename AllocatedType
+ ,const unsigned int objectPerAllocation>
+class BatchAllocator
+{
+public:
+ typedef AllocatedType Type;
+
+ BatchAllocator( unsigned int objectsPerPage = 255 )
+ : freeHead_( 0 )
+ , objectsPerPage_( objectsPerPage )
+ {
+// printf( "Size: %d => %s\n", sizeof(AllocatedType), typeid(AllocatedType).name() );
+ assert( sizeof(AllocatedType) * objectPerAllocation >= sizeof(AllocatedType *) ); // We must be able to store a slist in the object free space.
+ assert( objectsPerPage >= 16 );
+ batches_ = allocateBatch( 0 ); // allocated a dummy page
+ currentBatch_ = batches_;
+ }
+
+ ~BatchAllocator()
+ {
+ for ( BatchInfo *batch = batches_; batch; )
+ {
+ BatchInfo *nextBatch = batch->next_;
+ free( batch );
+ batch = nextBatch;
+ }
+ }
+
+ /// allocate space for an array of objectPerAllocation object.
+ /// @warning it is the responsability of the caller to call objects constructors.
+ AllocatedType *allocate()
+ {
+ if ( freeHead_ ) // returns node from free list.
+ {
+ AllocatedType *object = freeHead_;
+ freeHead_ = *(AllocatedType **)object;
+ return object;
+ }
+ if ( currentBatch_->used_ == currentBatch_->end_ )
+ {
+ currentBatch_ = currentBatch_->next_;
+ while ( currentBatch_ && currentBatch_->used_ == currentBatch_->end_ )
+ currentBatch_ = currentBatch_->next_;
+
+ if ( !currentBatch_ ) // no free batch found, allocate a new one
+ {
+ currentBatch_ = allocateBatch( objectsPerPage_ );
+ currentBatch_->next_ = batches_; // insert at the head of the list
+ batches_ = currentBatch_;
+ }
+ }
+ AllocatedType *allocated = currentBatch_->used_;
+ currentBatch_->used_ += objectPerAllocation;
+ return allocated;
+ }
+
+ /// Release the object.
+ /// @warning it is the responsability of the caller to actually destruct the object.
+ void release( AllocatedType *object )
+ {
+ assert( object != 0 );
+ *(AllocatedType **)object = freeHead_;
+ freeHead_ = object;
+ }
+
+private:
+ struct BatchInfo
+ {
+ BatchInfo *next_;
+ AllocatedType *used_;
+ AllocatedType *end_;
+ AllocatedType buffer_[objectPerAllocation];
+ };
+
+ // disabled copy constructor and assignement operator.
+ BatchAllocator( const BatchAllocator & );
+ void operator =( const BatchAllocator &);
+
+ static BatchInfo *allocateBatch( unsigned int objectsPerPage )
+ {
+ const unsigned int mallocSize = sizeof(BatchInfo) - sizeof(AllocatedType)* objectPerAllocation
+ + sizeof(AllocatedType) * objectPerAllocation * objectsPerPage;
+ BatchInfo *batch = static_cast<BatchInfo*>( malloc( mallocSize ) );
+ batch->next_ = 0;
+ batch->used_ = batch->buffer_;
+ batch->end_ = batch->buffer_ + objectsPerPage;
+ return batch;
+ }
+
+ BatchInfo *batches_;
+ BatchInfo *currentBatch_;
+ /// Head of a single linked list within the allocated space of freeed object
+ AllocatedType *freeHead_;
+ unsigned int objectsPerPage_;
+};
+
+
+} // namespace Json
+
+# endif // ifndef JSONCPP_DOC_INCLUDE_IMPLEMENTATION
+
+#endif // JSONCPP_BATCHALLOCATOR_H_INCLUDED
+
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#ifndef JSON_CONFIG_H_INCLUDED
+# define JSON_CONFIG_H_INCLUDED
+
+/// If defined, indicates that json library is embedded in CppTL library.
+//# define JSON_IN_CPPTL 1
+
+/// If defined, indicates that json may leverage CppTL library
+//# define JSON_USE_CPPTL 1
+/// If defined, indicates that cpptl vector based map should be used instead of std::map
+/// as Value container.
+//# define JSON_USE_CPPTL_SMALLMAP 1
+/// If defined, indicates that Json specific container should be used
+/// (hash table & simple deque container with customizable allocator).
+/// THIS FEATURE IS STILL EXPERIMENTAL!
+//# define JSON_VALUE_USE_INTERNAL_MAP 1
+/// Force usage of standard new/malloc based allocator instead of memory pool based allocator.
+/// The memory pools allocator used optimization (initializing Value and ValueInternalLink
+/// as if it was a POD) that may cause some validation tool to report errors.
+/// Only has effects if JSON_VALUE_USE_INTERNAL_MAP is defined.
+//# define JSON_USE_SIMPLE_INTERNAL_ALLOCATOR 1
+
+/// If defined, indicates that Json use exception to report invalid type manipulation
+/// instead of C assert macro.
+# define JSON_USE_EXCEPTION 1
+
+# ifdef JSON_IN_CPPTL
+# include <cpptl/config.h>
+# ifndef JSON_USE_CPPTL
+# define JSON_USE_CPPTL 1
+# endif
+# endif
+
+# ifdef JSON_IN_CPPTL
+# define JSON_API CPPTL_API
+# elif defined(JSON_DLL_BUILD)
+# define JSON_API __declspec(dllexport)
+# elif defined(JSON_DLL)
+# define JSON_API __declspec(dllimport)
+# else
+# define JSON_API
+# endif
+
+// If JSON_NO_INT64 is defined, then Json only support C++ "int" type for integer
+// Storages.
+// #define JSON_NO_INT64 1
+
+#if defined(_MSC_VER) && _MSC_VER <= 1200 // MSVC 6
+// Microsoft Visual Studio 6 only support conversion from __int64 to double
+// (no conversion from unsigned __int64).
+#define JSON_USE_INT64_DOUBLE_CONVERSION 1
+#endif // if defined(_MSC_VER) && _MSC_VER < 1200 // MSVC 6
+
+
+namespace Json {
+# if defined(JSON_NO_INT64)
+ typedef int Int;
+ typedef unsigned int UInt;
+# else // if defined(JSON_NO_INT64)
+ // For Microsoft Visual use specific types as long long is not supported
+# if defined(_MSC_VER) // Microsoft Visual Studio
+ typedef __int64 Int;
+ typedef unsigned __int64 UInt;
+# else // if defined(_MSC_VER) // Other platforms, use long long
+ typedef long long int Int;
+ typedef unsigned long long int UInt;
+# endif // if defined(_MSC_VER)
+# endif // if defined(JSON_NO_INT64)
+} // end namespace Json
+
+
+#endif // JSON_CONFIG_H_INCLUDED
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#ifndef CPPTL_JSON_FEATURES_H_INCLUDED
+# define CPPTL_JSON_FEATURES_H_INCLUDED
+
+# include "json_forwards.h"
+
+namespace Json {
+
+ /** \brief Configuration passed to reader and writer.
+ * This configuration object can be used to force the Reader or Writer
+ * to behave in a standard conforming way.
+ */
+ class JSON_API Features
+ {
+ public:
+ /** \brief A configuration that allows all features and assumes all strings are UTF-8.
+ * - C & C++ comments are allowed
+ * - Root object can be any JSON value
+ * - Assumes Value strings are encoded in UTF-8
+ */
+ static Features all();
+
+ /** \brief A configuration that is strictly compatible with the JSON specification.
+ * - Comments are forbidden.
+ * - Root object must be either an array or an object value.
+ * - Assumes Value strings are encoded in UTF-8
+ */
+ static Features strictMode();
+
+ /** \brief Initialize the configuration like JsonConfig::allFeatures;
+ */
+ Features();
+
+ /// \c true if comments are allowed. Default: \c true.
+ bool allowComments_;
+
+ /// \c true if root must be either an array or an object value. Default: \c false.
+ bool strictRoot_;
+ };
+
+} // namespace Json
+
+#endif // CPPTL_JSON_FEATURES_H_INCLUDED
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#ifndef JSON_FORWARDS_H_INCLUDED
+# define JSON_FORWARDS_H_INCLUDED
+
+# include "json_config.h"
+
+namespace Json {
+
+ // writer.h
+ class FastWriter;
+ class StyledWriter;
+
+ // reader.h
+ class Reader;
+
+ // features.h
+ class Features;
+
+ // value.h
+ typedef unsigned int ArrayIndex;
+ class StaticString;
+ class Path;
+ class PathArgument;
+ class Value;
+ class ValueIteratorBase;
+ class ValueIterator;
+ class ValueConstIterator;
+#ifdef JSON_VALUE_USE_INTERNAL_MAP
+ class ValueMapAllocator;
+ class ValueInternalLink;
+ class ValueInternalArray;
+ class ValueInternalMap;
+#endif // #ifdef JSON_VALUE_USE_INTERNAL_MAP
+
+} // namespace Json
+
+
+#endif // JSON_FORWARDS_H_INCLUDED
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+// included by json_value.cpp
+// everything is within Json namespace
+
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// class ValueInternalArray
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+
+ValueArrayAllocator::~ValueArrayAllocator()
+{
+}
+
+// //////////////////////////////////////////////////////////////////
+// class DefaultValueArrayAllocator
+// //////////////////////////////////////////////////////////////////
+#ifdef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
+class DefaultValueArrayAllocator : public ValueArrayAllocator
+{
+public: // overridden from ValueArrayAllocator
+ virtual ~DefaultValueArrayAllocator()
+ {
+ }
+
+ virtual ValueInternalArray *newArray()
+ {
+ return new ValueInternalArray();
+ }
+
+ virtual ValueInternalArray *newArrayCopy( const ValueInternalArray &other )
+ {
+ return new ValueInternalArray( other );
+ }
+
+ virtual void destructArray( ValueInternalArray *array )
+ {
+ delete array;
+ }
+
+ virtual void reallocateArrayPageIndex( Value **&indexes,
+ ValueInternalArray::PageIndex &indexCount,
+ ValueInternalArray::PageIndex minNewIndexCount )
+ {
+ ValueInternalArray::PageIndex newIndexCount = (indexCount*3)/2 + 1;
+ if ( minNewIndexCount > newIndexCount )
+ newIndexCount = minNewIndexCount;
+ void *newIndexes = realloc( indexes, sizeof(Value*) * newIndexCount );
+ if ( !newIndexes )
+ throw std::bad_alloc();
+ indexCount = newIndexCount;
+ indexes = static_cast<Value **>( newIndexes );
+ }
+ virtual void releaseArrayPageIndex( Value **indexes,
+ ValueInternalArray::PageIndex indexCount )
+ {
+ if ( indexes )
+ free( indexes );
+ }
+
+ virtual Value *allocateArrayPage()
+ {
+ return static_cast<Value *>( malloc( sizeof(Value) * ValueInternalArray::itemsPerPage ) );
+ }
+
+ virtual void releaseArrayPage( Value *value )
+ {
+ if ( value )
+ free( value );
+ }
+};
+
+#else // #ifdef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
+/// @todo make this thread-safe (lock when accessign batch allocator)
+class DefaultValueArrayAllocator : public ValueArrayAllocator
+{
+public: // overridden from ValueArrayAllocator
+ virtual ~DefaultValueArrayAllocator()
+ {
+ }
+
+ virtual ValueInternalArray *newArray()
+ {
+ ValueInternalArray *array = arraysAllocator_.allocate();
+ new (array) ValueInternalArray(); // placement new
+ return array;
+ }
+
+ virtual ValueInternalArray *newArrayCopy( const ValueInternalArray &other )
+ {
+ ValueInternalArray *array = arraysAllocator_.allocate();
+ new (array) ValueInternalArray( other ); // placement new
+ return array;
+ }
+
+ virtual void destructArray( ValueInternalArray *array )
+ {
+ if ( array )
+ {
+ array->~ValueInternalArray();
+ arraysAllocator_.release( array );
+ }
+ }
+
+ virtual void reallocateArrayPageIndex( Value **&indexes,
+ ValueInternalArray::PageIndex &indexCount,
+ ValueInternalArray::PageIndex minNewIndexCount )
+ {
+ ValueInternalArray::PageIndex newIndexCount = (indexCount*3)/2 + 1;
+ if ( minNewIndexCount > newIndexCount )
+ newIndexCount = minNewIndexCount;
+ void *newIndexes = realloc( indexes, sizeof(Value*) * newIndexCount );
+ if ( !newIndexes )
+ throw std::bad_alloc();
+ indexCount = newIndexCount;
+ indexes = static_cast<Value **>( newIndexes );
+ }
+ virtual void releaseArrayPageIndex( Value **indexes,
+ ValueInternalArray::PageIndex indexCount )
+ {
+ if ( indexes )
+ free( indexes );
+ }
+
+ virtual Value *allocateArrayPage()
+ {
+ return static_cast<Value *>( pagesAllocator_.allocate() );
+ }
+
+ virtual void releaseArrayPage( Value *value )
+ {
+ if ( value )
+ pagesAllocator_.release( value );
+ }
+private:
+ BatchAllocator<ValueInternalArray,1> arraysAllocator_;
+ BatchAllocator<Value,ValueInternalArray::itemsPerPage> pagesAllocator_;
+};
+#endif // #ifdef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
+
+static ValueArrayAllocator *&arrayAllocator()
+{
+ static DefaultValueArrayAllocator defaultAllocator;
+ static ValueArrayAllocator *arrayAllocator = &defaultAllocator;
+ return arrayAllocator;
+}
+
+static struct DummyArrayAllocatorInitializer {
+ DummyArrayAllocatorInitializer()
+ {
+ arrayAllocator(); // ensure arrayAllocator() statics are initialized before main().
+ }
+} dummyArrayAllocatorInitializer;
+
+// //////////////////////////////////////////////////////////////////
+// class ValueInternalArray
+// //////////////////////////////////////////////////////////////////
+bool
+ValueInternalArray::equals( const IteratorState &x,
+ const IteratorState &other )
+{
+ return x.array_ == other.array_
+ && x.currentItemIndex_ == other.currentItemIndex_
+ && x.currentPageIndex_ == other.currentPageIndex_;
+}
+
+
+void
+ValueInternalArray::increment( IteratorState &it )
+{
+ JSON_ASSERT_MESSAGE( it.array_ &&
+ (it.currentPageIndex_ - it.array_->pages_)*itemsPerPage + it.currentItemIndex_
+ != it.array_->size_,
+ "ValueInternalArray::increment(): moving iterator beyond end" );
+ ++(it.currentItemIndex_);
+ if ( it.currentItemIndex_ == itemsPerPage )
+ {
+ it.currentItemIndex_ = 0;
+ ++(it.currentPageIndex_);
+ }
+}
+
+
+void
+ValueInternalArray::decrement( IteratorState &it )
+{
+ JSON_ASSERT_MESSAGE( it.array_ && it.currentPageIndex_ == it.array_->pages_
+ && it.currentItemIndex_ == 0,
+ "ValueInternalArray::decrement(): moving iterator beyond end" );
+ if ( it.currentItemIndex_ == 0 )
+ {
+ it.currentItemIndex_ = itemsPerPage-1;
+ --(it.currentPageIndex_);
+ }
+ else
+ {
+ --(it.currentItemIndex_);
+ }
+}
+
+
+Value &
+ValueInternalArray::unsafeDereference( const IteratorState &it )
+{
+ return (*(it.currentPageIndex_))[it.currentItemIndex_];
+}
+
+
+Value &
+ValueInternalArray::dereference( const IteratorState &it )
+{
+ JSON_ASSERT_MESSAGE( it.array_ &&
+ (it.currentPageIndex_ - it.array_->pages_)*itemsPerPage + it.currentItemIndex_
+ < it.array_->size_,
+ "ValueInternalArray::dereference(): dereferencing invalid iterator" );
+ return unsafeDereference( it );
+}
+
+void
+ValueInternalArray::makeBeginIterator( IteratorState &it ) const
+{
+ it.array_ = const_cast<ValueInternalArray *>( this );
+ it.currentItemIndex_ = 0;
+ it.currentPageIndex_ = pages_;
+}
+
+
+void
+ValueInternalArray::makeIterator( IteratorState &it, ArrayIndex index ) const
+{
+ it.array_ = const_cast<ValueInternalArray *>( this );
+ it.currentItemIndex_ = index % itemsPerPage;
+ it.currentPageIndex_ = pages_ + index / itemsPerPage;
+}
+
+
+void
+ValueInternalArray::makeEndIterator( IteratorState &it ) const
+{
+ makeIterator( it, size_ );
+}
+
+
+ValueInternalArray::ValueInternalArray()
+ : pages_( 0 )
+ , size_( 0 )
+ , pageCount_( 0 )
+{
+}
+
+
+ValueInternalArray::ValueInternalArray( const ValueInternalArray &other )
+ : pages_( 0 )
+ , pageCount_( 0 )
+ , size_( other.size_ )
+{
+ PageIndex minNewPages = other.size_ / itemsPerPage;
+ arrayAllocator()->reallocateArrayPageIndex( pages_, pageCount_, minNewPages );
+ JSON_ASSERT_MESSAGE( pageCount_ >= minNewPages,
+ "ValueInternalArray::reserve(): bad reallocation" );
+ IteratorState itOther;
+ other.makeBeginIterator( itOther );
+ Value *value;
+ for ( ArrayIndex index = 0; index < size_; ++index, increment(itOther) )
+ {
+ if ( index % itemsPerPage == 0 )
+ {
+ PageIndex pageIndex = index / itemsPerPage;
+ value = arrayAllocator()->allocateArrayPage();
+ pages_[pageIndex] = value;
+ }
+ new (value) Value( dereference( itOther ) );
+ }
+}
+
+
+ValueInternalArray &
+ValueInternalArray::operator =( const ValueInternalArray &other )
+{
+ ValueInternalArray temp( other );
+ swap( temp );
+ return *this;
+}
+
+
+ValueInternalArray::~ValueInternalArray()
+{
+ // destroy all constructed items
+ IteratorState it;
+ IteratorState itEnd;
+ makeBeginIterator( it);
+ makeEndIterator( itEnd );
+ for ( ; !equals(it,itEnd); increment(it) )
+ {
+ Value *value = &dereference(it);
+ value->~Value();
+ }
+ // release all pages
+ PageIndex lastPageIndex = size_ / itemsPerPage;
+ for ( PageIndex pageIndex = 0; pageIndex < lastPageIndex; ++pageIndex )
+ arrayAllocator()->releaseArrayPage( pages_[pageIndex] );
+ // release pages index
+ arrayAllocator()->releaseArrayPageIndex( pages_, pageCount_ );
+}
+
+
+void
+ValueInternalArray::swap( ValueInternalArray &other )
+{
+ Value **tempPages = pages_;
+ pages_ = other.pages_;
+ other.pages_ = tempPages;
+ ArrayIndex tempSize = size_;
+ size_ = other.size_;
+ other.size_ = tempSize;
+ PageIndex tempPageCount = pageCount_;
+ pageCount_ = other.pageCount_;
+ other.pageCount_ = tempPageCount;
+}
+
+void
+ValueInternalArray::clear()
+{
+ ValueInternalArray dummy;
+ swap( dummy );
+}
+
+
+void
+ValueInternalArray::resize( ArrayIndex newSize )
+{
+ if ( newSize == 0 )
+ clear();
+ else if ( newSize < size_ )
+ {
+ IteratorState it;
+ IteratorState itEnd;
+ makeIterator( it, newSize );
+ makeIterator( itEnd, size_ );
+ for ( ; !equals(it,itEnd); increment(it) )
+ {
+ Value *value = &dereference(it);
+ value->~Value();
+ }
+ PageIndex pageIndex = (newSize + itemsPerPage - 1) / itemsPerPage;
+ PageIndex lastPageIndex = size_ / itemsPerPage;
+ for ( ; pageIndex < lastPageIndex; ++pageIndex )
+ arrayAllocator()->releaseArrayPage( pages_[pageIndex] );
+ size_ = newSize;
+ }
+ else if ( newSize > size_ )
+ resolveReference( newSize );
+}
+
+
+void
+ValueInternalArray::makeIndexValid( ArrayIndex index )
+{
+ // Need to enlarge page index ?
+ if ( index >= pageCount_ * itemsPerPage )
+ {
+ PageIndex minNewPages = (index + 1) / itemsPerPage;
+ arrayAllocator()->reallocateArrayPageIndex( pages_, pageCount_, minNewPages );
+ JSON_ASSERT_MESSAGE( pageCount_ >= minNewPages, "ValueInternalArray::reserve(): bad reallocation" );
+ }
+
+ // Need to allocate new pages ?
+ ArrayIndex nextPageIndex =
+ (size_ % itemsPerPage) != 0 ? size_ - (size_%itemsPerPage) + itemsPerPage
+ : size_;
+ if ( nextPageIndex <= index )
+ {
+ PageIndex pageIndex = nextPageIndex / itemsPerPage;
+ PageIndex pageToAllocate = (index - nextPageIndex) / itemsPerPage + 1;
+ for ( ; pageToAllocate-- > 0; ++pageIndex )
+ pages_[pageIndex] = arrayAllocator()->allocateArrayPage();
+ }
+
+ // Initialize all new entries
+ IteratorState it;
+ IteratorState itEnd;
+ makeIterator( it, size_ );
+ size_ = index + 1;
+ makeIterator( itEnd, size_ );
+ for ( ; !equals(it,itEnd); increment(it) )
+ {
+ Value *value = &dereference(it);
+ new (value) Value(); // Construct a default value using placement new
+ }
+}
+
+Value &
+ValueInternalArray::resolveReference( ArrayIndex index )
+{
+ if ( index >= size_ )
+ makeIndexValid( index );
+ return pages_[index/itemsPerPage][index%itemsPerPage];
+}
+
+Value *
+ValueInternalArray::find( ArrayIndex index ) const
+{
+ if ( index >= size_ )
+ return 0;
+ return &(pages_[index/itemsPerPage][index%itemsPerPage]);
+}
+
+ValueInternalArray::ArrayIndex
+ValueInternalArray::size() const
+{
+ return size_;
+}
+
+int
+ValueInternalArray::distance( const IteratorState &x, const IteratorState &y )
+{
+ return indexOf(y) - indexOf(x);
+}
+
+
+ValueInternalArray::ArrayIndex
+ValueInternalArray::indexOf( const IteratorState &iterator )
+{
+ if ( !iterator.array_ )
+ return ArrayIndex(-1);
+ return ArrayIndex(
+ (iterator.currentPageIndex_ - iterator.array_->pages_) * itemsPerPage
+ + iterator.currentItemIndex_ );
+}
+
+
+int
+ValueInternalArray::compare( const ValueInternalArray &other ) const
+{
+ int sizeDiff( size_ - other.size_ );
+ if ( sizeDiff != 0 )
+ return sizeDiff;
+
+ for ( ArrayIndex index =0; index < size_; ++index )
+ {
+ int diff = pages_[index/itemsPerPage][index%itemsPerPage].compare(
+ other.pages_[index/itemsPerPage][index%itemsPerPage] );
+ if ( diff != 0 )
+ return diff;
+ }
+ return 0;
+}
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+// included by json_value.cpp
+// everything is within Json namespace
+
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// class ValueInternalMap
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+
+/** \internal MUST be safely initialized using memset( this, 0, sizeof(ValueInternalLink) );
+ * This optimization is used by the fast allocator.
+ */
+ValueInternalLink::ValueInternalLink()
+ : previous_( 0 )
+ , next_( 0 )
+{
+}
+
+ValueInternalLink::~ValueInternalLink()
+{
+ for ( int index =0; index < itemPerLink; ++index )
+ {
+ if ( !items_[index].isItemAvailable() )
+ {
+ if ( !items_[index].isMemberNameStatic() )
+ free( keys_[index] );
+ }
+ else
+ break;
+ }
+}
+
+
+
+ValueMapAllocator::~ValueMapAllocator()
+{
+}
+
+#ifdef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
+class DefaultValueMapAllocator : public ValueMapAllocator
+{
+public: // overridden from ValueMapAllocator
+ virtual ValueInternalMap *newMap()
+ {
+ return new ValueInternalMap();
+ }
+
+ virtual ValueInternalMap *newMapCopy( const ValueInternalMap &other )
+ {
+ return new ValueInternalMap( other );
+ }
+
+ virtual void destructMap( ValueInternalMap *map )
+ {
+ delete map;
+ }
+
+ virtual ValueInternalLink *allocateMapBuckets( unsigned int size )
+ {
+ return new ValueInternalLink[size];
+ }
+
+ virtual void releaseMapBuckets( ValueInternalLink *links )
+ {
+ delete [] links;
+ }
+
+ virtual ValueInternalLink *allocateMapLink()
+ {
+ return new ValueInternalLink();
+ }
+
+ virtual void releaseMapLink( ValueInternalLink *link )
+ {
+ delete link;
+ }
+};
+#else
+/// @todo make this thread-safe (lock when accessign batch allocator)
+class DefaultValueMapAllocator : public ValueMapAllocator
+{
+public: // overridden from ValueMapAllocator
+ virtual ValueInternalMap *newMap()
+ {
+ ValueInternalMap *map = mapsAllocator_.allocate();
+ new (map) ValueInternalMap(); // placement new
+ return map;
+ }
+
+ virtual ValueInternalMap *newMapCopy( const ValueInternalMap &other )
+ {
+ ValueInternalMap *map = mapsAllocator_.allocate();
+ new (map) ValueInternalMap( other ); // placement new
+ return map;
+ }
+
+ virtual void destructMap( ValueInternalMap *map )
+ {
+ if ( map )
+ {
+ map->~ValueInternalMap();
+ mapsAllocator_.release( map );
+ }
+ }
+
+ virtual ValueInternalLink *allocateMapBuckets( unsigned int size )
+ {
+ return new ValueInternalLink[size];
+ }
+
+ virtual void releaseMapBuckets( ValueInternalLink *links )
+ {
+ delete [] links;
+ }
+
+ virtual ValueInternalLink *allocateMapLink()
+ {
+ ValueInternalLink *link = linksAllocator_.allocate();
+ memset( link, 0, sizeof(ValueInternalLink) );
+ return link;
+ }
+
+ virtual void releaseMapLink( ValueInternalLink *link )
+ {
+ link->~ValueInternalLink();
+ linksAllocator_.release( link );
+ }
+private:
+ BatchAllocator<ValueInternalMap,1> mapsAllocator_;
+ BatchAllocator<ValueInternalLink,1> linksAllocator_;
+};
+#endif
+
+static ValueMapAllocator *&mapAllocator()
+{
+ static DefaultValueMapAllocator defaultAllocator;
+ static ValueMapAllocator *mapAllocator = &defaultAllocator;
+ return mapAllocator;
+}
+
+static struct DummyMapAllocatorInitializer {
+ DummyMapAllocatorInitializer()
+ {
+ mapAllocator(); // ensure mapAllocator() statics are initialized before main().
+ }
+} dummyMapAllocatorInitializer;
+
+
+
+// h(K) = value * K >> w ; with w = 32 & K prime w.r.t. 2^32.
+
+/*
+use linked list hash map.
+buckets array is a container.
+linked list element contains 6 key/values. (memory = (16+4) * 6 + 4 = 124)
+value have extra state: valid, available, deleted
+*/
+
+
+ValueInternalMap::ValueInternalMap()
+ : buckets_( 0 )
+ , tailLink_( 0 )
+ , bucketsSize_( 0 )
+ , itemCount_( 0 )
+{
+}
+
+
+ValueInternalMap::ValueInternalMap( const ValueInternalMap &other )
+ : buckets_( 0 )
+ , tailLink_( 0 )
+ , bucketsSize_( 0 )
+ , itemCount_( 0 )
+{
+ reserve( other.itemCount_ );
+ IteratorState it;
+ IteratorState itEnd;
+ other.makeBeginIterator( it );
+ other.makeEndIterator( itEnd );
+ for ( ; !equals(it,itEnd); increment(it) )
+ {
+ bool isStatic;
+ const char *memberName = key( it, isStatic );
+ const Value &aValue = value( it );
+ resolveReference(memberName, isStatic) = aValue;
+ }
+}
+
+
+ValueInternalMap &
+ValueInternalMap::operator =( const ValueInternalMap &other )
+{
+ ValueInternalMap dummy( other );
+ swap( dummy );
+ return *this;
+}
+
+
+ValueInternalMap::~ValueInternalMap()
+{
+ if ( buckets_ )
+ {
+ for ( BucketIndex bucketIndex =0; bucketIndex < bucketsSize_; ++bucketIndex )
+ {
+ ValueInternalLink *link = buckets_[bucketIndex].next_;
+ while ( link )
+ {
+ ValueInternalLink *linkToRelease = link;
+ link = link->next_;
+ mapAllocator()->releaseMapLink( linkToRelease );
+ }
+ }
+ mapAllocator()->releaseMapBuckets( buckets_ );
+ }
+}
+
+
+void
+ValueInternalMap::swap( ValueInternalMap &other )
+{
+ ValueInternalLink *tempBuckets = buckets_;
+ buckets_ = other.buckets_;
+ other.buckets_ = tempBuckets;
+ ValueInternalLink *tempTailLink = tailLink_;
+ tailLink_ = other.tailLink_;
+ other.tailLink_ = tempTailLink;
+ BucketIndex tempBucketsSize = bucketsSize_;
+ bucketsSize_ = other.bucketsSize_;
+ other.bucketsSize_ = tempBucketsSize;
+ BucketIndex tempItemCount = itemCount_;
+ itemCount_ = other.itemCount_;
+ other.itemCount_ = tempItemCount;
+}
+
+
+void
+ValueInternalMap::clear()
+{
+ ValueInternalMap dummy;
+ swap( dummy );
+}
+
+
+ValueInternalMap::BucketIndex
+ValueInternalMap::size() const
+{
+ return itemCount_;
+}
+
+bool
+ValueInternalMap::reserveDelta( BucketIndex growth )
+{
+ return reserve( itemCount_ + growth );
+}
+
+bool
+ValueInternalMap::reserve( BucketIndex newItemCount )
+{
+ if ( !buckets_ && newItemCount > 0 )
+ {
+ buckets_ = mapAllocator()->allocateMapBuckets( 1 );
+ bucketsSize_ = 1;
+ tailLink_ = &buckets_[0];
+ }
+// BucketIndex idealBucketCount = (newItemCount + ValueInternalLink::itemPerLink) / ValueInternalLink::itemPerLink;
+ return true;
+}
+
+
+const Value *
+ValueInternalMap::find( const char *key ) const
+{
+ if ( !bucketsSize_ )
+ return 0;
+ HashKey hashedKey = hash( key );
+ BucketIndex bucketIndex = hashedKey % bucketsSize_;
+ for ( const ValueInternalLink *current = &buckets_[bucketIndex];
+ current != 0;
+ current = current->next_ )
+ {
+ for ( BucketIndex index=0; index < ValueInternalLink::itemPerLink; ++index )
+ {
+ if ( current->items_[index].isItemAvailable() )
+ return 0;
+ if ( strcmp( key, current->keys_[index] ) == 0 )
+ return ¤t->items_[index];
+ }
+ }
+ return 0;
+}
+
+
+Value *
+ValueInternalMap::find( const char *key )
+{
+ const ValueInternalMap *constThis = this;
+ return const_cast<Value *>( constThis->find( key ) );
+}
+
+
+Value &
+ValueInternalMap::resolveReference( const char *key,
+ bool isStatic )
+{
+ HashKey hashedKey = hash( key );
+ if ( bucketsSize_ )
+ {
+ BucketIndex bucketIndex = hashedKey % bucketsSize_;
+ ValueInternalLink **previous = 0;
+ BucketIndex index;
+ for ( ValueInternalLink *current = &buckets_[bucketIndex];
+ current != 0;
+ previous = ¤t->next_, current = current->next_ )
+ {
+ for ( index=0; index < ValueInternalLink::itemPerLink; ++index )
+ {
+ if ( current->items_[index].isItemAvailable() )
+ return setNewItem( key, isStatic, current, index );
+ if ( strcmp( key, current->keys_[index] ) == 0 )
+ return current->items_[index];
+ }
+ }
+ }
+
+ reserveDelta( 1 );
+ return unsafeAdd( key, isStatic, hashedKey );
+}
+
+
+void
+ValueInternalMap::remove( const char *key )
+{
+ HashKey hashedKey = hash( key );
+ if ( !bucketsSize_ )
+ return;
+ BucketIndex bucketIndex = hashedKey % bucketsSize_;
+ for ( ValueInternalLink *link = &buckets_[bucketIndex];
+ link != 0;
+ link = link->next_ )
+ {
+ BucketIndex index;
+ for ( index =0; index < ValueInternalLink::itemPerLink; ++index )
+ {
+ if ( link->items_[index].isItemAvailable() )
+ return;
+ if ( strcmp( key, link->keys_[index] ) == 0 )
+ {
+ doActualRemove( link, index, bucketIndex );
+ return;
+ }
+ }
+ }
+}
+
+void
+ValueInternalMap::doActualRemove( ValueInternalLink *link,
+ BucketIndex index,
+ BucketIndex bucketIndex )
+{
+ // find last item of the bucket and swap it with the 'removed' one.
+ // set removed items flags to 'available'.
+ // if last page only contains 'available' items, then desallocate it (it's empty)
+ ValueInternalLink *&lastLink = getLastLinkInBucket( index );
+ BucketIndex lastItemIndex = 1; // a link can never be empty, so start at 1
+ for ( ;
+ lastItemIndex < ValueInternalLink::itemPerLink;
+ ++lastItemIndex ) // may be optimized with dicotomic search
+ {
+ if ( lastLink->items_[lastItemIndex].isItemAvailable() )
+ break;
+ }
+
+ BucketIndex lastUsedIndex = lastItemIndex - 1;
+ Value *valueToDelete = &link->items_[index];
+ Value *valueToPreserve = &lastLink->items_[lastUsedIndex];
+ if ( valueToDelete != valueToPreserve )
+ valueToDelete->swap( *valueToPreserve );
+ if ( lastUsedIndex == 0 ) // page is now empty
+ { // remove it from bucket linked list and delete it.
+ ValueInternalLink *linkPreviousToLast = lastLink->previous_;
+ if ( linkPreviousToLast != 0 ) // can not deleted bucket link.
+ {
+ mapAllocator()->releaseMapLink( lastLink );
+ linkPreviousToLast->next_ = 0;
+ lastLink = linkPreviousToLast;
+ }
+ }
+ else
+ {
+ Value dummy;
+ valueToPreserve->swap( dummy ); // restore deleted to default Value.
+ valueToPreserve->setItemUsed( false );
+ }
+ --itemCount_;
+}
+
+
+ValueInternalLink *&
+ValueInternalMap::getLastLinkInBucket( BucketIndex bucketIndex )
+{
+ if ( bucketIndex == bucketsSize_ - 1 )
+ return tailLink_;
+ ValueInternalLink *&previous = buckets_[bucketIndex+1].previous_;
+ if ( !previous )
+ previous = &buckets_[bucketIndex];
+ return previous;
+}
+
+
+Value &
+ValueInternalMap::setNewItem( const char *key,
+ bool isStatic,
+ ValueInternalLink *link,
+ BucketIndex index )
+{
+ char *duplicatedKey = makeMemberName( key );
+ ++itemCount_;
+ link->keys_[index] = duplicatedKey;
+ link->items_[index].setItemUsed();
+ link->items_[index].setMemberNameIsStatic( isStatic );
+ return link->items_[index]; // items already default constructed.
+}
+
+
+Value &
+ValueInternalMap::unsafeAdd( const char *key,
+ bool isStatic,
+ HashKey hashedKey )
+{
+ JSON_ASSERT_MESSAGE( bucketsSize_ > 0, "ValueInternalMap::unsafeAdd(): internal logic error." );
+ BucketIndex bucketIndex = hashedKey % bucketsSize_;
+ ValueInternalLink *&previousLink = getLastLinkInBucket( bucketIndex );
+ ValueInternalLink *link = previousLink;
+ BucketIndex index;
+ for ( index =0; index < ValueInternalLink::itemPerLink; ++index )
+ {
+ if ( link->items_[index].isItemAvailable() )
+ break;
+ }
+ if ( index == ValueInternalLink::itemPerLink ) // need to add a new page
+ {
+ ValueInternalLink *newLink = mapAllocator()->allocateMapLink();
+ index = 0;
+ link->next_ = newLink;
+ previousLink = newLink;
+ link = newLink;
+ }
+ return setNewItem( key, isStatic, link, index );
+}
+
+
+ValueInternalMap::HashKey
+ValueInternalMap::hash( const char *key ) const
+{
+ HashKey hash = 0;
+ while ( *key )
+ hash += *key++ * 37;
+ return hash;
+}
+
+
+int
+ValueInternalMap::compare( const ValueInternalMap &other ) const
+{
+ int sizeDiff( itemCount_ - other.itemCount_ );
+ if ( sizeDiff != 0 )
+ return sizeDiff;
+ // Strict order guaranty is required. Compare all keys FIRST, then compare values.
+ IteratorState it;
+ IteratorState itEnd;
+ makeBeginIterator( it );
+ makeEndIterator( itEnd );
+ for ( ; !equals(it,itEnd); increment(it) )
+ {
+ if ( !other.find( key( it ) ) )
+ return 1;
+ }
+
+ // All keys are equals, let's compare values
+ makeBeginIterator( it );
+ for ( ; !equals(it,itEnd); increment(it) )
+ {
+ const Value *otherValue = other.find( key( it ) );
+ int valueDiff = value(it).compare( *otherValue );
+ if ( valueDiff != 0 )
+ return valueDiff;
+ }
+ return 0;
+}
+
+
+void
+ValueInternalMap::makeBeginIterator( IteratorState &it ) const
+{
+ it.map_ = const_cast<ValueInternalMap *>( this );
+ it.bucketIndex_ = 0;
+ it.itemIndex_ = 0;
+ it.link_ = buckets_;
+}
+
+
+void
+ValueInternalMap::makeEndIterator( IteratorState &it ) const
+{
+ it.map_ = const_cast<ValueInternalMap *>( this );
+ it.bucketIndex_ = bucketsSize_;
+ it.itemIndex_ = 0;
+ it.link_ = 0;
+}
+
+
+bool
+ValueInternalMap::equals( const IteratorState &x, const IteratorState &other )
+{
+ return x.map_ == other.map_
+ && x.bucketIndex_ == other.bucketIndex_
+ && x.link_ == other.link_
+ && x.itemIndex_ == other.itemIndex_;
+}
+
+
+void
+ValueInternalMap::incrementBucket( IteratorState &iterator )
+{
+ ++iterator.bucketIndex_;
+ JSON_ASSERT_MESSAGE( iterator.bucketIndex_ <= iterator.map_->bucketsSize_,
+ "ValueInternalMap::increment(): attempting to iterate beyond end." );
+ if ( iterator.bucketIndex_ == iterator.map_->bucketsSize_ )
+ iterator.link_ = 0;
+ else
+ iterator.link_ = &(iterator.map_->buckets_[iterator.bucketIndex_]);
+ iterator.itemIndex_ = 0;
+}
+
+
+void
+ValueInternalMap::increment( IteratorState &iterator )
+{
+ JSON_ASSERT_MESSAGE( iterator.map_, "Attempting to iterator using invalid iterator." );
+ ++iterator.itemIndex_;
+ if ( iterator.itemIndex_ == ValueInternalLink::itemPerLink )
+ {
+ JSON_ASSERT_MESSAGE( iterator.link_ != 0,
+ "ValueInternalMap::increment(): attempting to iterate beyond end." );
+ iterator.link_ = iterator.link_->next_;
+ if ( iterator.link_ == 0 )
+ incrementBucket( iterator );
+ }
+ else if ( iterator.link_->items_[iterator.itemIndex_].isItemAvailable() )
+ {
+ incrementBucket( iterator );
+ }
+}
+
+
+void
+ValueInternalMap::decrement( IteratorState &iterator )
+{
+ if ( iterator.itemIndex_ == 0 )
+ {
+ JSON_ASSERT_MESSAGE( iterator.map_, "Attempting to iterate using invalid iterator." );
+ if ( iterator.link_ == &iterator.map_->buckets_[iterator.bucketIndex_] )
+ {
+ JSON_ASSERT_MESSAGE( iterator.bucketIndex_ > 0, "Attempting to iterate beyond beginning." );
+ --(iterator.bucketIndex_);
+ }
+ iterator.link_ = iterator.link_->previous_;
+ iterator.itemIndex_ = ValueInternalLink::itemPerLink - 1;
+ }
+}
+
+
+const char *
+ValueInternalMap::key( const IteratorState &iterator )
+{
+ JSON_ASSERT_MESSAGE( iterator.link_, "Attempting to iterate using invalid iterator." );
+ return iterator.link_->keys_[iterator.itemIndex_];
+}
+
+const char *
+ValueInternalMap::key( const IteratorState &iterator, bool &isStatic )
+{
+ JSON_ASSERT_MESSAGE( iterator.link_, "Attempting to iterate using invalid iterator." );
+ isStatic = iterator.link_->items_[iterator.itemIndex_].isMemberNameStatic();
+ return iterator.link_->keys_[iterator.itemIndex_];
+}
+
+
+Value &
+ValueInternalMap::value( const IteratorState &iterator )
+{
+ JSON_ASSERT_MESSAGE( iterator.link_, "Attempting to iterate using invalid iterator." );
+ return iterator.link_->items_[iterator.itemIndex_];
+}
+
+
+int
+ValueInternalMap::distance( const IteratorState &x, const IteratorState &y )
+{
+ int offset = 0;
+ IteratorState it = x;
+ while ( !equals( it, y ) )
+ increment( it );
+ return offset;
+}
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#include "json_reader.h"
+#include "json_value.h"
+#include "json_tool.h"
+#include <utility>
+#include <cstdio>
+#include <cassert>
+#include <cstring>
+#include <iostream>
+#include <stdexcept>
+
+#if _MSC_VER >= 1400 // VC++ 8.0
+#pragma warning( disable : 4996 ) // disable warning about strdup being deprecated.
+#endif
+
+namespace Json {
+
+// Implementation of class Features
+// ////////////////////////////////
+
+Features::Features()
+ : allowComments_( true )
+ , strictRoot_( false )
+{
+}
+
+
+Features
+Features::all()
+{
+ return Features();
+}
+
+
+Features
+Features::strictMode()
+{
+ Features features;
+ features.allowComments_ = false;
+ features.strictRoot_ = true;
+ return features;
+}
+
+// Implementation of class Reader
+// ////////////////////////////////
+
+
+static inline bool
+in( Reader::Char c, Reader::Char c1, Reader::Char c2, Reader::Char c3, Reader::Char c4 )
+{
+ return c == c1 || c == c2 || c == c3 || c == c4;
+}
+
+static inline bool
+in( Reader::Char c, Reader::Char c1, Reader::Char c2, Reader::Char c3, Reader::Char c4, Reader::Char c5 )
+{
+ return c == c1 || c == c2 || c == c3 || c == c4 || c == c5;
+}
+
+
+static bool
+containsNewLine( Reader::Location begin,
+ Reader::Location end )
+{
+ for ( ;begin < end; ++begin )
+ if ( *begin == '\n' || *begin == '\r' )
+ return true;
+ return false;
+}
+
+
+// Class Reader
+// //////////////////////////////////////////////////////////////////
+
+Reader::Reader()
+ : features_( Features::all() )
+{
+}
+
+
+Reader::Reader( const Features &features )
+ : features_( features )
+{
+}
+
+
+bool
+Reader::parse( const std::string &document,
+ Value &root,
+ bool collectComments )
+{
+ document_ = document;
+ const char *begin = document_.c_str();
+ const char *end = begin + document_.length();
+ return parse( begin, end, root, collectComments );
+}
+
+
+bool
+Reader::parse( std::istream& sin,
+ Value &root,
+ bool collectComments )
+{
+ //std::istream_iterator<char> begin(sin);
+ //std::istream_iterator<char> end;
+ // Those would allow streamed input from a file, if parse() were a
+ // template function.
+
+ // Since std::string is reference-counted, this at least does not
+ // create an extra copy.
+ std::string doc;
+ std::getline(sin, doc, (char)EOF);
+ return parse( doc, root, collectComments );
+}
+
+bool
+Reader::parse( const char *beginDoc, const char *endDoc,
+ Value &root,
+ bool collectComments )
+{
+ if ( !features_.allowComments_ )
+ {
+ collectComments = false;
+ }
+
+ begin_ = beginDoc;
+ end_ = endDoc;
+ collectComments_ = collectComments;
+ current_ = begin_;
+ lastValueEnd_ = 0;
+ lastValue_ = 0;
+ commentsBefore_ = "";
+ errors_.clear();
+ while ( !nodes_.empty() )
+ nodes_.pop();
+ nodes_.push( &root );
+
+ bool successful = readValue();
+ Token token;
+ skipCommentTokens( token );
+ if ( collectComments_ && !commentsBefore_.empty() )
+ root.setComment( commentsBefore_, commentAfter );
+ if ( features_.strictRoot_ )
+ {
+ if ( !root.isArray() && !root.isObject() )
+ {
+ // Set error location to start of doc, ideally should be first token found in doc
+ token.type_ = tokenError;
+ token.start_ = beginDoc;
+ token.end_ = endDoc;
+ addError( "A valid JSON document must be either an array or an object value.",
+ token );
+ return false;
+ }
+ }
+ return successful;
+}
+
+
+bool
+Reader::readValue()
+{
+ Token token;
+ skipCommentTokens( token );
+ bool successful = true;
+
+ if ( collectComments_ && !commentsBefore_.empty() )
+ {
+ currentValue().setComment( commentsBefore_, commentBefore );
+ commentsBefore_ = "";
+ }
+
+
+ switch ( token.type_ )
+ {
+ case tokenObjectBegin:
+ successful = readObject( token );
+ break;
+ case tokenArrayBegin:
+ successful = readArray( token );
+ break;
+ case tokenNumber:
+ successful = decodeNumber( token );
+ break;
+ case tokenString:
+ successful = decodeString( token );
+ break;
+ case tokenTrue:
+ currentValue() = true;
+ break;
+ case tokenFalse:
+ currentValue() = false;
+ break;
+ case tokenNull:
+ currentValue() = Value();
+ break;
+ default:
+ return addError( "Syntax error: value, object or array expected.", token );
+ }
+
+ if ( collectComments_ )
+ {
+ lastValueEnd_ = current_;
+ lastValue_ = ¤tValue();
+ }
+
+ return successful;
+}
+
+
+void
+Reader::skipCommentTokens( Token &token )
+{
+ if ( features_.allowComments_ )
+ {
+ do
+ {
+ readToken( token );
+ }
+ while ( token.type_ == tokenComment );
+ }
+ else
+ {
+ readToken( token );
+ }
+}
+
+
+bool
+Reader::expectToken( TokenType type, Token &token, const char *message )
+{
+ readToken( token );
+ if ( token.type_ != type )
+ return addError( message, token );
+ return true;
+}
+
+
+bool
+Reader::readToken( Token &token )
+{
+ skipSpaces();
+ token.start_ = current_;
+ Char c = getNextChar();
+ bool ok = true;
+ switch ( c )
+ {
+ case '{':
+ token.type_ = tokenObjectBegin;
+ break;
+ case '}':
+ token.type_ = tokenObjectEnd;
+ break;
+ case '[':
+ token.type_ = tokenArrayBegin;
+ break;
+ case ']':
+ token.type_ = tokenArrayEnd;
+ break;
+ case '"':
+ token.type_ = tokenString;
+ ok = readString();
+ break;
+ case '/':
+ token.type_ = tokenComment;
+ ok = readComment();
+ break;
+ case '0':
+ case '1':
+ case '2':
+ case '3':
+ case '4':
+ case '5':
+ case '6':
+ case '7':
+ case '8':
+ case '9':
+ case '-':
+ token.type_ = tokenNumber;
+ readNumber();
+ break;
+ case 't':
+ token.type_ = tokenTrue;
+ ok = match( "rue", 3 );
+ break;
+ case 'f':
+ token.type_ = tokenFalse;
+ ok = match( "alse", 4 );
+ break;
+ case 'n':
+ token.type_ = tokenNull;
+ ok = match( "ull", 3 );
+ break;
+ case ',':
+ token.type_ = tokenArraySeparator;
+ break;
+ case ':':
+ token.type_ = tokenMemberSeparator;
+ break;
+ case 0:
+ token.type_ = tokenEndOfStream;
+ break;
+ default:
+ ok = false;
+ break;
+ }
+ if ( !ok )
+ token.type_ = tokenError;
+ token.end_ = current_;
+ return true;
+}
+
+
+void
+Reader::skipSpaces()
+{
+ while ( current_ != end_ )
+ {
+ Char c = *current_;
+ if ( c == ' ' || c == '\t' || c == '\r' || c == '\n' )
+ ++current_;
+ else
+ break;
+ }
+}
+
+
+bool
+Reader::match( Location pattern,
+ int patternLength )
+{
+ if ( end_ - current_ < patternLength )
+ return false;
+ int index = patternLength;
+ while ( index-- )
+ if ( current_[index] != pattern[index] )
+ return false;
+ current_ += patternLength;
+ return true;
+}
+
+
+bool
+Reader::readComment()
+{
+ Location commentBegin = current_ - 1;
+ Char c = getNextChar();
+ bool successful = false;
+ if ( c == '*' )
+ successful = readCStyleComment();
+ else if ( c == '/' )
+ successful = readCppStyleComment();
+ if ( !successful )
+ return false;
+
+ if ( collectComments_ )
+ {
+ CommentPlacement placement = commentBefore;
+ if ( lastValueEnd_ && !containsNewLine( lastValueEnd_, commentBegin ) )
+ {
+ if ( c != '*' || !containsNewLine( commentBegin, current_ ) )
+ placement = commentAfterOnSameLine;
+ }
+
+ addComment( commentBegin, current_, placement );
+ }
+ return true;
+}
+
+
+void
+Reader::addComment( Location begin,
+ Location end,
+ CommentPlacement placement )
+{
+ assert( collectComments_ );
+ if ( placement == commentAfterOnSameLine )
+ {
+ assert( lastValue_ != 0 );
+ lastValue_->setComment( std::string( begin, end ), placement );
+ }
+ else
+ {
+ if ( !commentsBefore_.empty() )
+ commentsBefore_ += "\n";
+ commentsBefore_ += std::string( begin, end );
+ }
+}
+
+
+bool
+Reader::readCStyleComment()
+{
+ while ( current_ != end_ )
+ {
+ Char c = getNextChar();
+ if ( c == '*' && *current_ == '/' )
+ break;
+ }
+ return getNextChar() == '/';
+}
+
+
+bool
+Reader::readCppStyleComment()
+{
+ while ( current_ != end_ )
+ {
+ Char c = getNextChar();
+ if ( c == '\r' || c == '\n' )
+ break;
+ }
+ return true;
+}
+
+
+void
+Reader::readNumber()
+{
+ while ( current_ != end_ )
+ {
+ if ( !(*current_ >= '0' && *current_ <= '9') &&
+ !in( *current_, '.', 'e', 'E', '+', '-' ) )
+ break;
+ ++current_;
+ }
+}
+
+bool
+Reader::readString()
+{
+ Char c = 0;
+ while ( current_ != end_ )
+ {
+ c = getNextChar();
+ if ( c == '\\' )
+ getNextChar();
+ else if ( c == '"' )
+ break;
+ }
+ return c == '"';
+}
+
+
+bool
+Reader::readObject( Token &tokenStart )
+{
+ Token tokenName;
+ std::string name;
+ currentValue() = Value( objectValue );
+ while ( readToken( tokenName ) )
+ {
+ bool initialTokenOk = true;
+ while ( tokenName.type_ == tokenComment && initialTokenOk )
+ initialTokenOk = readToken( tokenName );
+ if ( !initialTokenOk )
+ break;
+ if ( tokenName.type_ == tokenObjectEnd && name.empty() ) // empty object
+ return true;
+ if ( tokenName.type_ != tokenString )
+ break;
+
+ name = "";
+ if ( !decodeString( tokenName, name ) )
+ return recoverFromError( tokenObjectEnd );
+
+ Token colon;
+ if ( !readToken( colon ) || colon.type_ != tokenMemberSeparator )
+ {
+ return addErrorAndRecover( "Missing ':' after object member name",
+ colon,
+ tokenObjectEnd );
+ }
+ Value &value = currentValue()[ name ];
+ nodes_.push( &value );
+ bool ok = readValue();
+ nodes_.pop();
+ if ( !ok ) // error already set
+ return recoverFromError( tokenObjectEnd );
+
+ Token comma;
+ if ( !readToken( comma )
+ || ( comma.type_ != tokenObjectEnd &&
+ comma.type_ != tokenArraySeparator &&
+ comma.type_ != tokenComment ) )
+ {
+ return addErrorAndRecover( "Missing ',' or '}' in object declaration",
+ comma,
+ tokenObjectEnd );
+ }
+ bool finalizeTokenOk = true;
+ while ( comma.type_ == tokenComment &&
+ finalizeTokenOk )
+ finalizeTokenOk = readToken( comma );
+ if ( comma.type_ == tokenObjectEnd )
+ return true;
+ }
+ return addErrorAndRecover( "Missing '}' or object member name",
+ tokenName,
+ tokenObjectEnd );
+}
+
+
+bool
+Reader::readArray( Token &tokenStart )
+{
+ currentValue() = Value( arrayValue );
+ skipSpaces();
+ if ( *current_ == ']' ) // empty array
+ {
+ Token endArray;
+ readToken( endArray );
+ return true;
+ }
+ int index = 0;
+ while ( true )
+ {
+ Value &value = currentValue()[ index++ ];
+ nodes_.push( &value );
+ bool ok = readValue();
+ nodes_.pop();
+ if ( !ok ) // error already set
+ return recoverFromError( tokenArrayEnd );
+
+ Token token;
+ // Accept Comment after last item in the array.
+ ok = readToken( token );
+ while ( token.type_ == tokenComment && ok )
+ {
+ ok = readToken( token );
+ }
+ bool badTokenType = ( token.type_ == tokenArraySeparator &&
+ token.type_ == tokenArrayEnd );
+ if ( !ok || badTokenType )
+ {
+ return addErrorAndRecover( "Missing ',' or ']' in array declaration",
+ token,
+ tokenArrayEnd );
+ }
+ if ( token.type_ == tokenArrayEnd )
+ break;
+ }
+ return true;
+}
+
+
+bool
+Reader::decodeNumber( Token &token )
+{
+ bool isDouble = false;
+ for ( Location inspect = token.start_; inspect != token.end_; ++inspect )
+ {
+ isDouble = isDouble
+ || in( *inspect, '.', 'e', 'E', '+' )
+ || ( *inspect == '-' && inspect != token.start_ );
+ }
+ if ( isDouble )
+ return decodeDouble( token );
+ // Attempts to parse the number as an integer. If the number is
+ // larger than the maximum supported value of an integer then
+ // we decode the number as a double.
+ Location current = token.start_;
+ bool isNegative = *current == '-';
+ if ( isNegative )
+ ++current;
+ Value::UInt maxIntegerValue = isNegative ? Value::UInt(-Value::minInt)
+ : Value::maxUInt;
+ Value::UInt threshold = maxIntegerValue / 10;
+ Value::UInt lastDigitThreshold = maxIntegerValue % 10;
+ assert( lastDigitThreshold >=0 && lastDigitThreshold <= 9 );
+ Value::UInt value = 0;
+ while ( current < token.end_ )
+ {
+ Char c = *current++;
+ if ( c < '0' || c > '9' )
+ return addError( "'" + std::string( token.start_, token.end_ ) + "' is not a number.", token );
+ Value::UInt digit(c - '0');
+ if ( value >= threshold )
+ {
+ // If the current digit is not the last one, or if it is
+ // greater than the last digit of the maximum integer value,
+ // the parse the number as a double.
+ if ( current != token.end_ || digit > lastDigitThreshold )
+ {
+ return decodeDouble( token );
+ }
+ }
+ value = value * 10 + digit;
+ }
+ if ( isNegative )
+ currentValue() = -Value::Int( value );
+ else if ( value <= Value::UInt(Value::maxInt) )
+ currentValue() = Value::Int( value );
+ else
+ currentValue() = value;
+ return true;
+}
+
+
+bool
+Reader::decodeDouble( Token &token )
+{
+ double value = 0;
+ const int bufferSize = 32;
+ int count;
+ int length = int(token.end_ - token.start_);
+ if ( length <= bufferSize )
+ {
+ Char buffer[bufferSize];
+ memcpy( buffer, token.start_, length );
+ buffer[length] = 0;
+ count = sscanf( buffer, "%lf", &value );
+ }
+ else
+ {
+ std::string buffer( token.start_, token.end_ );
+ count = sscanf( buffer.c_str(), "%lf", &value );
+ }
+
+ if ( count != 1 )
+ return addError( "'" + std::string( token.start_, token.end_ ) + "' is not a number.", token );
+ currentValue() = value;
+ return true;
+}
+
+
+bool
+Reader::decodeString( Token &token )
+{
+ std::string decoded;
+ if ( !decodeString( token, decoded ) )
+ return false;
+ currentValue() = decoded;
+ return true;
+}
+
+
+bool
+Reader::decodeString( Token &token, std::string &decoded )
+{
+ decoded.reserve( token.end_ - token.start_ - 2 );
+ Location current = token.start_ + 1; // skip '"'
+ Location end = token.end_ - 1; // do not include '"'
+ while ( current != end )
+ {
+ Char c = *current++;
+ if ( c == '"' )
+ break;
+ else if ( c == '\\' )
+ {
+ if ( current == end )
+ return addError( "Empty escape sequence in string", token, current );
+ Char escape = *current++;
+ switch ( escape )
+ {
+ case '"': decoded += '"'; break;
+ case '/': decoded += '/'; break;
+ case '\\': decoded += '\\'; break;
+ case 'b': decoded += '\b'; break;
+ case 'f': decoded += '\f'; break;
+ case 'n': decoded += '\n'; break;
+ case 'r': decoded += '\r'; break;
+ case 't': decoded += '\t'; break;
+ case 'u':
+ {
+ unsigned int unicode;
+ if ( !decodeUnicodeCodePoint( token, current, end, unicode ) )
+ return false;
+ decoded += codePointToUTF8(unicode);
+ }
+ break;
+ default:
+ return addError( "Bad escape sequence in string", token, current );
+ }
+ }
+ else
+ {
+ decoded += c;
+ }
+ }
+ return true;
+}
+
+bool
+Reader::decodeUnicodeCodePoint( Token &token,
+ Location ¤t,
+ Location end,
+ unsigned int &unicode )
+{
+
+ if ( !decodeUnicodeEscapeSequence( token, current, end, unicode ) )
+ return false;
+ if (unicode >= 0xD800 && unicode <= 0xDBFF)
+ {
+ // surrogate pairs
+ if (end - current < 6)
+ return addError( "additional six characters expected to parse unicode surrogate pair.", token, current );
+ unsigned int surrogatePair;
+ if (*(current++) == '\\' && *(current++)== 'u')
+ {
+ if (decodeUnicodeEscapeSequence( token, current, end, surrogatePair ))
+ {
+ unicode = 0x10000 + ((unicode & 0x3FF) << 10) + (surrogatePair & 0x3FF);
+ }
+ else
+ return false;
+ }
+ else
+ return addError( "expecting another \\u token to begin the second half of a unicode surrogate pair", token, current );
+ }
+ return true;
+}
+
+bool
+Reader::decodeUnicodeEscapeSequence( Token &token,
+ Location ¤t,
+ Location end,
+ unsigned int &unicode )
+{
+ if ( end - current < 4 )
+ return addError( "Bad unicode escape sequence in string: four digits expected.", token, current );
+ unicode = 0;
+ for ( int index =0; index < 4; ++index )
+ {
+ Char c = *current++;
+ unicode *= 16;
+ if ( c >= '0' && c <= '9' )
+ unicode += c - '0';
+ else if ( c >= 'a' && c <= 'f' )
+ unicode += c - 'a' + 10;
+ else if ( c >= 'A' && c <= 'F' )
+ unicode += c - 'A' + 10;
+ else
+ return addError( "Bad unicode escape sequence in string: hexadecimal digit expected.", token, current );
+ }
+ return true;
+}
+
+
+bool
+Reader::addError( const std::string &message,
+ Token &token,
+ Location extra )
+{
+ ErrorInfo info;
+ info.token_ = token;
+ info.message_ = message;
+ info.extra_ = extra;
+ errors_.push_back( info );
+ return false;
+}
+
+
+bool
+Reader::recoverFromError( TokenType skipUntilToken )
+{
+ int errorCount = int(errors_.size());
+ Token skip;
+ while ( true )
+ {
+ if ( !readToken(skip) )
+ errors_.resize( errorCount ); // discard errors caused by recovery
+ if ( skip.type_ == skipUntilToken || skip.type_ == tokenEndOfStream )
+ break;
+ }
+ errors_.resize( errorCount );
+ return false;
+}
+
+
+bool
+Reader::addErrorAndRecover( const std::string &message,
+ Token &token,
+ TokenType skipUntilToken )
+{
+ addError( message, token );
+ return recoverFromError( skipUntilToken );
+}
+
+
+Value &
+Reader::currentValue()
+{
+ return *(nodes_.top());
+}
+
+
+Reader::Char
+Reader::getNextChar()
+{
+ if ( current_ == end_ )
+ return 0;
+ return *current_++;
+}
+
+
+void
+Reader::getLocationLineAndColumn( Location location,
+ int &line,
+ int &column ) const
+{
+ Location current = begin_;
+ Location lastLineStart = current;
+ line = 0;
+ while ( current < location && current != end_ )
+ {
+ Char c = *current++;
+ if ( c == '\r' )
+ {
+ if ( *current == '\n' )
+ ++current;
+ lastLineStart = current;
+ ++line;
+ }
+ else if ( c == '\n' )
+ {
+ lastLineStart = current;
+ ++line;
+ }
+ }
+ // column & line start at 1
+ column = int(location - lastLineStart) + 1;
+ ++line;
+}
+
+
+std::string
+Reader::getLocationLineAndColumn( Location location ) const
+{
+ int line, column;
+ getLocationLineAndColumn( location, line, column );
+ char buffer[18+16+16+1];
+ sprintf( buffer, "Line %d, Column %d", line, column );
+ return buffer;
+}
+
+
+std::string
+Reader::getFormatedErrorMessages() const
+{
+ std::string formattedMessage;
+ for ( Errors::const_iterator itError = errors_.begin();
+ itError != errors_.end();
+ ++itError )
+ {
+ const ErrorInfo &error = *itError;
+ formattedMessage += "* " + getLocationLineAndColumn( error.token_.start_ ) + "\n";
+ formattedMessage += " " + error.message_ + "\n";
+ if ( error.extra_ )
+ formattedMessage += "See " + getLocationLineAndColumn( error.extra_ ) + " for detail.\n";
+ }
+ return formattedMessage;
+}
+
+
+std::istream& operator>>( std::istream &sin, Value &root )
+{
+ Json::Reader reader;
+ bool ok = reader.parse(sin, root, true);
+ //JSON_ASSERT( ok );
+ if (!ok) throw std::runtime_error(reader.getFormatedErrorMessages());
+ return sin;
+}
+
+
+} // namespace Json
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#ifndef CPPTL_JSON_READER_H_INCLUDED
+# define CPPTL_JSON_READER_H_INCLUDED
+
+# include "json_features.h"
+# include "json_value.h"
+# include <deque>
+# include <stack>
+# include <string>
+# include <iostream>
+
+namespace Json {
+
+ /** \brief Unserialize a <a HREF="http://www.json.org">JSON</a> document into a Value.
+ *
+ */
+ class JSON_API Reader
+ {
+ public:
+ typedef char Char;
+ typedef const Char *Location;
+
+ /** \brief Constructs a Reader allowing all features
+ * for parsing.
+ */
+ Reader();
+
+ /** \brief Constructs a Reader allowing the specified feature set
+ * for parsing.
+ */
+ Reader( const Features &features );
+
+ /** \brief Read a Value from a <a HREF="http://www.json.org">JSON</a> document.
+ * \param document UTF-8 encoded string containing the document to read.
+ * \param root [out] Contains the root value of the document if it was
+ * successfully parsed.
+ * \param collectComments \c true to collect comment and allow writing them back during
+ * serialization, \c false to discard comments.
+ * This parameter is ignored if Features::allowComments_
+ * is \c false.
+ * \return \c true if the document was successfully parsed, \c false if an error occurred.
+ */
+ bool parse( const std::string &document,
+ Value &root,
+ bool collectComments = true );
+
+ /** \brief Read a Value from a <a HREF="http://www.json.org">JSON</a> document.
+ * \param document UTF-8 encoded string containing the document to read.
+ * \param root [out] Contains the root value of the document if it was
+ * successfully parsed.
+ * \param collectComments \c true to collect comment and allow writing them back during
+ * serialization, \c false to discard comments.
+ * This parameter is ignored if Features::allowComments_
+ * is \c false.
+ * \return \c true if the document was successfully parsed, \c false if an error occurred.
+ */
+ bool parse( const char *beginDoc, const char *endDoc,
+ Value &root,
+ bool collectComments = true );
+
+ /// \brief Parse from input stream.
+ /// \see Json::operator>>(std::istream&, Json::Value&).
+ bool parse( std::istream &is,
+ Value &root,
+ bool collectComments = true );
+
+ /** \brief Returns a user friendly string that list errors in the parsed document.
+ * \return Formatted error message with the list of errors with their location in
+ * the parsed document. An empty string is returned if no error occurred
+ * during parsing.
+ */
+ std::string getFormatedErrorMessages() const;
+
+ private:
+ enum TokenType
+ {
+ tokenEndOfStream = 0,
+ tokenObjectBegin,
+ tokenObjectEnd,
+ tokenArrayBegin,
+ tokenArrayEnd,
+ tokenString,
+ tokenNumber,
+ tokenTrue,
+ tokenFalse,
+ tokenNull,
+ tokenArraySeparator,
+ tokenMemberSeparator,
+ tokenComment,
+ tokenError
+ };
+
+ class Token
+ {
+ public:
+ TokenType type_;
+ Location start_;
+ Location end_;
+ };
+
+ class ErrorInfo
+ {
+ public:
+ Token token_;
+ std::string message_;
+ Location extra_;
+ };
+
+ typedef std::deque<ErrorInfo> Errors;
+
+ bool expectToken( TokenType type, Token &token, const char *message );
+ bool readToken( Token &token );
+ void skipSpaces();
+ bool match( Location pattern,
+ int patternLength );
+ bool readComment();
+ bool readCStyleComment();
+ bool readCppStyleComment();
+ bool readString();
+ void readNumber();
+ bool readValue();
+ bool readObject( Token &token );
+ bool readArray( Token &token );
+ bool decodeNumber( Token &token );
+ bool decodeString( Token &token );
+ bool decodeString( Token &token, std::string &decoded );
+ bool decodeDouble( Token &token );
+ bool decodeUnicodeCodePoint( Token &token,
+ Location ¤t,
+ Location end,
+ unsigned int &unicode );
+ bool decodeUnicodeEscapeSequence( Token &token,
+ Location ¤t,
+ Location end,
+ unsigned int &unicode );
+ bool addError( const std::string &message,
+ Token &token,
+ Location extra = 0 );
+ bool recoverFromError( TokenType skipUntilToken );
+ bool addErrorAndRecover( const std::string &message,
+ Token &token,
+ TokenType skipUntilToken );
+ void skipUntilSpace();
+ Value ¤tValue();
+ Char getNextChar();
+ void getLocationLineAndColumn( Location location,
+ int &line,
+ int &column ) const;
+ std::string getLocationLineAndColumn( Location location ) const;
+ void addComment( Location begin,
+ Location end,
+ CommentPlacement placement );
+ void skipCommentTokens( Token &token );
+
+ typedef std::stack<Value *> Nodes;
+ Nodes nodes_;
+ Errors errors_;
+ std::string document_;
+ Location begin_;
+ Location end_;
+ Location current_;
+ Location lastValueEnd_;
+ Value *lastValue_;
+ std::string commentsBefore_;
+ Features features_;
+ bool collectComments_;
+ };
+
+ /** \brief Read from 'sin' into 'root'.
+
+ Always keep comments from the input JSON.
+
+ This can be used to read a file into a particular sub-object.
+ For example:
+ \code
+ Json::Value root;
+ cin >> root["dir"]["file"];
+ cout << root;
+ \endcode
+ Result:
+ \verbatim
+ {
+ "dir": {
+ "file": {
+ // The input stream JSON would be nested here.
+ }
+ }
+ }
+ \endverbatim
+ \throw std::exception on parse error.
+ \see Json::operator<<()
+ */
+ std::istream& operator>>( std::istream&, Value& );
+
+} // namespace Json
+
+#endif // CPPTL_JSON_READER_H_INCLUDED
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#ifndef LIB_JSONCPP_JSON_TOOL_H_INCLUDED
+# define LIB_JSONCPP_JSON_TOOL_H_INCLUDED
+
+/* This header provides common string manipulation support, such as UTF-8,
+ * portable conversion from/to string...
+ *
+ * It is an internal header that must not be exposed.
+ */
+
+namespace Json {
+
+/// Converts a unicode code-point to UTF-8.
+static inline std::string
+codePointToUTF8(unsigned int cp)
+{
+ std::string result;
+
+ // based on description from http://en.wikipedia.org/wiki/UTF-8
+
+ if (cp <= 0x7f)
+ {
+ result.resize(1);
+ result[0] = static_cast<char>(cp);
+ }
+ else if (cp <= 0x7FF)
+ {
+ result.resize(2);
+ result[1] = static_cast<char>(0x80 | (0x3f & cp));
+ result[0] = static_cast<char>(0xC0 | (0x1f & (cp >> 6)));
+ }
+ else if (cp <= 0xFFFF)
+ {
+ result.resize(3);
+ result[2] = static_cast<char>(0x80 | (0x3f & cp));
+ result[1] = 0x80 | static_cast<char>((0x3f & (cp >> 6)));
+ result[0] = 0xE0 | static_cast<char>((0xf & (cp >> 12)));
+ }
+ else if (cp <= 0x10FFFF)
+ {
+ result.resize(4);
+ result[3] = static_cast<char>(0x80 | (0x3f & cp));
+ result[2] = static_cast<char>(0x80 | (0x3f & (cp >> 6)));
+ result[1] = static_cast<char>(0x80 | (0x3f & (cp >> 12)));
+ result[0] = static_cast<char>(0xF0 | (0x7 & (cp >> 18)));
+ }
+
+ return result;
+}
+
+
+/// Returns true if ch is a control character (in range [0,32[).
+static inline bool
+isControlCharacter(char ch)
+{
+ return ch > 0 && ch <= 0x1F;
+}
+
+
+enum {
+ /// Constant that specify the size of the buffer that must be passed to uintToString.
+ uintToStringBufferSize = 3*sizeof(UInt)+1
+};
+
+// Defines a char buffer for use with uintToString().
+typedef char UIntToStringBuffer[uintToStringBufferSize];
+
+
+/** Converts an unsigned integer to string.
+ * @param value Unsigned interger to convert to string
+ * @param current Input/Output string buffer.
+ * Must have at least uintToStringBufferSize chars free.
+ */
+static inline void
+uintToString( UInt value,
+ char *¤t )
+{
+ *--current = 0;
+ do
+ {
+ *--current = char(value % 10) + '0';
+ value /= 10;
+ }
+ while ( value != 0 );
+}
+
+} // namespace Json {
+
+#endif // LIB_JSONCPP_JSON_TOOL_H_INCLUDED
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#include <iostream>
+#include "json_value.h"
+#include "json_writer.h"
+#include <utility>
+#include <stdexcept>
+#include <cstring>
+#include <cassert>
+#ifdef JSON_USE_CPPTL
+# include <cpptl/conststring.h>
+#endif
+#include <cstddef> // size_t
+#ifndef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
+# include "json_batchallocator.h"
+#endif // #ifndef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
+
+#define JSON_ASSERT_UNREACHABLE assert( false )
+#define JSON_ASSERT( condition ) assert( condition ); // @todo <= change this into an exception throw
+#define JSON_ASSERT_MESSAGE( condition, message ) if (!( condition )) throw std::runtime_error( message );
+
+namespace Json {
+
+const Value Value::null;
+const Int Value::minInt = Int( ~(UInt(-1)/2) );
+const Int Value::maxInt = Int( UInt(-1)/2 );
+const UInt Value::maxUInt = UInt(-1);
+
+/// Unknown size marker
+enum { unknown = (unsigned)-1 };
+
+
+/** Duplicates the specified string value.
+ * @param value Pointer to the string to duplicate. Must be zero-terminated if
+ * length is "unknown".
+ * @param length Length of the value. if equals to unknown, then it will be
+ * computed using strlen(value).
+ * @return Pointer on the duplicate instance of string.
+ */
+static inline char *
+duplicateStringValue( const char *value,
+ unsigned int length = unknown )
+{
+ if ( length == unknown )
+ length = (unsigned int)strlen(value);
+ char *newString = static_cast<char *>( malloc( length + 1 ) );
+ memcpy( newString, value, length );
+ newString[length] = 0;
+ return newString;
+}
+
+
+/** Free the string duplicated by duplicateStringValue().
+ */
+static inline void
+releaseStringValue( char *value )
+{
+ if ( value )
+ free( value );
+}
+
+
+
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// ValueInternals...
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+#ifdef JSON_VALUE_USE_INTERNAL_MAP
+# include "json_internalarray.inl"
+# include "json_internalmap.inl"
+#endif // JSON_VALUE_USE_INTERNAL_MAP
+
+# include "json_valueiterator.inl"
+
+
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// class Value::CommentInfo
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+
+
+Value::CommentInfo::CommentInfo()
+ : comment_( 0 )
+{
+}
+
+Value::CommentInfo::~CommentInfo()
+{
+ if ( comment_ )
+ releaseStringValue( comment_ );
+}
+
+
+void
+Value::CommentInfo::setComment( const char *text )
+{
+ if ( comment_ )
+ releaseStringValue( comment_ );
+ JSON_ASSERT( text );
+ JSON_ASSERT_MESSAGE( text[0]=='\0' || text[0]=='/', "Comments must start with /");
+ // It seems that /**/ style comments are acceptable as well.
+ comment_ = duplicateStringValue( text );
+}
+
+
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// class Value::CZString
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+# ifndef JSON_VALUE_USE_INTERNAL_MAP
+
+// Notes: index_ indicates if the string was allocated when
+// a string is stored.
+
+Value::CZString::CZString( ArrayIndex index )
+ : cstr_( 0 )
+ , index_( index )
+{
+}
+
+Value::CZString::CZString( const char *cstr, DuplicationPolicy allocate )
+ : cstr_( allocate == duplicate ? duplicateStringValue(cstr)
+ : cstr )
+ , index_( allocate )
+{
+}
+
+Value::CZString::CZString( const CZString &other )
+: cstr_( other.index_ != noDuplication && other.cstr_ != 0
+ ? duplicateStringValue( other.cstr_ )
+ : other.cstr_ )
+ , index_( other.cstr_ ? (other.index_ == noDuplication ? noDuplication : duplicate)
+ : other.index_ )
+{
+}
+
+Value::CZString::~CZString()
+{
+ if ( cstr_ && index_ == duplicate )
+ releaseStringValue( const_cast<char *>( cstr_ ) );
+}
+
+void
+Value::CZString::swap( CZString &other )
+{
+ std::swap( cstr_, other.cstr_ );
+ std::swap( index_, other.index_ );
+}
+
+Value::CZString &
+Value::CZString::operator =( const CZString &other )
+{
+ CZString temp( other );
+ swap( temp );
+ return *this;
+}
+
+bool
+Value::CZString::operator<( const CZString &other ) const
+{
+ if ( cstr_ )
+ return strcmp( cstr_, other.cstr_ ) < 0;
+ return index_ < other.index_;
+}
+
+bool
+Value::CZString::operator==( const CZString &other ) const
+{
+ if ( cstr_ )
+ return strcmp( cstr_, other.cstr_ ) == 0;
+ return index_ == other.index_;
+}
+
+
+ArrayIndex
+Value::CZString::index() const
+{
+ return index_;
+}
+
+
+const char *
+Value::CZString::c_str() const
+{
+ return cstr_;
+}
+
+bool
+Value::CZString::isStaticString() const
+{
+ return index_ == noDuplication;
+}
+
+#endif // ifndef JSON_VALUE_USE_INTERNAL_MAP
+
+
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// class Value::Value
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+
+/*! \internal Default constructor initialization must be equivalent to:
+ * memset( this, 0, sizeof(Value) )
+ * This optimization is used in ValueInternalMap fast allocator.
+ */
+Value::Value( ValueType type )
+ : type_( type )
+ , allocated_( 0 )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ switch ( type )
+ {
+ case nullValue:
+ break;
+ case intValue:
+ case uintValue:
+ value_.int_ = 0;
+ break;
+ case realValue:
+ value_.real_ = 0.0;
+ break;
+ case stringValue:
+ value_.string_ = 0;
+ break;
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ case arrayValue:
+ case objectValue:
+ value_.map_ = new ObjectValues();
+ break;
+#else
+ case arrayValue:
+ value_.array_ = arrayAllocator()->newArray();
+ break;
+ case objectValue:
+ value_.map_ = mapAllocator()->newMap();
+ break;
+#endif
+ case booleanValue:
+ value_.bool_ = false;
+ break;
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+}
+
+
+#if !defined(JSON_NO_INT64)
+Value::Value( ArrayIndex value )
+ : type_( uintValue )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ value_.uint_ = value;
+}
+
+Value::Value( int value )
+ : type_( intValue )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ value_.int_ = value;
+}
+
+#endif // if !defined(JSON_NO_INT64)
+
+
+Value::Value( Int value )
+ : type_( intValue )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ value_.int_ = value;
+}
+
+
+Value::Value( UInt value )
+ : type_( uintValue )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ value_.uint_ = value;
+}
+
+Value::Value( double value )
+ : type_( realValue )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ value_.real_ = value;
+}
+
+Value::Value( const char *value )
+ : type_( stringValue )
+ , allocated_( true )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ value_.string_ = duplicateStringValue( value );
+}
+
+
+Value::Value( const char *beginValue,
+ const char *endValue )
+ : type_( stringValue )
+ , allocated_( true )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ value_.string_ = duplicateStringValue( beginValue,
+ (unsigned int)(endValue - beginValue) );
+}
+
+
+Value::Value( const std::string &value )
+ : type_( stringValue )
+ , allocated_( true )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ value_.string_ = duplicateStringValue( value.c_str(),
+ (unsigned int)value.length() );
+
+}
+
+Value::Value( const StaticString &value )
+ : type_( stringValue )
+ , allocated_( false )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ value_.string_ = const_cast<char *>( value.c_str() );
+}
+
+
+# ifdef JSON_USE_CPPTL
+Value::Value( const CppTL::ConstString &value )
+ : type_( stringValue )
+ , allocated_( true )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ value_.string_ = duplicateStringValue( value, value.length() );
+}
+# endif
+
+Value::Value( bool value )
+ : type_( booleanValue )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ value_.bool_ = value;
+}
+
+
+Value::Value( const Value &other )
+ : type_( other.type_ )
+ , comments_( 0 )
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ , itemIsUsed_( 0 )
+#endif
+{
+ switch ( type_ )
+ {
+ case nullValue:
+ case intValue:
+ case uintValue:
+ case realValue:
+ case booleanValue:
+ value_ = other.value_;
+ break;
+ case stringValue:
+ if ( other.value_.string_ )
+ {
+ value_.string_ = duplicateStringValue( other.value_.string_ );
+ allocated_ = true;
+ }
+ else
+ value_.string_ = 0;
+ break;
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ case arrayValue:
+ case objectValue:
+ value_.map_ = new ObjectValues( *other.value_.map_ );
+ break;
+#else
+ case arrayValue:
+ value_.array_ = arrayAllocator()->newArrayCopy( *other.value_.array_ );
+ break;
+ case objectValue:
+ value_.map_ = mapAllocator()->newMapCopy( *other.value_.map_ );
+ break;
+#endif
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+ if ( other.comments_ )
+ {
+ comments_ = new CommentInfo[numberOfCommentPlacement];
+ for ( int comment =0; comment < numberOfCommentPlacement; ++comment )
+ {
+ const CommentInfo &otherComment = other.comments_[comment];
+ if ( otherComment.comment_ )
+ comments_[comment].setComment( otherComment.comment_ );
+ }
+ }
+}
+
+
+Value::~Value()
+{
+ switch ( type_ )
+ {
+ case nullValue:
+ case intValue:
+ case uintValue:
+ case realValue:
+ case booleanValue:
+ break;
+ case stringValue:
+ if ( allocated_ )
+ releaseStringValue( value_.string_ );
+ break;
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ case arrayValue:
+ case objectValue:
+ delete value_.map_;
+ break;
+#else
+ case arrayValue:
+ arrayAllocator()->destructArray( value_.array_ );
+ break;
+ case objectValue:
+ mapAllocator()->destructMap( value_.map_ );
+ break;
+#endif
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+
+ if ( comments_ )
+ delete[] comments_;
+}
+
+Value &
+Value::operator=( const Value &other )
+{
+ Value temp( other );
+ swap( temp );
+ return *this;
+}
+
+void
+Value::swap( Value &other )
+{
+ ValueType temp = type_;
+ type_ = other.type_;
+ other.type_ = temp;
+ std::swap( value_, other.value_ );
+ int temp2 = allocated_;
+ allocated_ = other.allocated_;
+ other.allocated_ = temp2;
+}
+
+ValueType
+Value::type() const
+{
+ return type_;
+}
+
+
+int
+Value::compare( const Value &other )
+{
+ /*
+ int typeDelta = other.type_ - type_;
+ switch ( type_ )
+ {
+ case nullValue:
+
+ return other.type_ == type_;
+ case intValue:
+ if ( other.type_.isNumeric()
+ case uintValue:
+ case realValue:
+ case booleanValue:
+ break;
+ case stringValue,
+ break;
+ case arrayValue:
+ delete value_.array_;
+ break;
+ case objectValue:
+ delete value_.map_;
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+ */
+ return 0; // unreachable
+}
+
+bool
+Value::operator <( const Value &other ) const
+{
+ int typeDelta = type_ - other.type_;
+ if ( typeDelta )
+ return typeDelta < 0 ? true : false;
+ switch ( type_ )
+ {
+ case nullValue:
+ return false;
+ case intValue:
+ return value_.int_ < other.value_.int_;
+ case uintValue:
+ return value_.uint_ < other.value_.uint_;
+ case realValue:
+ return value_.real_ < other.value_.real_;
+ case booleanValue:
+ return value_.bool_ < other.value_.bool_;
+ case stringValue:
+ return ( value_.string_ == 0 && other.value_.string_ )
+ || ( other.value_.string_
+ && value_.string_
+ && strcmp( value_.string_, other.value_.string_ ) < 0 );
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ case arrayValue:
+ case objectValue:
+ {
+ int delta = int( value_.map_->size() - other.value_.map_->size() );
+ if ( delta )
+ return delta < 0;
+ return (*value_.map_) < (*other.value_.map_);
+ }
+#else
+ case arrayValue:
+ return value_.array_->compare( *(other.value_.array_) ) < 0;
+ case objectValue:
+ return value_.map_->compare( *(other.value_.map_) ) < 0;
+#endif
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+ return 0; // unreachable
+}
+
+bool
+Value::operator <=( const Value &other ) const
+{
+ return !(other > *this);
+}
+
+bool
+Value::operator >=( const Value &other ) const
+{
+ return !(*this < other);
+}
+
+bool
+Value::operator >( const Value &other ) const
+{
+ return other < *this;
+}
+
+bool
+Value::operator ==( const Value &other ) const
+{
+ //if ( type_ != other.type_ )
+ // GCC 2.95.3 says:
+ // attempt to take address of bit-field structure member `Json::Value::type_'
+ // Beats me, but a temp solves the problem.
+ int temp = other.type_;
+ if ( type_ != temp )
+ return false;
+ switch ( type_ )
+ {
+ case nullValue:
+ return true;
+ case intValue:
+ return value_.int_ == other.value_.int_;
+ case uintValue:
+ return value_.uint_ == other.value_.uint_;
+ case realValue:
+ return value_.real_ == other.value_.real_;
+ case booleanValue:
+ return value_.bool_ == other.value_.bool_;
+ case stringValue:
+ return ( value_.string_ == other.value_.string_ )
+ || ( other.value_.string_
+ && value_.string_
+ && strcmp( value_.string_, other.value_.string_ ) == 0 );
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ case arrayValue:
+ case objectValue:
+ return value_.map_->size() == other.value_.map_->size()
+ && (*value_.map_) == (*other.value_.map_);
+#else
+ case arrayValue:
+ return value_.array_->compare( *(other.value_.array_) ) == 0;
+ case objectValue:
+ return value_.map_->compare( *(other.value_.map_) ) == 0;
+#endif
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+ return 0; // unreachable
+}
+
+bool
+Value::operator !=( const Value &other ) const
+{
+ return !( *this == other );
+}
+
+const char *
+Value::asCString() const
+{
+ JSON_ASSERT( type_ == stringValue );
+ return value_.string_;
+}
+
+
+std::string
+Value::asString() const
+{
+ switch ( type_ )
+ {
+ case nullValue:
+ return "";
+ case stringValue:
+ return value_.string_ ? value_.string_ : "";
+ case booleanValue:
+ return value_.bool_ ? "true" : "false";
+ case intValue:
+ case uintValue:
+ case realValue:
+ case arrayValue:
+ case objectValue:
+ JSON_ASSERT_MESSAGE( false, "Type is not convertible to string" );
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+ return ""; // unreachable
+}
+
+# ifdef JSON_USE_CPPTL
+CppTL::ConstString
+Value::asConstString() const
+{
+ return CppTL::ConstString( asString().c_str() );
+}
+# endif
+
+Value::Int
+Value::asInt() const
+{
+ switch ( type_ )
+ {
+ case nullValue:
+ return 0;
+ case intValue:
+ return value_.int_;
+ case uintValue:
+ JSON_ASSERT_MESSAGE( value_.uint_ < (unsigned)maxInt, "integer out of signed integer range" );
+ return value_.uint_;
+ case realValue:
+ JSON_ASSERT_MESSAGE( value_.real_ >= minInt && value_.real_ <= maxInt, "Real out of signed integer range" );
+ return Int( value_.real_ );
+ case booleanValue:
+ return value_.bool_ ? 1 : 0;
+ case stringValue:
+ case arrayValue:
+ case objectValue:
+ JSON_ASSERT_MESSAGE( false, "Type is not convertible to int" );
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+ return 0; // unreachable;
+}
+
+Value::UInt
+Value::asUInt() const
+{
+ switch ( type_ )
+ {
+ case nullValue:
+ return 0;
+ case intValue:
+ JSON_ASSERT_MESSAGE( value_.int_ >= 0, "Negative integer can not be converted to unsigned integer" );
+ return value_.int_;
+ case uintValue:
+ return value_.uint_;
+ case realValue:
+ JSON_ASSERT_MESSAGE( value_.real_ >= 0 && value_.real_ <= maxUInt, "Real out of unsigned integer range" );
+ return UInt( value_.real_ );
+ case booleanValue:
+ return value_.bool_ ? 1 : 0;
+ case stringValue:
+ case arrayValue:
+ case objectValue:
+ JSON_ASSERT_MESSAGE( false, "Type is not convertible to uint" );
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+ return 0; // unreachable;
+}
+
+double
+Value::asDouble() const
+{
+ switch ( type_ )
+ {
+ case nullValue:
+ return 0.0;
+ case intValue:
+ return static_cast<double>( value_.int_ );
+ case uintValue:
+#if !defined(JSON_USE_INT64_DOUBLE_CONVERSION)
+ return static_cast<double>( value_.uint_ );
+#else // if !defined(JSON_USE_INT64_DOUBLE_CONVERSION)
+ return static_cast<double>( Int(value_.uint_/2) ) * 2 + Int(value_.uint_ & 1);
+#endif // if !defined(JSON_USE_INT64_DOUBLE_CONVERSION)
+ case realValue:
+ return value_.real_;
+ case booleanValue:
+ return value_.bool_ ? 1.0 : 0.0;
+ case stringValue:
+ case arrayValue:
+ case objectValue:
+ JSON_ASSERT_MESSAGE( false, "Type is not convertible to double" );
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+ return 0; // unreachable;
+}
+
+bool
+Value::asBool() const
+{
+ switch ( type_ )
+ {
+ case nullValue:
+ return false;
+ case intValue:
+ case uintValue:
+ return value_.int_ != 0;
+ case realValue:
+ return value_.real_ != 0.0;
+ case booleanValue:
+ return value_.bool_;
+ case stringValue:
+ return value_.string_ && value_.string_[0] != 0;
+ case arrayValue:
+ case objectValue:
+ return value_.map_->size() != 0;
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+ return false; // unreachable;
+}
+
+
+bool
+Value::isConvertibleTo( ValueType other ) const
+{
+ switch ( type_ )
+ {
+ case nullValue:
+ return true;
+ case intValue:
+ return ( other == nullValue && value_.int_ == 0 )
+ || other == intValue
+ || ( other == uintValue && value_.int_ >= 0 )
+ || other == realValue
+ || other == stringValue
+ || other == booleanValue;
+ case uintValue:
+ return ( other == nullValue && value_.uint_ == 0 )
+ || ( other == intValue && value_.uint_ <= (unsigned)maxInt )
+ || other == uintValue
+ || other == realValue
+ || other == stringValue
+ || other == booleanValue;
+ case realValue:
+ return ( other == nullValue && value_.real_ == 0.0 )
+ || ( other == intValue && value_.real_ >= minInt && value_.real_ <= maxInt )
+ || ( other == uintValue && value_.real_ >= 0 && value_.real_ <= maxUInt )
+ || other == realValue
+ || other == stringValue
+ || other == booleanValue;
+ case booleanValue:
+ return ( other == nullValue && value_.bool_ == false )
+ || other == intValue
+ || other == uintValue
+ || other == realValue
+ || other == stringValue
+ || other == booleanValue;
+ case stringValue:
+ return other == stringValue
+ || ( other == nullValue && (!value_.string_ || value_.string_[0] == 0) );
+ case arrayValue:
+ return other == arrayValue
+ || ( other == nullValue && value_.map_->size() == 0 );
+ case objectValue:
+ return other == objectValue
+ || ( other == nullValue && value_.map_->size() == 0 );
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+ return false; // unreachable;
+}
+
+
+/// Number of values in array or object
+ArrayIndex
+Value::size() const
+{
+ switch ( type_ )
+ {
+ case nullValue:
+ case intValue:
+ case uintValue:
+ case realValue:
+ case booleanValue:
+ case stringValue:
+ return 0;
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ case arrayValue: // size of the array is highest index + 1
+ if ( !value_.map_->empty() )
+ {
+ ObjectValues::const_iterator itLast = value_.map_->end();
+ --itLast;
+ return (*itLast).first.index()+1;
+ }
+ return 0;
+ case objectValue:
+ return ArrayIndex( value_.map_->size() );
+#else
+ case arrayValue:
+ return Int( value_.array_->size() );
+ case objectValue:
+ return Int( value_.map_->size() );
+#endif
+ default:
+ JSON_ASSERT_UNREACHABLE;
+ }
+ return 0; // unreachable;
+}
+
+
+bool
+Value::empty() const
+{
+ if ( isNull() || isArray() || isObject() )
+ return size() == 0u;
+ else
+ return false;
+}
+
+
+bool
+Value::operator!() const
+{
+ return isNull();
+}
+
+
+void
+Value::clear()
+{
+ JSON_ASSERT( type_ == nullValue || type_ == arrayValue || type_ == objectValue );
+
+ switch ( type_ )
+ {
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ case arrayValue:
+ case objectValue:
+ value_.map_->clear();
+ break;
+#else
+ case arrayValue:
+ value_.array_->clear();
+ break;
+ case objectValue:
+ value_.map_->clear();
+ break;
+#endif
+ default:
+ break;
+ }
+}
+
+void
+Value::resize( ArrayIndex newSize )
+{
+ JSON_ASSERT( type_ == nullValue || type_ == arrayValue );
+ if ( type_ == nullValue )
+ *this = Value( arrayValue );
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ ArrayIndex oldSize = size();
+ if ( newSize == 0 )
+ clear();
+ else if ( newSize > oldSize )
+ (*this)[ newSize - 1 ];
+ else
+ {
+ for ( ArrayIndex index = newSize; index < oldSize; ++index )
+ {
+ value_.map_->erase( index );
+ }
+ assert( size() == newSize );
+ }
+#else
+ value_.array_->resize( newSize );
+#endif
+}
+
+
+Value &
+Value::operator[]( ArrayIndex index )
+{
+ JSON_ASSERT( type_ == nullValue || type_ == arrayValue );
+ if ( type_ == nullValue )
+ *this = Value( arrayValue );
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ CZString key( index );
+ ObjectValues::iterator it = value_.map_->lower_bound( key );
+ if ( it != value_.map_->end() && (*it).first == key )
+ return (*it).second;
+
+ ObjectValues::value_type defaultValue( key, null );
+ it = value_.map_->insert( it, defaultValue );
+ return (*it).second;
+#else
+ return value_.array_->resolveReference( index );
+#endif
+}
+
+
+const Value &
+Value::operator[]( ArrayIndex index ) const
+{
+ JSON_ASSERT( type_ == nullValue || type_ == arrayValue );
+ if ( type_ == nullValue )
+ return null;
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ CZString key( index );
+ ObjectValues::const_iterator it = value_.map_->find( key );
+ if ( it == value_.map_->end() )
+ return null;
+ return (*it).second;
+#else
+ Value *value = value_.array_->find( index );
+ return value ? *value : null;
+#endif
+}
+
+
+Value &
+Value::operator[]( const char *key )
+{
+ return resolveReference( key, false );
+}
+
+
+Value &
+Value::resolveReference( const char *key,
+ bool isStatic )
+{
+ JSON_ASSERT( type_ == nullValue || type_ == objectValue );
+ if ( type_ == nullValue )
+ *this = Value( objectValue );
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ CZString actualKey( key, isStatic ? CZString::noDuplication
+ : CZString::duplicateOnCopy );
+ ObjectValues::iterator it = value_.map_->lower_bound( actualKey );
+ if ( it != value_.map_->end() && (*it).first == actualKey )
+ return (*it).second;
+
+ ObjectValues::value_type defaultValue( actualKey, null );
+ it = value_.map_->insert( it, defaultValue );
+ Value &value = (*it).second;
+ return value;
+#else
+ return value_.map_->resolveReference( key, isStatic );
+#endif
+}
+
+
+Value
+Value::get( ArrayIndex index,
+ const Value &defaultValue ) const
+{
+ const Value *value = &((*this)[index]);
+ return value == &null ? defaultValue : *value;
+}
+
+
+bool
+Value::isValidIndex( ArrayIndex index ) const
+{
+ return index < size();
+}
+
+
+
+const Value &
+Value::operator[]( const char *key ) const
+{
+ JSON_ASSERT( type_ == nullValue || type_ == objectValue );
+ if ( type_ == nullValue )
+ return null;
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ CZString actualKey( key, CZString::noDuplication );
+ ObjectValues::const_iterator it = value_.map_->find( actualKey );
+ if ( it == value_.map_->end() )
+ return null;
+ return (*it).second;
+#else
+ const Value *value = value_.map_->find( key );
+ return value ? *value : null;
+#endif
+}
+
+
+Value &
+Value::operator[]( const std::string &key )
+{
+ return (*this)[ key.c_str() ];
+}
+
+
+const Value &
+Value::operator[]( const std::string &key ) const
+{
+ return (*this)[ key.c_str() ];
+}
+
+Value &
+Value::operator[]( const StaticString &key )
+{
+ return resolveReference( key, true );
+}
+
+
+# ifdef JSON_USE_CPPTL
+Value &
+Value::operator[]( const CppTL::ConstString &key )
+{
+ return (*this)[ key.c_str() ];
+}
+
+
+const Value &
+Value::operator[]( const CppTL::ConstString &key ) const
+{
+ return (*this)[ key.c_str() ];
+}
+# endif
+
+
+Value &
+Value::append( const Value &value )
+{
+ return (*this)[size()] = value;
+}
+
+
+Value
+Value::get( const char *key,
+ const Value &defaultValue ) const
+{
+ const Value *value = &((*this)[key]);
+ return value == &null ? defaultValue : *value;
+}
+
+
+Value
+Value::get( const std::string &key,
+ const Value &defaultValue ) const
+{
+ return get( key.c_str(), defaultValue );
+}
+
+Value
+Value::removeMember( const char* key )
+{
+ JSON_ASSERT( type_ == nullValue || type_ == objectValue );
+ if ( type_ == nullValue )
+ return null;
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ CZString actualKey( key, CZString::noDuplication );
+ ObjectValues::iterator it = value_.map_->find( actualKey );
+ if ( it == value_.map_->end() )
+ return null;
+ Value old(it->second);
+ value_.map_->erase(it);
+ return old;
+#else
+ Value *value = value_.map_->find( key );
+ if (value){
+ Value old(*value);
+ value_.map_.remove( key );
+ return old;
+ } else {
+ return null;
+ }
+#endif
+}
+
+Value
+Value::removeMember( const std::string &key )
+{
+ return removeMember( key.c_str() );
+}
+
+# ifdef JSON_USE_CPPTL
+Value
+Value::get( const CppTL::ConstString &key,
+ const Value &defaultValue ) const
+{
+ return get( key.c_str(), defaultValue );
+}
+# endif
+
+bool
+Value::isMember( const char *key ) const
+{
+ const Value *value = &((*this)[key]);
+ return value != &null;
+}
+
+
+bool
+Value::isMember( const std::string &key ) const
+{
+ return isMember( key.c_str() );
+}
+
+
+# ifdef JSON_USE_CPPTL
+bool
+Value::isMember( const CppTL::ConstString &key ) const
+{
+ return isMember( key.c_str() );
+}
+#endif
+
+Value::Members
+Value::getMemberNames() const
+{
+ JSON_ASSERT( type_ == nullValue || type_ == objectValue );
+ if ( type_ == nullValue )
+ return Value::Members();
+ Members members;
+ members.reserve( value_.map_->size() );
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ ObjectValues::const_iterator it = value_.map_->begin();
+ ObjectValues::const_iterator itEnd = value_.map_->end();
+ for ( ; it != itEnd; ++it )
+ members.push_back( std::string( (*it).first.c_str() ) );
+#else
+ ValueInternalMap::IteratorState it;
+ ValueInternalMap::IteratorState itEnd;
+ value_.map_->makeBeginIterator( it );
+ value_.map_->makeEndIterator( itEnd );
+ for ( ; !ValueInternalMap::equals( it, itEnd ); ValueInternalMap::increment(it) )
+ members.push_back( std::string( ValueInternalMap::key( it ) ) );
+#endif
+ return members;
+}
+//
+//# ifdef JSON_USE_CPPTL
+//EnumMemberNames
+//Value::enumMemberNames() const
+//{
+// if ( type_ == objectValue )
+// {
+// return CppTL::Enum::any( CppTL::Enum::transform(
+// CppTL::Enum::keys( *(value_.map_), CppTL::Type<const CZString &>() ),
+// MemberNamesTransform() ) );
+// }
+// return EnumMemberNames();
+//}
+//
+//
+//EnumValues
+//Value::enumValues() const
+//{
+// if ( type_ == objectValue || type_ == arrayValue )
+// return CppTL::Enum::anyValues( *(value_.map_),
+// CppTL::Type<const Value &>() );
+// return EnumValues();
+//}
+//
+//# endif
+
+
+bool
+Value::isNull() const
+{
+ return type_ == nullValue;
+}
+
+
+bool
+Value::isBool() const
+{
+ return type_ == booleanValue;
+}
+
+
+bool
+Value::isInt() const
+{
+ return type_ == intValue;
+}
+
+
+bool
+Value::isUInt() const
+{
+ return type_ == uintValue;
+}
+
+
+bool
+Value::isIntegral() const
+{
+ return type_ == intValue
+ || type_ == uintValue
+ || type_ == booleanValue;
+}
+
+
+bool
+Value::isDouble() const
+{
+ return type_ == realValue;
+}
+
+
+bool
+Value::isNumeric() const
+{
+ return isIntegral() || isDouble();
+}
+
+
+bool
+Value::isString() const
+{
+ return type_ == stringValue;
+}
+
+
+bool
+Value::isArray() const
+{
+ return type_ == nullValue || type_ == arrayValue;
+}
+
+
+bool
+Value::isObject() const
+{
+ return type_ == nullValue || type_ == objectValue;
+}
+
+
+void
+Value::setComment( const char *comment,
+ CommentPlacement placement )
+{
+ if ( !comments_ )
+ comments_ = new CommentInfo[numberOfCommentPlacement];
+ comments_[placement].setComment( comment );
+}
+
+
+void
+Value::setComment( const std::string &comment,
+ CommentPlacement placement )
+{
+ setComment( comment.c_str(), placement );
+}
+
+
+bool
+Value::hasComment( CommentPlacement placement ) const
+{
+ return comments_ != 0 && comments_[placement].comment_ != 0;
+}
+
+std::string
+Value::getComment( CommentPlacement placement ) const
+{
+ if ( hasComment(placement) )
+ return comments_[placement].comment_;
+ return "";
+}
+
+
+std::string
+Value::toStyledString() const
+{
+ StyledWriter writer;
+ return writer.write( *this );
+}
+
+
+Value::const_iterator
+Value::begin() const
+{
+ switch ( type_ )
+ {
+#ifdef JSON_VALUE_USE_INTERNAL_MAP
+ case arrayValue:
+ if ( value_.array_ )
+ {
+ ValueInternalArray::IteratorState it;
+ value_.array_->makeBeginIterator( it );
+ return const_iterator( it );
+ }
+ break;
+ case objectValue:
+ if ( value_.map_ )
+ {
+ ValueInternalMap::IteratorState it;
+ value_.map_->makeBeginIterator( it );
+ return const_iterator( it );
+ }
+ break;
+#else
+ case arrayValue:
+ case objectValue:
+ if ( value_.map_ )
+ return const_iterator( value_.map_->begin() );
+ break;
+#endif
+ default:
+ break;
+ }
+ return const_iterator();
+}
+
+Value::const_iterator
+Value::end() const
+{
+ switch ( type_ )
+ {
+#ifdef JSON_VALUE_USE_INTERNAL_MAP
+ case arrayValue:
+ if ( value_.array_ )
+ {
+ ValueInternalArray::IteratorState it;
+ value_.array_->makeEndIterator( it );
+ return const_iterator( it );
+ }
+ break;
+ case objectValue:
+ if ( value_.map_ )
+ {
+ ValueInternalMap::IteratorState it;
+ value_.map_->makeEndIterator( it );
+ return const_iterator( it );
+ }
+ break;
+#else
+ case arrayValue:
+ case objectValue:
+ if ( value_.map_ )
+ return const_iterator( value_.map_->end() );
+ break;
+#endif
+ default:
+ break;
+ }
+ return const_iterator();
+}
+
+
+Value::iterator
+Value::begin()
+{
+ switch ( type_ )
+ {
+#ifdef JSON_VALUE_USE_INTERNAL_MAP
+ case arrayValue:
+ if ( value_.array_ )
+ {
+ ValueInternalArray::IteratorState it;
+ value_.array_->makeBeginIterator( it );
+ return iterator( it );
+ }
+ break;
+ case objectValue:
+ if ( value_.map_ )
+ {
+ ValueInternalMap::IteratorState it;
+ value_.map_->makeBeginIterator( it );
+ return iterator( it );
+ }
+ break;
+#else
+ case arrayValue:
+ case objectValue:
+ if ( value_.map_ )
+ return iterator( value_.map_->begin() );
+ break;
+#endif
+ default:
+ break;
+ }
+ return iterator();
+}
+
+Value::iterator
+Value::end()
+{
+ switch ( type_ )
+ {
+#ifdef JSON_VALUE_USE_INTERNAL_MAP
+ case arrayValue:
+ if ( value_.array_ )
+ {
+ ValueInternalArray::IteratorState it;
+ value_.array_->makeEndIterator( it );
+ return iterator( it );
+ }
+ break;
+ case objectValue:
+ if ( value_.map_ )
+ {
+ ValueInternalMap::IteratorState it;
+ value_.map_->makeEndIterator( it );
+ return iterator( it );
+ }
+ break;
+#else
+ case arrayValue:
+ case objectValue:
+ if ( value_.map_ )
+ return iterator( value_.map_->end() );
+ break;
+#endif
+ default:
+ break;
+ }
+ return iterator();
+}
+
+
+// class PathArgument
+// //////////////////////////////////////////////////////////////////
+
+PathArgument::PathArgument()
+ : kind_( kindNone )
+{
+}
+
+
+PathArgument::PathArgument( ArrayIndex index )
+ : index_( index )
+ , kind_( kindIndex )
+{
+}
+
+
+PathArgument::PathArgument( const char *key )
+ : key_( key )
+ , kind_( kindKey )
+{
+}
+
+
+PathArgument::PathArgument( const std::string &key )
+ : key_( key.c_str() )
+ , kind_( kindKey )
+{
+}
+
+// class Path
+// //////////////////////////////////////////////////////////////////
+
+Path::Path( const std::string &path,
+ const PathArgument &a1,
+ const PathArgument &a2,
+ const PathArgument &a3,
+ const PathArgument &a4,
+ const PathArgument &a5 )
+{
+ InArgs in;
+ in.push_back( &a1 );
+ in.push_back( &a2 );
+ in.push_back( &a3 );
+ in.push_back( &a4 );
+ in.push_back( &a5 );
+ makePath( path, in );
+}
+
+
+void
+Path::makePath( const std::string &path,
+ const InArgs &in )
+{
+ const char *current = path.c_str();
+ const char *end = current + path.length();
+ InArgs::const_iterator itInArg = in.begin();
+ while ( current != end )
+ {
+ if ( *current == '[' )
+ {
+ ++current;
+ if ( *current == '%' )
+ addPathInArg( path, in, itInArg, PathArgument::kindIndex );
+ else
+ {
+ ArrayIndex index = 0;
+ for ( ; current != end && *current >= '0' && *current <= '9'; ++current )
+ index = index * 10 + ArrayIndex(*current - '0');
+ args_.push_back( index );
+ }
+ if ( current == end || *current++ != ']' )
+ invalidPath( path, int(current - path.c_str()) );
+ }
+ else if ( *current == '%' )
+ {
+ addPathInArg( path, in, itInArg, PathArgument::kindKey );
+ ++current;
+ }
+ else if ( *current == '.' )
+ {
+ ++current;
+ }
+ else
+ {
+ const char *beginName = current;
+ while ( current != end && !strchr( "[.", *current ) )
+ ++current;
+ args_.push_back( std::string( beginName, current ) );
+ }
+ }
+}
+
+
+void
+Path::addPathInArg( const std::string &path,
+ const InArgs &in,
+ InArgs::const_iterator &itInArg,
+ PathArgument::Kind kind )
+{
+ if ( itInArg == in.end() )
+ {
+ // Error: missing argument %d
+ }
+ else if ( (*itInArg)->kind_ != kind )
+ {
+ // Error: bad argument type
+ }
+ else
+ {
+ args_.push_back( **itInArg );
+ }
+}
+
+
+void
+Path::invalidPath( const std::string &path,
+ int location )
+{
+ // Error: invalid path.
+}
+
+
+const Value &
+Path::resolve( const Value &root ) const
+{
+ const Value *node = &root;
+ for ( Args::const_iterator it = args_.begin(); it != args_.end(); ++it )
+ {
+ const PathArgument &arg = *it;
+ if ( arg.kind_ == PathArgument::kindIndex )
+ {
+ if ( !node->isArray() || node->isValidIndex( arg.index_ ) )
+ {
+ // Error: unable to resolve path (array value expected at position...
+ }
+ node = &((*node)[arg.index_]);
+ }
+ else if ( arg.kind_ == PathArgument::kindKey )
+ {
+ if ( !node->isObject() )
+ {
+ // Error: unable to resolve path (object value expected at position...)
+ }
+ node = &((*node)[arg.key_]);
+ if ( node == &Value::null )
+ {
+ // Error: unable to resolve path (object has no member named '' at position...)
+ }
+ }
+ }
+ return *node;
+}
+
+
+Value
+Path::resolve( const Value &root,
+ const Value &defaultValue ) const
+{
+ const Value *node = &root;
+ for ( Args::const_iterator it = args_.begin(); it != args_.end(); ++it )
+ {
+ const PathArgument &arg = *it;
+ if ( arg.kind_ == PathArgument::kindIndex )
+ {
+ if ( !node->isArray() || node->isValidIndex( arg.index_ ) )
+ return defaultValue;
+ node = &((*node)[arg.index_]);
+ }
+ else if ( arg.kind_ == PathArgument::kindKey )
+ {
+ if ( !node->isObject() )
+ return defaultValue;
+ node = &((*node)[arg.key_]);
+ if ( node == &Value::null )
+ return defaultValue;
+ }
+ }
+ return *node;
+}
+
+
+Value &
+Path::make( Value &root ) const
+{
+ Value *node = &root;
+ for ( Args::const_iterator it = args_.begin(); it != args_.end(); ++it )
+ {
+ const PathArgument &arg = *it;
+ if ( arg.kind_ == PathArgument::kindIndex )
+ {
+ if ( !node->isArray() )
+ {
+ // Error: node is not an array at position ...
+ }
+ node = &((*node)[arg.index_]);
+ }
+ else if ( arg.kind_ == PathArgument::kindKey )
+ {
+ if ( !node->isObject() )
+ {
+ // Error: node is not an object at position...
+ }
+ node = &((*node)[arg.key_]);
+ }
+ }
+ return *node;
+}
+
+
+} // namespace Json
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#ifndef CPPTL_JSON_H_INCLUDED
+# define CPPTL_JSON_H_INCLUDED
+
+# include "json_forwards.h"
+# include <string>
+# include <vector>
+
+# ifndef JSON_USE_CPPTL_SMALLMAP
+# include <map>
+# else
+# include <cpptl/smallmap.h>
+# endif
+# ifdef JSON_USE_CPPTL
+# include <cpptl/forwards.h>
+# endif
+
+/** \brief JSON (JavaScript Object Notation).
+ */
+namespace Json {
+
+ /** \brief Type of the value held by a Value object.
+ */
+ enum ValueType
+ {
+ nullValue = 0, ///< 'null' value
+ intValue, ///< signed integer value
+ uintValue, ///< unsigned integer value
+ realValue, ///< double value
+ stringValue, ///< UTF-8 string value
+ booleanValue, ///< bool value
+ arrayValue, ///< array value (ordered list)
+ objectValue ///< object value (collection of name/value pairs).
+ };
+
+ enum CommentPlacement
+ {
+ commentBefore = 0, ///< a comment placed on the line before a value
+ commentAfterOnSameLine, ///< a comment just after a value on the same line
+ commentAfter, ///< a comment on the line after a value (only make sense for root value)
+ numberOfCommentPlacement
+ };
+
+//# ifdef JSON_USE_CPPTL
+// typedef CppTL::AnyEnumerator<const char *> EnumMemberNames;
+// typedef CppTL::AnyEnumerator<const Value &> EnumValues;
+//# endif
+
+ /** \brief Lightweight wrapper to tag static string.
+ *
+ * Value constructor and objectValue member assignement takes advantage of the
+ * StaticString and avoid the cost of string duplication when storing the
+ * string or the member name.
+ *
+ * Example of usage:
+ * \code
+ * Json::Value aValue( StaticString("some text") );
+ * Json::Value object;
+ * static const StaticString code("code");
+ * object[code] = 1234;
+ * \endcode
+ */
+ class JSON_API StaticString
+ {
+ public:
+ explicit StaticString( const char *czstring )
+ : str_( czstring )
+ {
+ }
+
+ operator const char *() const
+ {
+ return str_;
+ }
+
+ const char *c_str() const
+ {
+ return str_;
+ }
+
+ private:
+ const char *str_;
+ };
+
+ /** \brief Represents a <a HREF="http://www.json.org">JSON</a> value.
+ *
+ * This class is a discriminated union wrapper that can represents a:
+ * - signed integer [range: Value::minInt - Value::maxInt]
+ * - unsigned integer (range: 0 - Value::maxUInt)
+ * - double
+ * - UTF-8 string
+ * - boolean
+ * - 'null'
+ * - an ordered list of Value
+ * - collection of name/value pairs (javascript object)
+ *
+ * The type of the held value is represented by a #ValueType and
+ * can be obtained using type().
+ *
+ * values of an #objectValue or #arrayValue can be accessed using operator[]() methods.
+ * Non const methods will automatically create the a #nullValue element
+ * if it does not exist.
+ * The sequence of an #arrayValue will be automatically resize and initialized
+ * with #nullValue. resize() can be used to enlarge or truncate an #arrayValue.
+ *
+ * The get() methods can be used to obtanis default value in the case the required element
+ * does not exist.
+ *
+ * It is possible to iterate over the list of a #objectValue values using
+ * the getMemberNames() method.
+ */
+ class JSON_API Value
+ {
+ friend class ValueIteratorBase;
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ friend class ValueInternalLink;
+ friend class ValueInternalMap;
+# endif
+ public:
+ typedef std::vector<std::string> Members;
+ typedef ValueIterator iterator;
+ typedef ValueConstIterator const_iterator;
+ typedef Json::UInt UInt;
+ typedef Json::Int Int;
+ typedef Json::ArrayIndex ArrayIndex;
+
+ static const Value null;
+ static const Int minInt;
+ static const Int maxInt;
+ static const UInt maxUInt;
+
+ private:
+#ifndef JSONCPP_DOC_EXCLUDE_IMPLEMENTATION
+# ifndef JSON_VALUE_USE_INTERNAL_MAP
+ class CZString
+ {
+ public:
+ enum DuplicationPolicy
+ {
+ noDuplication = 0,
+ duplicate,
+ duplicateOnCopy
+ };
+ CZString( ArrayIndex index );
+ CZString( const char *cstr, DuplicationPolicy allocate );
+ CZString( const CZString &other );
+ ~CZString();
+ CZString &operator =( const CZString &other );
+ bool operator<( const CZString &other ) const;
+ bool operator==( const CZString &other ) const;
+ ArrayIndex index() const;
+ const char *c_str() const;
+ bool isStaticString() const;
+ private:
+ void swap( CZString &other );
+ const char *cstr_;
+ ArrayIndex index_;
+ };
+
+ public:
+# ifndef JSON_USE_CPPTL_SMALLMAP
+ typedef std::map<CZString, Value> ObjectValues;
+# else
+ typedef CppTL::SmallMap<CZString, Value> ObjectValues;
+# endif // ifndef JSON_USE_CPPTL_SMALLMAP
+# endif // ifndef JSON_VALUE_USE_INTERNAL_MAP
+#endif // ifndef JSONCPP_DOC_EXCLUDE_IMPLEMENTATION
+
+ public:
+ /** \brief Create a default Value of the given type.
+
+ This is a very useful constructor.
+ To create an empty array, pass arrayValue.
+ To create an empty object, pass objectValue.
+ Another Value can then be set to this one by assignment.
+ This is useful since clear() and resize() will not alter types.
+
+ Examples:
+ \code
+ Json::Value null_value; // null
+ Json::Value arr_value(Json::arrayValue); // []
+ Json::Value obj_value(Json::objectValue); // {}
+ \endcode
+ */
+ Value( ValueType type = nullValue );
+#if !defined(JSON_NO_INT64)
+ Value( int value );
+ Value( ArrayIndex value );
+#endif // if !defined(JSON_NO_INT64)
+ Value( Int value );
+ Value( UInt value );
+ Value( double value );
+ Value( const char *value );
+ Value( const char *beginValue, const char *endValue );
+ /** \brief Constructs a value from a static string.
+
+ * Like other value string constructor but do not duplicate the string for
+ * internal storage. The given string must remain alive after the call to this
+ * constructor.
+ * Example of usage:
+ * \code
+ * Json::Value aValue( StaticString("some text") );
+ * \endcode
+ */
+ Value( const StaticString &value );
+ Value( const std::string &value );
+# ifdef JSON_USE_CPPTL
+ Value( const CppTL::ConstString &value );
+# endif
+ Value( bool value );
+ Value( const Value &other );
+ ~Value();
+
+ Value &operator=( const Value &other );
+ /// Swap values.
+ /// \note Currently, comments are intentionally not swapped, for
+ /// both logic and efficiency.
+ void swap( Value &other );
+
+ ValueType type() const;
+
+ bool operator <( const Value &other ) const;
+ bool operator <=( const Value &other ) const;
+ bool operator >=( const Value &other ) const;
+ bool operator >( const Value &other ) const;
+
+ bool operator ==( const Value &other ) const;
+ bool operator !=( const Value &other ) const;
+
+ int compare( const Value &other );
+
+ const char *asCString() const;
+ std::string asString() const;
+# ifdef JSON_USE_CPPTL
+ CppTL::ConstString asConstString() const;
+# endif
+ Int asInt() const;
+ UInt asUInt() const;
+ double asDouble() const;
+ bool asBool() const;
+
+ bool isNull() const;
+ bool isBool() const;
+ bool isInt() const;
+ bool isUInt() const;
+ bool isIntegral() const;
+ bool isDouble() const;
+ bool isNumeric() const;
+ bool isString() const;
+ bool isArray() const;
+ bool isObject() const;
+
+ bool isConvertibleTo( ValueType other ) const;
+
+ /// Number of values in array or object
+ ArrayIndex size() const;
+
+ /// \brief Return true if empty array, empty object, or null;
+ /// otherwise, false.
+ bool empty() const;
+
+ /// Return isNull()
+ bool operator!() const;
+
+ /// Remove all object members and array elements.
+ /// \pre type() is arrayValue, objectValue, or nullValue
+ /// \post type() is unchanged
+ void clear();
+
+ /// Resize the array to size elements.
+ /// New elements are initialized to null.
+ /// May only be called on nullValue or arrayValue.
+ /// \pre type() is arrayValue or nullValue
+ /// \post type() is arrayValue
+ void resize( ArrayIndex size );
+
+ /// Access an array element (zero based index ).
+ /// If the array contains less than index element, then null value are inserted
+ /// in the array so that its size is index+1.
+ /// (You may need to say 'value[0u]' to get your compiler to distinguish
+ /// this from the operator[] which takes a string.)
+ Value &operator[]( ArrayIndex index );
+ /// Access an array element (zero based index )
+ /// (You may need to say 'value[0u]' to get your compiler to distinguish
+ /// this from the operator[] which takes a string.)
+ const Value &operator[]( ArrayIndex index ) const;
+ /// If the array contains at least index+1 elements, returns the element value,
+ /// otherwise returns defaultValue.
+ Value get( ArrayIndex index,
+ const Value &defaultValue ) const;
+ /// Return true if index < size().
+ bool isValidIndex( ArrayIndex index ) const;
+ /// \brief Append value to array at the end.
+ ///
+ /// Equivalent to jsonvalue[jsonvalue.size()] = value;
+ Value &append( const Value &value );
+
+ /// Access an object value by name, create a null member if it does not exist.
+ Value &operator[]( const char *key );
+ /// Access an object value by name, returns null if there is no member with that name.
+ const Value &operator[]( const char *key ) const;
+ /// Access an object value by name, create a null member if it does not exist.
+ Value &operator[]( const std::string &key );
+ /// Access an object value by name, returns null if there is no member with that name.
+ const Value &operator[]( const std::string &key ) const;
+ /** \brief Access an object value by name, create a null member if it does not exist.
+
+ * If the object as no entry for that name, then the member name used to store
+ * the new entry is not duplicated.
+ * Example of use:
+ * \code
+ * Json::Value object;
+ * static const StaticString code("code");
+ * object[code] = 1234;
+ * \endcode
+ */
+ Value &operator[]( const StaticString &key );
+# ifdef JSON_USE_CPPTL
+ /// Access an object value by name, create a null member if it does not exist.
+ Value &operator[]( const CppTL::ConstString &key );
+ /// Access an object value by name, returns null if there is no member with that name.
+ const Value &operator[]( const CppTL::ConstString &key ) const;
+# endif
+ /// Return the member named key if it exist, defaultValue otherwise.
+ Value get( const char *key,
+ const Value &defaultValue ) const;
+ /// Return the member named key if it exist, defaultValue otherwise.
+ Value get( const std::string &key,
+ const Value &defaultValue ) const;
+# ifdef JSON_USE_CPPTL
+ /// Return the member named key if it exist, defaultValue otherwise.
+ Value get( const CppTL::ConstString &key,
+ const Value &defaultValue ) const;
+# endif
+ /// \brief Remove and return the named member.
+ ///
+ /// Do nothing if it did not exist.
+ /// \return the removed Value, or null.
+ /// \pre type() is objectValue or nullValue
+ /// \post type() is unchanged
+ Value removeMember( const char* key );
+ /// Same as removeMember(const char*)
+ Value removeMember( const std::string &key );
+
+ /// Return true if the object has a member named key.
+ bool isMember( const char *key ) const;
+ /// Return true if the object has a member named key.
+ bool isMember( const std::string &key ) const;
+# ifdef JSON_USE_CPPTL
+ /// Return true if the object has a member named key.
+ bool isMember( const CppTL::ConstString &key ) const;
+# endif
+
+ /// \brief Return a list of the member names.
+ ///
+ /// If null, return an empty list.
+ /// \pre type() is objectValue or nullValue
+ /// \post if type() was nullValue, it remains nullValue
+ Members getMemberNames() const;
+
+//# ifdef JSON_USE_CPPTL
+// EnumMemberNames enumMemberNames() const;
+// EnumValues enumValues() const;
+//# endif
+
+ /// Comments must be //... or /* ... */
+ void setComment( const char *comment,
+ CommentPlacement placement );
+ /// Comments must be //... or /* ... */
+ void setComment( const std::string &comment,
+ CommentPlacement placement );
+ bool hasComment( CommentPlacement placement ) const;
+ /// Include delimiters and embedded newlines.
+ std::string getComment( CommentPlacement placement ) const;
+
+ std::string toStyledString() const;
+
+ const_iterator begin() const;
+ const_iterator end() const;
+
+ iterator begin();
+ iterator end();
+
+ private:
+ Value &resolveReference( const char *key,
+ bool isStatic );
+
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ inline bool isItemAvailable() const
+ {
+ return itemIsUsed_ == 0;
+ }
+
+ inline void setItemUsed( bool isUsed = true )
+ {
+ itemIsUsed_ = isUsed ? 1 : 0;
+ }
+
+ inline bool isMemberNameStatic() const
+ {
+ return memberNameIsStatic_ == 0;
+ }
+
+ inline void setMemberNameIsStatic( bool isStatic )
+ {
+ memberNameIsStatic_ = isStatic ? 1 : 0;
+ }
+# endif // # ifdef JSON_VALUE_USE_INTERNAL_MAP
+
+ private:
+ struct CommentInfo
+ {
+ CommentInfo();
+ ~CommentInfo();
+
+ void setComment( const char *text );
+
+ char *comment_;
+ };
+
+ //struct MemberNamesTransform
+ //{
+ // typedef const char *result_type;
+ // const char *operator()( const CZString &name ) const
+ // {
+ // return name.c_str();
+ // }
+ //};
+
+ union ValueHolder
+ {
+ Int int_;
+ UInt uint_;
+ double real_;
+ bool bool_;
+ char *string_;
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ ValueInternalArray *array_;
+ ValueInternalMap *map_;
+#else
+ ObjectValues *map_;
+# endif
+ } value_;
+ ValueType type_ : 8;
+ int allocated_ : 1; // Notes: if declared as bool, bitfield is useless.
+# ifdef JSON_VALUE_USE_INTERNAL_MAP
+ unsigned int itemIsUsed_ : 1; // used by the ValueInternalMap container.
+ int memberNameIsStatic_ : 1; // used by the ValueInternalMap container.
+# endif
+ CommentInfo *comments_;
+ };
+
+
+ /** \brief Experimental and untested: represents an element of the "path" to access a node.
+ */
+ class PathArgument
+ {
+ public:
+ friend class Path;
+
+ PathArgument();
+ PathArgument( ArrayIndex index );
+ PathArgument( const char *key );
+ PathArgument( const std::string &key );
+
+ private:
+ enum Kind
+ {
+ kindNone = 0,
+ kindIndex,
+ kindKey
+ };
+ std::string key_;
+ ArrayIndex index_;
+ Kind kind_;
+ };
+
+ /** \brief Experimental and untested: represents a "path" to access a node.
+ *
+ * Syntax:
+ * - "." => root node
+ * - ".[n]" => elements at index 'n' of root node (an array value)
+ * - ".name" => member named 'name' of root node (an object value)
+ * - ".name1.name2.name3"
+ * - ".[0][1][2].name1[3]"
+ * - ".%" => member name is provided as parameter
+ * - ".[%]" => index is provied as parameter
+ */
+ class Path
+ {
+ public:
+ Path( const std::string &path,
+ const PathArgument &a1 = PathArgument(),
+ const PathArgument &a2 = PathArgument(),
+ const PathArgument &a3 = PathArgument(),
+ const PathArgument &a4 = PathArgument(),
+ const PathArgument &a5 = PathArgument() );
+
+ const Value &resolve( const Value &root ) const;
+ Value resolve( const Value &root,
+ const Value &defaultValue ) const;
+ /// Creates the "path" to access the specified node and returns a reference on the node.
+ Value &make( Value &root ) const;
+
+ private:
+ typedef std::vector<const PathArgument *> InArgs;
+ typedef std::vector<PathArgument> Args;
+
+ void makePath( const std::string &path,
+ const InArgs &in );
+ void addPathInArg( const std::string &path,
+ const InArgs &in,
+ InArgs::const_iterator &itInArg,
+ PathArgument::Kind kind );
+ void invalidPath( const std::string &path,
+ int location );
+
+ Args args_;
+ };
+
+
+
+#ifdef JSON_VALUE_USE_INTERNAL_MAP
+ /** \brief Allocator to customize Value internal map.
+ * Below is an example of a simple implementation (default implementation actually
+ * use memory pool for speed).
+ * \code
+ class DefaultValueMapAllocator : public ValueMapAllocator
+ {
+ public: // overridden from ValueMapAllocator
+ virtual ValueInternalMap *newMap()
+ {
+ return new ValueInternalMap();
+ }
+
+ virtual ValueInternalMap *newMapCopy( const ValueInternalMap &other )
+ {
+ return new ValueInternalMap( other );
+ }
+
+ virtual void destructMap( ValueInternalMap *map )
+ {
+ delete map;
+ }
+
+ virtual ValueInternalLink *allocateMapBuckets( unsigned int size )
+ {
+ return new ValueInternalLink[size];
+ }
+
+ virtual void releaseMapBuckets( ValueInternalLink *links )
+ {
+ delete [] links;
+ }
+
+ virtual ValueInternalLink *allocateMapLink()
+ {
+ return new ValueInternalLink();
+ }
+
+ virtual void releaseMapLink( ValueInternalLink *link )
+ {
+ delete link;
+ }
+ };
+ * \endcode
+ */
+ class JSON_API ValueMapAllocator
+ {
+ public:
+ virtual ~ValueMapAllocator();
+ virtual ValueInternalMap *newMap() = 0;
+ virtual ValueInternalMap *newMapCopy( const ValueInternalMap &other ) = 0;
+ virtual void destructMap( ValueInternalMap *map ) = 0;
+ virtual ValueInternalLink *allocateMapBuckets( unsigned int size ) = 0;
+ virtual void releaseMapBuckets( ValueInternalLink *links ) = 0;
+ virtual ValueInternalLink *allocateMapLink() = 0;
+ virtual void releaseMapLink( ValueInternalLink *link ) = 0;
+ };
+
+ /** \brief ValueInternalMap hash-map bucket chain link (for internal use only).
+ * \internal previous_ & next_ allows for bidirectional traversal.
+ */
+ class JSON_API ValueInternalLink
+ {
+ public:
+ enum { itemPerLink = 6 }; // sizeof(ValueInternalLink) = 128 on 32 bits architecture.
+ enum InternalFlags {
+ flagAvailable = 0,
+ flagUsed = 1
+ };
+
+ ValueInternalLink();
+
+ ~ValueInternalLink();
+
+ Value items_[itemPerLink];
+ char *keys_[itemPerLink];
+ ValueInternalLink *previous_;
+ ValueInternalLink *next_;
+ };
+
+
+ /** \brief A linked page based hash-table implementation used internally by Value.
+ * \internal ValueInternalMap is a tradional bucket based hash-table, with a linked
+ * list in each bucket to handle collision. There is an addional twist in that
+ * each node of the collision linked list is a page containing a fixed amount of
+ * value. This provides a better compromise between memory usage and speed.
+ *
+ * Each bucket is made up of a chained list of ValueInternalLink. The last
+ * link of a given bucket can be found in the 'previous_' field of the following bucket.
+ * The last link of the last bucket is stored in tailLink_ as it has no following bucket.
+ * Only the last link of a bucket may contains 'available' item. The last link always
+ * contains at least one element unless is it the bucket one very first link.
+ */
+ class JSON_API ValueInternalMap
+ {
+ friend class ValueIteratorBase;
+ friend class Value;
+ public:
+ typedef unsigned int HashKey;
+ typedef unsigned int BucketIndex;
+
+# ifndef JSONCPP_DOC_EXCLUDE_IMPLEMENTATION
+ struct IteratorState
+ {
+ IteratorState()
+ : map_(0)
+ , link_(0)
+ , itemIndex_(0)
+ , bucketIndex_(0)
+ {
+ }
+ ValueInternalMap *map_;
+ ValueInternalLink *link_;
+ BucketIndex itemIndex_;
+ BucketIndex bucketIndex_;
+ };
+# endif // ifndef JSONCPP_DOC_EXCLUDE_IMPLEMENTATION
+
+ ValueInternalMap();
+ ValueInternalMap( const ValueInternalMap &other );
+ ValueInternalMap &operator =( const ValueInternalMap &other );
+ ~ValueInternalMap();
+
+ void swap( ValueInternalMap &other );
+
+ BucketIndex size() const;
+
+ void clear();
+
+ bool reserveDelta( BucketIndex growth );
+
+ bool reserve( BucketIndex newItemCount );
+
+ const Value *find( const char *key ) const;
+
+ Value *find( const char *key );
+
+ Value &resolveReference( const char *key,
+ bool isStatic );
+
+ void remove( const char *key );
+
+ void doActualRemove( ValueInternalLink *link,
+ BucketIndex index,
+ BucketIndex bucketIndex );
+
+ ValueInternalLink *&getLastLinkInBucket( BucketIndex bucketIndex );
+
+ Value &setNewItem( const char *key,
+ bool isStatic,
+ ValueInternalLink *link,
+ BucketIndex index );
+
+ Value &unsafeAdd( const char *key,
+ bool isStatic,
+ HashKey hashedKey );
+
+ HashKey hash( const char *key ) const;
+
+ int compare( const ValueInternalMap &other ) const;
+
+ private:
+ void makeBeginIterator( IteratorState &it ) const;
+ void makeEndIterator( IteratorState &it ) const;
+ static bool equals( const IteratorState &x, const IteratorState &other );
+ static void increment( IteratorState &iterator );
+ static void incrementBucket( IteratorState &iterator );
+ static void decrement( IteratorState &iterator );
+ static const char *key( const IteratorState &iterator );
+ static const char *key( const IteratorState &iterator, bool &isStatic );
+ static Value &value( const IteratorState &iterator );
+ static int distance( const IteratorState &x, const IteratorState &y );
+
+ private:
+ ValueInternalLink *buckets_;
+ ValueInternalLink *tailLink_;
+ BucketIndex bucketsSize_;
+ BucketIndex itemCount_;
+ };
+
+ /** \brief A simplified deque implementation used internally by Value.
+ * \internal
+ * It is based on a list of fixed "page", each page contains a fixed number of items.
+ * Instead of using a linked-list, a array of pointer is used for fast item look-up.
+ * Look-up for an element is as follow:
+ * - compute page index: pageIndex = itemIndex / itemsPerPage
+ * - look-up item in page: pages_[pageIndex][itemIndex % itemsPerPage]
+ *
+ * Insertion is amortized constant time (only the array containing the index of pointers
+ * need to be reallocated when items are appended).
+ */
+ class JSON_API ValueInternalArray
+ {
+ friend class Value;
+ friend class ValueIteratorBase;
+ public:
+ enum { itemsPerPage = 8 }; // should be a power of 2 for fast divide and modulo.
+ typedef Value::ArrayIndex ArrayIndex;
+ typedef unsigned int PageIndex;
+
+# ifndef JSONCPP_DOC_EXCLUDE_IMPLEMENTATION
+ struct IteratorState // Must be a POD
+ {
+ IteratorState()
+ : array_(0)
+ , currentPageIndex_(0)
+ , currentItemIndex_(0)
+ {
+ }
+ ValueInternalArray *array_;
+ Value **currentPageIndex_;
+ unsigned int currentItemIndex_;
+ };
+# endif // ifndef JSONCPP_DOC_EXCLUDE_IMPLEMENTATION
+
+ ValueInternalArray();
+ ValueInternalArray( const ValueInternalArray &other );
+ ValueInternalArray &operator =( const ValueInternalArray &other );
+ ~ValueInternalArray();
+ void swap( ValueInternalArray &other );
+
+ void clear();
+ void resize( ArrayIndex newSize );
+
+ Value &resolveReference( ArrayIndex index );
+
+ Value *find( ArrayIndex index ) const;
+
+ ArrayIndex size() const;
+
+ int compare( const ValueInternalArray &other ) const;
+
+ private:
+ static bool equals( const IteratorState &x, const IteratorState &other );
+ static void increment( IteratorState &iterator );
+ static void decrement( IteratorState &iterator );
+ static Value &dereference( const IteratorState &iterator );
+ static Value &unsafeDereference( const IteratorState &iterator );
+ static int distance( const IteratorState &x, const IteratorState &y );
+ static ArrayIndex indexOf( const IteratorState &iterator );
+ void makeBeginIterator( IteratorState &it ) const;
+ void makeEndIterator( IteratorState &it ) const;
+ void makeIterator( IteratorState &it, ArrayIndex index ) const;
+
+ void makeIndexValid( ArrayIndex index );
+
+ Value **pages_;
+ ArrayIndex size_;
+ PageIndex pageCount_;
+ };
+
+ /** \brief Experimental: do not use. Allocator to customize Value internal array.
+ * Below is an example of a simple implementation (actual implementation use
+ * memory pool).
+ \code
+class DefaultValueArrayAllocator : public ValueArrayAllocator
+{
+public: // overridden from ValueArrayAllocator
+ virtual ~DefaultValueArrayAllocator()
+ {
+ }
+
+ virtual ValueInternalArray *newArray()
+ {
+ return new ValueInternalArray();
+ }
+
+ virtual ValueInternalArray *newArrayCopy( const ValueInternalArray &other )
+ {
+ return new ValueInternalArray( other );
+ }
+
+ virtual void destruct( ValueInternalArray *array )
+ {
+ delete array;
+ }
+
+ virtual void reallocateArrayPageIndex( Value **&indexes,
+ ValueInternalArray::PageIndex &indexCount,
+ ValueInternalArray::PageIndex minNewIndexCount )
+ {
+ ValueInternalArray::PageIndex newIndexCount = (indexCount*3)/2 + 1;
+ if ( minNewIndexCount > newIndexCount )
+ newIndexCount = minNewIndexCount;
+ void *newIndexes = realloc( indexes, sizeof(Value*) * newIndexCount );
+ if ( !newIndexes )
+ throw std::bad_alloc();
+ indexCount = newIndexCount;
+ indexes = static_cast<Value **>( newIndexes );
+ }
+ virtual void releaseArrayPageIndex( Value **indexes,
+ ValueInternalArray::PageIndex indexCount )
+ {
+ if ( indexes )
+ free( indexes );
+ }
+
+ virtual Value *allocateArrayPage()
+ {
+ return static_cast<Value *>( malloc( sizeof(Value) * ValueInternalArray::itemsPerPage ) );
+ }
+
+ virtual void releaseArrayPage( Value *value )
+ {
+ if ( value )
+ free( value );
+ }
+};
+ \endcode
+ */
+ class JSON_API ValueArrayAllocator
+ {
+ public:
+ virtual ~ValueArrayAllocator();
+ virtual ValueInternalArray *newArray() = 0;
+ virtual ValueInternalArray *newArrayCopy( const ValueInternalArray &other ) = 0;
+ virtual void destructArray( ValueInternalArray *array ) = 0;
+ /** \brief Reallocate array page index.
+ * Reallocates an array of pointer on each page.
+ * \param indexes [input] pointer on the current index. May be \c NULL.
+ * [output] pointer on the new index of at least
+ * \a minNewIndexCount pages.
+ * \param indexCount [input] current number of pages in the index.
+ * [output] number of page the reallocated index can handle.
+ * \b MUST be >= \a minNewIndexCount.
+ * \param minNewIndexCount Minimum number of page the new index must be able to
+ * handle.
+ */
+ virtual void reallocateArrayPageIndex( Value **&indexes,
+ ValueInternalArray::PageIndex &indexCount,
+ ValueInternalArray::PageIndex minNewIndexCount ) = 0;
+ virtual void releaseArrayPageIndex( Value **indexes,
+ ValueInternalArray::PageIndex indexCount ) = 0;
+ virtual Value *allocateArrayPage() = 0;
+ virtual void releaseArrayPage( Value *value ) = 0;
+ };
+#endif // #ifdef JSON_VALUE_USE_INTERNAL_MAP
+
+
+ /** \brief base class for Value iterators.
+ *
+ */
+ class ValueIteratorBase
+ {
+ public:
+ typedef unsigned int size_t;
+ typedef int difference_type;
+ typedef ValueIteratorBase SelfType;
+
+ ValueIteratorBase();
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ explicit ValueIteratorBase( const Value::ObjectValues::iterator ¤t );
+#else
+ ValueIteratorBase( const ValueInternalArray::IteratorState &state );
+ ValueIteratorBase( const ValueInternalMap::IteratorState &state );
+#endif
+
+ bool operator ==( const SelfType &other ) const
+ {
+ return isEqual( other );
+ }
+
+ bool operator !=( const SelfType &other ) const
+ {
+ return !isEqual( other );
+ }
+
+ difference_type operator -( const SelfType &other ) const
+ {
+ return computeDistance( other );
+ }
+
+ /// Return either the index or the member name of the referenced value as a Value.
+ Value key() const;
+
+ /// Return the index of the referenced Value. -1 if it is not an arrayValue.
+ UInt index() const;
+
+ /// Return the member name of the referenced Value. "" if it is not an objectValue.
+ const char *memberName() const;
+
+ protected:
+ Value &deref() const;
+
+ void increment();
+
+ void decrement();
+
+ difference_type computeDistance( const SelfType &other ) const;
+
+ bool isEqual( const SelfType &other ) const;
+
+ void copy( const SelfType &other );
+
+ private:
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ Value::ObjectValues::iterator current_;
+ // Indicates that iterator is for a null value.
+ bool isNull_;
+#else
+ union
+ {
+ ValueInternalArray::IteratorState array_;
+ ValueInternalMap::IteratorState map_;
+ } iterator_;
+ bool isArray_;
+#endif
+ };
+
+ /** \brief const iterator for object and array value.
+ *
+ */
+ class ValueConstIterator : public ValueIteratorBase
+ {
+ friend class Value;
+ public:
+ typedef unsigned int size_t;
+ typedef int difference_type;
+ typedef const Value &reference;
+ typedef const Value *pointer;
+ typedef ValueConstIterator SelfType;
+
+ ValueConstIterator();
+ private:
+ /*! \internal Use by Value to create an iterator.
+ */
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ explicit ValueConstIterator( const Value::ObjectValues::iterator ¤t );
+#else
+ ValueConstIterator( const ValueInternalArray::IteratorState &state );
+ ValueConstIterator( const ValueInternalMap::IteratorState &state );
+#endif
+ public:
+ SelfType &operator =( const ValueIteratorBase &other );
+
+ SelfType operator++( int )
+ {
+ SelfType temp( *this );
+ ++*this;
+ return temp;
+ }
+
+ SelfType operator--( int )
+ {
+ SelfType temp( *this );
+ --*this;
+ return temp;
+ }
+
+ SelfType &operator--()
+ {
+ decrement();
+ return *this;
+ }
+
+ SelfType &operator++()
+ {
+ increment();
+ return *this;
+ }
+
+ reference operator *() const
+ {
+ return deref();
+ }
+ };
+
+
+ /** \brief Iterator for object and array value.
+ */
+ class ValueIterator : public ValueIteratorBase
+ {
+ friend class Value;
+ public:
+ typedef unsigned int size_t;
+ typedef int difference_type;
+ typedef Value &reference;
+ typedef Value *pointer;
+ typedef ValueIterator SelfType;
+
+ ValueIterator();
+ ValueIterator( const ValueConstIterator &other );
+ ValueIterator( const ValueIterator &other );
+ private:
+ /*! \internal Use by Value to create an iterator.
+ */
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ explicit ValueIterator( const Value::ObjectValues::iterator ¤t );
+#else
+ ValueIterator( const ValueInternalArray::IteratorState &state );
+ ValueIterator( const ValueInternalMap::IteratorState &state );
+#endif
+ public:
+
+ SelfType &operator =( const SelfType &other );
+
+ SelfType operator++( int )
+ {
+ SelfType temp( *this );
+ ++*this;
+ return temp;
+ }
+
+ SelfType operator--( int )
+ {
+ SelfType temp( *this );
+ --*this;
+ return temp;
+ }
+
+ SelfType &operator--()
+ {
+ decrement();
+ return *this;
+ }
+
+ SelfType &operator++()
+ {
+ increment();
+ return *this;
+ }
+
+ reference operator *() const
+ {
+ return deref();
+ }
+ };
+
+
+} // namespace Json
+
+
+#endif // CPPTL_JSON_H_INCLUDED
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+// included by json_value.cpp
+// everything is within Json namespace
+
+
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// class ValueIteratorBase
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+
+ValueIteratorBase::ValueIteratorBase()
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ : current_()
+ , isNull_( true )
+{
+}
+#else
+ : isArray_( true )
+ , isNull_( true )
+{
+ iterator_.array_ = ValueInternalArray::IteratorState();
+}
+#endif
+
+
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ValueIteratorBase::ValueIteratorBase( const Value::ObjectValues::iterator ¤t )
+ : current_( current )
+ , isNull_( false )
+{
+}
+#else
+ValueIteratorBase::ValueIteratorBase( const ValueInternalArray::IteratorState &state )
+ : isArray_( true )
+{
+ iterator_.array_ = state;
+}
+
+
+ValueIteratorBase::ValueIteratorBase( const ValueInternalMap::IteratorState &state )
+ : isArray_( false )
+{
+ iterator_.map_ = state;
+}
+#endif
+
+Value &
+ValueIteratorBase::deref() const
+{
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ return current_->second;
+#else
+ if ( isArray_ )
+ return ValueInternalArray::dereference( iterator_.array_ );
+ return ValueInternalMap::value( iterator_.map_ );
+#endif
+}
+
+
+void
+ValueIteratorBase::increment()
+{
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ ++current_;
+#else
+ if ( isArray_ )
+ ValueInternalArray::increment( iterator_.array_ );
+ ValueInternalMap::increment( iterator_.map_ );
+#endif
+}
+
+
+void
+ValueIteratorBase::decrement()
+{
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ --current_;
+#else
+ if ( isArray_ )
+ ValueInternalArray::decrement( iterator_.array_ );
+ ValueInternalMap::decrement( iterator_.map_ );
+#endif
+}
+
+
+ValueIteratorBase::difference_type
+ValueIteratorBase::computeDistance( const SelfType &other ) const
+{
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+# ifdef JSON_USE_CPPTL_SMALLMAP
+ return current_ - other.current_;
+# else
+ // Iterator for null value are initialized using the default
+ // constructor, which initialize current_ to the default
+ // std::map::iterator. As begin() and end() are two instance
+ // of the default std::map::iterator, they can not be compared.
+ // To allow this, we handle this comparison specifically.
+ if ( isNull_ && other.isNull_ )
+ {
+ return 0;
+ }
+
+
+ // Usage of std::distance is not portable (does not compile with Sun Studio 12 RogueWave STL,
+ // which is the one used by default).
+ // Using a portable hand-made version for non random iterator instead:
+ // return difference_type( std::distance( current_, other.current_ ) );
+ difference_type myDistance = 0;
+ for ( Value::ObjectValues::iterator it = current_; it != other.current_; ++it )
+ {
+ ++myDistance;
+ }
+ return myDistance;
+# endif
+#else
+ if ( isArray_ )
+ return ValueInternalArray::distance( iterator_.array_, other.iterator_.array_ );
+ return ValueInternalMap::distance( iterator_.map_, other.iterator_.map_ );
+#endif
+}
+
+
+bool
+ValueIteratorBase::isEqual( const SelfType &other ) const
+{
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ if ( isNull_ )
+ {
+ return other.isNull_;
+ }
+ return current_ == other.current_;
+#else
+ if ( isArray_ )
+ return ValueInternalArray::equals( iterator_.array_, other.iterator_.array_ );
+ return ValueInternalMap::equals( iterator_.map_, other.iterator_.map_ );
+#endif
+}
+
+
+void
+ValueIteratorBase::copy( const SelfType &other )
+{
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ current_ = other.current_;
+#else
+ if ( isArray_ )
+ iterator_.array_ = other.iterator_.array_;
+ iterator_.map_ = other.iterator_.map_;
+#endif
+}
+
+
+Value
+ValueIteratorBase::key() const
+{
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ const Value::CZString czstring = (*current_).first;
+ if ( czstring.c_str() )
+ {
+ if ( czstring.isStaticString() )
+ return Value( StaticString( czstring.c_str() ) );
+ return Value( czstring.c_str() );
+ }
+ return Value( czstring.index() );
+#else
+ if ( isArray_ )
+ return Value( ValueInternalArray::indexOf( iterator_.array_ ) );
+ bool isStatic;
+ const char *memberName = ValueInternalMap::key( iterator_.map_, isStatic );
+ if ( isStatic )
+ return Value( StaticString( memberName ) );
+ return Value( memberName );
+#endif
+}
+
+
+UInt
+ValueIteratorBase::index() const
+{
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ const Value::CZString czstring = (*current_).first;
+ if ( !czstring.c_str() )
+ return czstring.index();
+ return Value::UInt( -1 );
+#else
+ if ( isArray_ )
+ return Value::UInt( ValueInternalArray::indexOf( iterator_.array_ ) );
+ return Value::UInt( -1 );
+#endif
+}
+
+
+const char *
+ValueIteratorBase::memberName() const
+{
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ const char *name = (*current_).first.c_str();
+ return name ? name : "";
+#else
+ if ( !isArray_ )
+ return ValueInternalMap::key( iterator_.map_ );
+ return "";
+#endif
+}
+
+
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// class ValueConstIterator
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+
+ValueConstIterator::ValueConstIterator()
+{
+}
+
+
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ValueConstIterator::ValueConstIterator( const Value::ObjectValues::iterator ¤t )
+ : ValueIteratorBase( current )
+{
+}
+#else
+ValueConstIterator::ValueConstIterator( const ValueInternalArray::IteratorState &state )
+ : ValueIteratorBase( state )
+{
+}
+
+ValueConstIterator::ValueConstIterator( const ValueInternalMap::IteratorState &state )
+ : ValueIteratorBase( state )
+{
+}
+#endif
+
+ValueConstIterator &
+ValueConstIterator::operator =( const ValueIteratorBase &other )
+{
+ copy( other );
+ return *this;
+}
+
+
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// class ValueIterator
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+// //////////////////////////////////////////////////////////////////
+
+ValueIterator::ValueIterator()
+{
+}
+
+
+#ifndef JSON_VALUE_USE_INTERNAL_MAP
+ValueIterator::ValueIterator( const Value::ObjectValues::iterator ¤t )
+ : ValueIteratorBase( current )
+{
+}
+#else
+ValueIterator::ValueIterator( const ValueInternalArray::IteratorState &state )
+ : ValueIteratorBase( state )
+{
+}
+
+ValueIterator::ValueIterator( const ValueInternalMap::IteratorState &state )
+ : ValueIteratorBase( state )
+{
+}
+#endif
+
+ValueIterator::ValueIterator( const ValueConstIterator &other )
+ : ValueIteratorBase( other )
+{
+}
+
+ValueIterator::ValueIterator( const ValueIterator &other )
+ : ValueIteratorBase( other )
+{
+}
+
+ValueIterator &
+ValueIterator::operator =( const SelfType &other )
+{
+ copy( other );
+ return *this;
+}
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#include "json_writer.h"
+#include "json_tool.h"
+#include <utility>
+#include <assert.h>
+#include <stdio.h>
+#include <string.h>
+#include <iostream>
+#include <sstream>
+#include <iomanip>
+
+#if _MSC_VER >= 1400 // VC++ 8.0
+#pragma warning( disable : 4996 ) // disable warning about strdup being deprecated.
+#endif
+
+namespace Json {
+
+static bool containsControlCharacter( const char* str )
+{
+ while ( *str )
+ {
+ if ( isControlCharacter( *(str++) ) )
+ return true;
+ }
+ return false;
+}
+
+std::string valueToString( Int value )
+{
+ UIntToStringBuffer buffer;
+ char *current = buffer + sizeof(buffer);
+ bool isNegative = value < 0;
+ if ( isNegative )
+ value = -value;
+ uintToString( UInt(value), current );
+ if ( isNegative )
+ *--current = '-';
+ assert( current >= buffer );
+ return current;
+}
+
+
+std::string valueToString( UInt value )
+{
+ UIntToStringBuffer buffer;
+ char *current = buffer + sizeof(buffer);
+ uintToString( value, current );
+ assert( current >= buffer );
+ return current;
+}
+
+std::string valueToString( double value )
+{
+ char buffer[32];
+#if defined(_MSC_VER) && defined(__STDC_SECURE_LIB__) // Use secure version with visual studio 2005 to avoid warning.
+ sprintf_s(buffer, sizeof(buffer), "%#.16g", value);
+#else
+ sprintf(buffer, "%#.16g", value);
+#endif
+ char* ch = buffer + strlen(buffer) - 1;
+ if (*ch != '0') return buffer; // nothing to truncate, so save time
+ while(ch > buffer && *ch == '0'){
+ --ch;
+ }
+ char* last_nonzero = ch;
+ while(ch >= buffer){
+ switch(*ch){
+ case '0':
+ case '1':
+ case '2':
+ case '3':
+ case '4':
+ case '5':
+ case '6':
+ case '7':
+ case '8':
+ case '9':
+ --ch;
+ continue;
+ case '.':
+ // Truncate zeroes to save bytes in output, but keep one.
+ *(last_nonzero+2) = '\0';
+ return buffer;
+ default:
+ return buffer;
+ }
+ }
+ return buffer;
+}
+
+
+std::string valueToString( bool value )
+{
+ return value ? "true" : "false";
+}
+
+std::string valueToQuotedString( const char *value )
+{
+ // Not sure how to handle unicode...
+ if (strpbrk(value, "\"\\\b\f\n\r\t") == NULL && !containsControlCharacter( value ))
+ return std::string("\"") + value + "\"";
+ // We have to walk value and escape any special characters.
+ // Appending to std::string is not efficient, but this should be rare.
+ // (Note: forward slashes are *not* rare, but I am not escaping them.)
+ std::string::size_type maxsize = strlen(value)*2 + 3; // allescaped+quotes+NULL
+ std::string result;
+ result.reserve(maxsize); // to avoid lots of mallocs
+ result += "\"";
+ for (const char* c=value; *c != 0; ++c)
+ {
+ switch(*c)
+ {
+ case '\"':
+ result += "\\\"";
+ break;
+ case '\\':
+ result += "\\\\";
+ break;
+ case '\b':
+ result += "\\b";
+ break;
+ case '\f':
+ result += "\\f";
+ break;
+ case '\n':
+ result += "\\n";
+ break;
+ case '\r':
+ result += "\\r";
+ break;
+ case '\t':
+ result += "\\t";
+ break;
+ //case '/':
+ // Even though \/ is considered a legal escape in JSON, a bare
+ // slash is also legal, so I see no reason to escape it.
+ // (I hope I am not misunderstanding something.
+ // blep notes: actually escaping \/ may be useful in javascript to avoid </
+ // sequence.
+ // Should add a flag to allow this compatibility mode and prevent this
+ // sequence from occurring.
+ default:
+ if ( isControlCharacter( *c ) )
+ {
+ std::ostringstream oss;
+ oss << "\\u" << std::hex << std::uppercase << std::setfill('0') << std::setw(4) << static_cast<int>(*c);
+ result += oss.str();
+ }
+ else
+ {
+ result += *c;
+ }
+ break;
+ }
+ }
+ result += "\"";
+ return result;
+}
+
+// Class Writer
+// //////////////////////////////////////////////////////////////////
+Writer::~Writer()
+{
+}
+
+
+// Class FastWriter
+// //////////////////////////////////////////////////////////////////
+
+FastWriter::FastWriter()
+ : yamlCompatiblityEnabled_( false )
+{
+}
+
+
+void
+FastWriter::enableYAMLCompatibility()
+{
+ yamlCompatiblityEnabled_ = true;
+}
+
+
+std::string
+FastWriter::write( const Value &root )
+{
+ document_ = "";
+ writeValue( root );
+ document_ += "\n";
+ return document_;
+}
+
+
+void
+FastWriter::writeValue( const Value &value )
+{
+ switch ( value.type() )
+ {
+ case nullValue:
+ document_ += "null";
+ break;
+ case intValue:
+ document_ += valueToString( value.asInt() );
+ break;
+ case uintValue:
+ document_ += valueToString( value.asUInt() );
+ break;
+ case realValue:
+ document_ += valueToString( value.asDouble() );
+ break;
+ case stringValue:
+ document_ += valueToQuotedString( value.asCString() );
+ break;
+ case booleanValue:
+ document_ += valueToString( value.asBool() );
+ break;
+ case arrayValue:
+ {
+ document_ += "[";
+ int size = value.size();
+ for ( int index =0; index < size; ++index )
+ {
+ if ( index > 0 )
+ document_ += ",";
+ writeValue( value[index] );
+ }
+ document_ += "]";
+ }
+ break;
+ case objectValue:
+ {
+ Value::Members members( value.getMemberNames() );
+ document_ += "{";
+ for ( Value::Members::iterator it = members.begin();
+ it != members.end();
+ ++it )
+ {
+ const std::string &name = *it;
+ if ( it != members.begin() )
+ document_ += ",";
+ document_ += valueToQuotedString( name.c_str() );
+ document_ += yamlCompatiblityEnabled_ ? ": "
+ : ":";
+ writeValue( value[name] );
+ }
+ document_ += "}";
+ }
+ break;
+ }
+}
+
+
+// Class StyledWriter
+// //////////////////////////////////////////////////////////////////
+
+StyledWriter::StyledWriter()
+ : rightMargin_( 74 )
+ , indentSize_( 3 )
+{
+}
+
+
+std::string
+StyledWriter::write( const Value &root )
+{
+ document_ = "";
+ addChildValues_ = false;
+ indentString_ = "";
+ writeCommentBeforeValue( root );
+ writeValue( root );
+ writeCommentAfterValueOnSameLine( root );
+ document_ += "\n";
+ return document_;
+}
+
+
+void
+StyledWriter::writeValue( const Value &value )
+{
+ switch ( value.type() )
+ {
+ case nullValue:
+ pushValue( "null" );
+ break;
+ case intValue:
+ pushValue( valueToString( value.asInt() ) );
+ break;
+ case uintValue:
+ pushValue( valueToString( value.asUInt() ) );
+ break;
+ case realValue:
+ pushValue( valueToString( value.asDouble() ) );
+ break;
+ case stringValue:
+ pushValue( valueToQuotedString( value.asCString() ) );
+ break;
+ case booleanValue:
+ pushValue( valueToString( value.asBool() ) );
+ break;
+ case arrayValue:
+ writeArrayValue( value);
+ break;
+ case objectValue:
+ {
+ Value::Members members( value.getMemberNames() );
+ if ( members.empty() )
+ pushValue( "{}" );
+ else
+ {
+ writeWithIndent( "{" );
+ indent();
+ Value::Members::iterator it = members.begin();
+ while ( true )
+ {
+ const std::string &name = *it;
+ const Value &childValue = value[name];
+ writeCommentBeforeValue( childValue );
+ writeWithIndent( valueToQuotedString( name.c_str() ) );
+ document_ += " : ";
+ writeValue( childValue );
+ if ( ++it == members.end() )
+ {
+ writeCommentAfterValueOnSameLine( childValue );
+ break;
+ }
+ document_ += ",";
+ writeCommentAfterValueOnSameLine( childValue );
+ }
+ unindent();
+ writeWithIndent( "}" );
+ }
+ }
+ break;
+ }
+}
+
+
+void
+StyledWriter::writeArrayValue( const Value &value )
+{
+ unsigned size = value.size();
+ if ( size == 0 )
+ pushValue( "[]" );
+ else
+ {
+ bool isArrayMultiLine = isMultineArray( value );
+ if ( isArrayMultiLine )
+ {
+ writeWithIndent( "[" );
+ indent();
+ bool hasChildValue = !childValues_.empty();
+ unsigned index =0;
+ while ( true )
+ {
+ const Value &childValue = value[index];
+ writeCommentBeforeValue( childValue );
+ if ( hasChildValue )
+ writeWithIndent( childValues_[index] );
+ else
+ {
+ writeIndent();
+ writeValue( childValue );
+ }
+ if ( ++index == size )
+ {
+ writeCommentAfterValueOnSameLine( childValue );
+ break;
+ }
+ document_ += ",";
+ writeCommentAfterValueOnSameLine( childValue );
+ }
+ unindent();
+ writeWithIndent( "]" );
+ }
+ else // output on a single line
+ {
+ assert( childValues_.size() == size );
+ document_ += "[ ";
+ for ( unsigned index =0; index < size; ++index )
+ {
+ if ( index > 0 )
+ document_ += ", ";
+ document_ += childValues_[index];
+ }
+ document_ += " ]";
+ }
+ }
+}
+
+
+bool
+StyledWriter::isMultineArray( const Value &value )
+{
+ int size = value.size();
+ bool isMultiLine = size*3 >= rightMargin_ ;
+ childValues_.clear();
+ for ( int index =0; index < size && !isMultiLine; ++index )
+ {
+ const Value &childValue = value[index];
+ isMultiLine = isMultiLine ||
+ ( (childValue.isArray() || childValue.isObject()) &&
+ childValue.size() > 0 );
+ }
+ if ( !isMultiLine ) // check if line length > max line length
+ {
+ childValues_.reserve( size );
+ addChildValues_ = true;
+ int lineLength = 4 + (size-1)*2; // '[ ' + ', '*n + ' ]'
+ for ( int index =0; index < size && !isMultiLine; ++index )
+ {
+ writeValue( value[index] );
+ lineLength += int( childValues_[index].length() );
+ isMultiLine = isMultiLine && hasCommentForValue( value[index] );
+ }
+ addChildValues_ = false;
+ isMultiLine = isMultiLine || lineLength >= rightMargin_;
+ }
+ return isMultiLine;
+}
+
+
+void
+StyledWriter::pushValue( const std::string &value )
+{
+ if ( addChildValues_ )
+ childValues_.push_back( value );
+ else
+ document_ += value;
+}
+
+
+void
+StyledWriter::writeIndent()
+{
+ if ( !document_.empty() )
+ {
+ char last = document_[document_.length()-1];
+ if ( last == ' ' ) // already indented
+ return;
+ if ( last != '\n' ) // Comments may add new-line
+ document_ += '\n';
+ }
+ document_ += indentString_;
+}
+
+
+void
+StyledWriter::writeWithIndent( const std::string &value )
+{
+ writeIndent();
+ document_ += value;
+}
+
+
+void
+StyledWriter::indent()
+{
+ indentString_ += std::string( indentSize_, ' ' );
+}
+
+
+void
+StyledWriter::unindent()
+{
+ assert( int(indentString_.size()) >= indentSize_ );
+ indentString_.resize( indentString_.size() - indentSize_ );
+}
+
+
+void
+StyledWriter::writeCommentBeforeValue( const Value &root )
+{
+ if ( !root.hasComment( commentBefore ) )
+ return;
+ document_ += normalizeEOL( root.getComment( commentBefore ) );
+ document_ += "\n";
+}
+
+
+void
+StyledWriter::writeCommentAfterValueOnSameLine( const Value &root )
+{
+ if ( root.hasComment( commentAfterOnSameLine ) )
+ document_ += " " + normalizeEOL( root.getComment( commentAfterOnSameLine ) );
+
+ if ( root.hasComment( commentAfter ) )
+ {
+ document_ += "\n";
+ document_ += normalizeEOL( root.getComment( commentAfter ) );
+ document_ += "\n";
+ }
+}
+
+
+bool
+StyledWriter::hasCommentForValue( const Value &value )
+{
+ return value.hasComment( commentBefore )
+ || value.hasComment( commentAfterOnSameLine )
+ || value.hasComment( commentAfter );
+}
+
+
+std::string
+StyledWriter::normalizeEOL( const std::string &text )
+{
+ std::string normalized;
+ normalized.reserve( text.length() );
+ const char *begin = text.c_str();
+ const char *end = begin + text.length();
+ const char *current = begin;
+ while ( current != end )
+ {
+ char c = *current++;
+ if ( c == '\r' ) // mac or dos EOL
+ {
+ if ( *current == '\n' ) // convert dos EOL
+ ++current;
+ normalized += '\n';
+ }
+ else // handle unix EOL & other char
+ normalized += c;
+ }
+ return normalized;
+}
+
+
+// Class StyledStreamWriter
+// //////////////////////////////////////////////////////////////////
+
+StyledStreamWriter::StyledStreamWriter( std::string indentation )
+ : document_(NULL)
+ , rightMargin_( 74 )
+ , indentation_( indentation )
+{
+}
+
+
+void
+StyledStreamWriter::write( std::ostream &out, const Value &root )
+{
+ document_ = &out;
+ addChildValues_ = false;
+ indentString_ = "";
+ writeCommentBeforeValue( root );
+ writeValue( root );
+ writeCommentAfterValueOnSameLine( root );
+ *document_ << "\n";
+ document_ = NULL; // Forget the stream, for safety.
+}
+
+
+void
+StyledStreamWriter::writeValue( const Value &value )
+{
+ switch ( value.type() )
+ {
+ case nullValue:
+ pushValue( "null" );
+ break;
+ case intValue:
+ pushValue( valueToString( value.asInt() ) );
+ break;
+ case uintValue:
+ pushValue( valueToString( value.asUInt() ) );
+ break;
+ case realValue:
+ pushValue( valueToString( value.asDouble() ) );
+ break;
+ case stringValue:
+ pushValue( valueToQuotedString( value.asCString() ) );
+ break;
+ case booleanValue:
+ pushValue( valueToString( value.asBool() ) );
+ break;
+ case arrayValue:
+ writeArrayValue( value);
+ break;
+ case objectValue:
+ {
+ Value::Members members( value.getMemberNames() );
+ if ( members.empty() )
+ pushValue( "{}" );
+ else
+ {
+ writeWithIndent( "{" );
+ indent();
+ Value::Members::iterator it = members.begin();
+ while ( true )
+ {
+ const std::string &name = *it;
+ const Value &childValue = value[name];
+ writeCommentBeforeValue( childValue );
+ writeWithIndent( valueToQuotedString( name.c_str() ) );
+ *document_ << " : ";
+ writeValue( childValue );
+ if ( ++it == members.end() )
+ {
+ writeCommentAfterValueOnSameLine( childValue );
+ break;
+ }
+ *document_ << ",";
+ writeCommentAfterValueOnSameLine( childValue );
+ }
+ unindent();
+ writeWithIndent( "}" );
+ }
+ }
+ break;
+ }
+}
+
+
+void
+StyledStreamWriter::writeArrayValue( const Value &value )
+{
+ unsigned size = value.size();
+ if ( size == 0 )
+ pushValue( "[]" );
+ else
+ {
+ bool isArrayMultiLine = isMultineArray( value );
+ if ( isArrayMultiLine )
+ {
+ writeWithIndent( "[" );
+ indent();
+ bool hasChildValue = !childValues_.empty();
+ unsigned index =0;
+ while ( true )
+ {
+ const Value &childValue = value[index];
+ writeCommentBeforeValue( childValue );
+ if ( hasChildValue )
+ writeWithIndent( childValues_[index] );
+ else
+ {
+ writeIndent();
+ writeValue( childValue );
+ }
+ if ( ++index == size )
+ {
+ writeCommentAfterValueOnSameLine( childValue );
+ break;
+ }
+ *document_ << ",";
+ writeCommentAfterValueOnSameLine( childValue );
+ }
+ unindent();
+ writeWithIndent( "]" );
+ }
+ else // output on a single line
+ {
+ assert( childValues_.size() == size );
+ *document_ << "[ ";
+ for ( unsigned index =0; index < size; ++index )
+ {
+ if ( index > 0 )
+ *document_ << ", ";
+ *document_ << childValues_[index];
+ }
+ *document_ << " ]";
+ }
+ }
+}
+
+
+bool
+StyledStreamWriter::isMultineArray( const Value &value )
+{
+ int size = value.size();
+ bool isMultiLine = size*3 >= rightMargin_ ;
+ childValues_.clear();
+ for ( int index =0; index < size && !isMultiLine; ++index )
+ {
+ const Value &childValue = value[index];
+ isMultiLine = isMultiLine ||
+ ( (childValue.isArray() || childValue.isObject()) &&
+ childValue.size() > 0 );
+ }
+ if ( !isMultiLine ) // check if line length > max line length
+ {
+ childValues_.reserve( size );
+ addChildValues_ = true;
+ int lineLength = 4 + (size-1)*2; // '[ ' + ', '*n + ' ]'
+ for ( int index =0; index < size && !isMultiLine; ++index )
+ {
+ writeValue( value[index] );
+ lineLength += int( childValues_[index].length() );
+ isMultiLine = isMultiLine && hasCommentForValue( value[index] );
+ }
+ addChildValues_ = false;
+ isMultiLine = isMultiLine || lineLength >= rightMargin_;
+ }
+ return isMultiLine;
+}
+
+
+void
+StyledStreamWriter::pushValue( const std::string &value )
+{
+ if ( addChildValues_ )
+ childValues_.push_back( value );
+ else
+ *document_ << value;
+}
+
+
+void
+StyledStreamWriter::writeIndent()
+{
+ /*
+ Some comments in this method would have been nice. ;-)
+
+ if ( !document_.empty() )
+ {
+ char last = document_[document_.length()-1];
+ if ( last == ' ' ) // already indented
+ return;
+ if ( last != '\n' ) // Comments may add new-line
+ *document_ << '\n';
+ }
+ */
+ *document_ << '\n' << indentString_;
+}
+
+
+void
+StyledStreamWriter::writeWithIndent( const std::string &value )
+{
+ writeIndent();
+ *document_ << value;
+}
+
+
+void
+StyledStreamWriter::indent()
+{
+ indentString_ += indentation_;
+}
+
+
+void
+StyledStreamWriter::unindent()
+{
+ assert( indentString_.size() >= indentation_.size() );
+ indentString_.resize( indentString_.size() - indentation_.size() );
+}
+
+
+void
+StyledStreamWriter::writeCommentBeforeValue( const Value &root )
+{
+ if ( !root.hasComment( commentBefore ) )
+ return;
+ *document_ << normalizeEOL( root.getComment( commentBefore ) );
+ *document_ << "\n";
+}
+
+
+void
+StyledStreamWriter::writeCommentAfterValueOnSameLine( const Value &root )
+{
+ if ( root.hasComment( commentAfterOnSameLine ) )
+ *document_ << " " + normalizeEOL( root.getComment( commentAfterOnSameLine ) );
+
+ if ( root.hasComment( commentAfter ) )
+ {
+ *document_ << "\n";
+ *document_ << normalizeEOL( root.getComment( commentAfter ) );
+ *document_ << "\n";
+ }
+}
+
+
+bool
+StyledStreamWriter::hasCommentForValue( const Value &value )
+{
+ return value.hasComment( commentBefore )
+ || value.hasComment( commentAfterOnSameLine )
+ || value.hasComment( commentAfter );
+}
+
+
+std::string
+StyledStreamWriter::normalizeEOL( const std::string &text )
+{
+ std::string normalized;
+ normalized.reserve( text.length() );
+ const char *begin = text.c_str();
+ const char *end = begin + text.length();
+ const char *current = begin;
+ while ( current != end )
+ {
+ char c = *current++;
+ if ( c == '\r' ) // mac or dos EOL
+ {
+ if ( *current == '\n' ) // convert dos EOL
+ ++current;
+ normalized += '\n';
+ }
+ else // handle unix EOL & other char
+ normalized += c;
+ }
+ return normalized;
+}
+
+
+std::ostream& operator<<( std::ostream &sout, const Value &root )
+{
+ Json::StyledStreamWriter writer;
+ writer.write(sout, root);
+ return sout;
+}
+
+
+} // namespace Json
--- /dev/null
+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#ifndef JSON_WRITER_H_INCLUDED
+# define JSON_WRITER_H_INCLUDED
+
+# include "json_value.h"
+# include <vector>
+# include <string>
+# include <iostream>
+
+namespace Json {
+
+ class Value;
+
+ /** \brief Abstract class for writers.
+ */
+ class JSON_API Writer
+ {
+ public:
+ virtual ~Writer();
+
+ virtual std::string write( const Value &root ) = 0;
+ };
+
+ /** \brief Outputs a Value in <a HREF="http://www.json.org">JSON</a> format without formatting (not human friendly).
+ *
+ * The JSON document is written in a single line. It is not intended for 'human' consumption,
+ * but may be usefull to support feature such as RPC where bandwith is limited.
+ * \sa Reader, Value
+ */
+ class JSON_API FastWriter : public Writer
+ {
+ public:
+ FastWriter();
+ virtual ~FastWriter(){}
+
+ void enableYAMLCompatibility();
+
+ public: // overridden from Writer
+ virtual std::string write( const Value &root );
+
+ private:
+ void writeValue( const Value &value );
+
+ std::string document_;
+ bool yamlCompatiblityEnabled_;
+ };
+
+ /** \brief Writes a Value in <a HREF="http://www.json.org">JSON</a> format in a human friendly way.
+ *
+ * The rules for line break and indent are as follow:
+ * - Object value:
+ * - if empty then print {} without indent and line break
+ * - if not empty the print '{', line break & indent, print one value per line
+ * and then unindent and line break and print '}'.
+ * - Array value:
+ * - if empty then print [] without indent and line break
+ * - if the array contains no object value, empty array or some other value types,
+ * and all the values fit on one lines, then print the array on a single line.
+ * - otherwise, it the values do not fit on one line, or the array contains
+ * object or non empty array, then print one value per line.
+ *
+ * If the Value have comments then they are outputed according to their #CommentPlacement.
+ *
+ * \sa Reader, Value, Value::setComment()
+ */
+ class JSON_API StyledWriter: public Writer
+ {
+ public:
+ StyledWriter();
+ virtual ~StyledWriter(){}
+
+ public: // overridden from Writer
+ /** \brief Serialize a Value in <a HREF="http://www.json.org">JSON</a> format.
+ * \param root Value to serialize.
+ * \return String containing the JSON document that represents the root value.
+ */
+ virtual std::string write( const Value &root );
+
+ private:
+ void writeValue( const Value &value );
+ void writeArrayValue( const Value &value );
+ bool isMultineArray( const Value &value );
+ void pushValue( const std::string &value );
+ void writeIndent();
+ void writeWithIndent( const std::string &value );
+ void indent();
+ void unindent();
+ void writeCommentBeforeValue( const Value &root );
+ void writeCommentAfterValueOnSameLine( const Value &root );
+ bool hasCommentForValue( const Value &value );
+ static std::string normalizeEOL( const std::string &text );
+
+ typedef std::vector<std::string> ChildValues;
+
+ ChildValues childValues_;
+ std::string document_;
+ std::string indentString_;
+ int rightMargin_;
+ int indentSize_;
+ bool addChildValues_;
+ };
+
+ /** \brief Writes a Value in <a HREF="http://www.json.org">JSON</a> format in a human friendly way,
+ to a stream rather than to a string.
+ *
+ * The rules for line break and indent are as follow:
+ * - Object value:
+ * - if empty then print {} without indent and line break
+ * - if not empty the print '{', line break & indent, print one value per line
+ * and then unindent and line break and print '}'.
+ * - Array value:
+ * - if empty then print [] without indent and line break
+ * - if the array contains no object value, empty array or some other value types,
+ * and all the values fit on one lines, then print the array on a single line.
+ * - otherwise, it the values do not fit on one line, or the array contains
+ * object or non empty array, then print one value per line.
+ *
+ * If the Value have comments then they are outputed according to their #CommentPlacement.
+ *
+ * \param indentation Each level will be indented by this amount extra.
+ * \sa Reader, Value, Value::setComment()
+ */
+ class JSON_API StyledStreamWriter
+ {
+ public:
+ StyledStreamWriter( std::string indentation="\t" );
+ ~StyledStreamWriter(){}
+
+ public:
+ /** \brief Serialize a Value in <a HREF="http://www.json.org">JSON</a> format.
+ * \param out Stream to write to. (Can be ostringstream, e.g.)
+ * \param root Value to serialize.
+ * \note There is no point in deriving from Writer, since write() should not return a value.
+ */
+ void write( std::ostream &out, const Value &root );
+
+ private:
+ void writeValue( const Value &value );
+ void writeArrayValue( const Value &value );
+ bool isMultineArray( const Value &value );
+ void pushValue( const std::string &value );
+ void writeIndent();
+ void writeWithIndent( const std::string &value );
+ void indent();
+ void unindent();
+ void writeCommentBeforeValue( const Value &root );
+ void writeCommentAfterValueOnSameLine( const Value &root );
+ bool hasCommentForValue( const Value &value );
+ static std::string normalizeEOL( const std::string &text );
+
+ typedef std::vector<std::string> ChildValues;
+
+ ChildValues childValues_;
+ std::ostream* document_;
+ std::string indentString_;
+ int rightMargin_;
+ std::string indentation_;
+ bool addChildValues_;
+ };
+
+ std::string JSON_API valueToString( Int value );
+ std::string JSON_API valueToString( UInt value );
+ std::string JSON_API valueToString( double value );
+ std::string JSON_API valueToString( bool value );
+ std::string JSON_API valueToQuotedString( const char *value );
+
+ /// \brief Output using the StyledStreamWriter.
+ /// \see Json::operator>>()
+ std::ostream& operator<<( std::ostream&, const Value &root );
+
+} // namespace Json
+
+
+
+#endif // JSON_WRITER_H_INCLUDED
UTILS_DIR = ../utils
OBJ_DIR = ../../obj
BIN_DIR = ../../bin
+THIRD_PARTY_DIR = ../third_party
-INCLUDES = -I$(API_DIR)/ -I$(UTILS_DIR)
+INCLUDES = -I$(API_DIR)/ -I$(UTILS_DIR) -I$(THIRD_PARTY_DIR)
# ----------------------------------
# define our source and object files
cerr << "usage: bamtools [--help] COMMAND [ARGS]" << endl;
cerr << endl;
cerr << "Available bamtools commands:" << endl;
- cerr << "\tconvert Converts between BAM and a number of other formats" << endl;
- cerr << "\tcount Prints number of alignments in BAM file" << endl;
- cerr << "\tcoverage Prints coverage statistics from the input BAM file" << endl;
- cerr << "\tfilter Filters BAM file(s) by user-specified criteria" << endl;
- cerr << "\theader Prints BAM header information" << endl;
- cerr << "\tindex Generates index for BAM file" << endl;
- cerr << "\tmerge Merge multiple BAM files into single file" << endl;
- cerr << "\trandom Grab a random subset of alignments" << endl;
- cerr << "\tsort Sorts the BAM file according to some criteria" << endl;
- cerr << "\tstats Prints general alignment statistics" << endl;
+ cerr << "\tconvert Converts between BAM and a number of other formats" << endl;
+ cerr << "\tcount Prints number of alignments in BAM file(s)" << endl;
+ cerr << "\tcoverage Prints coverage statistics from the input BAM file" << endl;
+ cerr << "\tfilter Filters BAM file(s) by user-specified criteria" << endl;
+ cerr << "\theader Prints BAM header information" << endl;
+ cerr << "\tindex Generates index for BAM file" << endl;
+ cerr << "\tmerge Merge multiple BAM files into single file" << endl;
+ cerr << "\trandom Select random alignments from existing BAM file(s)" << endl;
+ cerr << "\tsort Sorts the BAM file according to some criteria" << endl;
+ cerr << "\tstats Prints some basic statistics from input BAM file(s)" << endl;
cerr << endl;
cerr << "See 'bamtools help COMMAND' for more information on a specific command." << endl;
cerr << endl;
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
+// Last modified: 3 September 2010
// ---------------------------------------------------------------------------
-// Prints alignment count for BAM file
-//
-// ** Expand to multiple??
-//
+// Prints alignment count for BAM file(s)
// ***************************************************************************
#include <iostream>
-#include <sstream>
#include <string>
#include <vector>
, m_settings(new CountSettings)
{
// set program details
- Options::SetProgramInfo("bamtools count", "prints alignment counts for a BAM file", "-in <filename> [-region <REGION>]");
+ Options::SetProgramInfo("bamtools count", "prints alignment counts for a BAM file", "[-in <filename> -in <filename> ...] [-region <REGION>]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
- Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts);
- //Options::AddValueOption("-index", "BAM index filename", "the BAM index file", "", m_settings->HasBamIndexFilename, m_settings->BamIndexFilename, IO_Opts);
+ Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
- Options::AddValueOption("-region", "REGION", "genomic region. Index file is recommended for better performance, and is read automatically if it exists as <filename>.bai or <filename>.bti. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
+ Options::AddValueOption("-region", "REGION", "genomic region. Index file is required and is read automatically if it exists as <filename>.bai or <filename>.bti. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
}
CountTool::~CountTool(void) {
// parse command line arguments
Options::Parse(argc, argv, 1);
+ // if no '-in' args supplied, default to stdin
if ( !m_settings->HasInput )
m_settings->InputFiles.push_back(Options::StandardIn());
+ // open reader without index
BamMultiReader reader;
reader.Open(m_settings->InputFiles, false, true);
// alignment counter
+ BamAlignment al;
int alignmentCount(0);
- // set up error handling
- ostringstream errorStream("");
- bool foundError(false);
-
// if no region specified, count entire file
if ( !m_settings->HasRegion ) {
- BamAlignment al;
while ( reader.GetNextAlignmentCore(al) )
++alignmentCount;
}
- // more complicated - region specified
+ // otherwise attempt to use region as constraint
else {
+ // if region string parses OK
BamRegion region;
if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
- // check if there are index files *.bai/*.bti corresponding to the input files
- bool hasDefaultIndex = false;
- bool hasBamtoolsIndex = false;
- bool hasNoIndex = false;
- int defaultIndexCount = 0;
- int bamtoolsIndexCount = 0;
- for (vector<string>::const_iterator f = m_settings->InputFiles.begin(); f != m_settings->InputFiles.end(); ++f) {
-
- if ( Utilities::FileExists(*f + ".bai") ) {
- hasDefaultIndex = true;
- ++defaultIndexCount;
- }
-
- if ( Utilities::FileExists(*f + ".bti") ) {
- hasBamtoolsIndex = true;
- ++bamtoolsIndexCount;
- }
-
- if ( !hasDefaultIndex && !hasBamtoolsIndex ) {
- hasNoIndex = true;
- cerr << "*WARNING - could not find index file for " << *f
- << ", parsing whole file(s) to get alignment counts for target region"
- << " (could be slow)" << endl;
- break;
- }
- }
+ // attempt to re-open reader with index files
+ reader.Close();
+ bool openedOK = reader.Open(m_settings->InputFiles, true, true );
- // determine if index file types are heterogeneous
- bool hasDifferentIndexTypes = false;
- if ( defaultIndexCount > 0 && bamtoolsIndexCount > 0 ) {
- hasDifferentIndexTypes = true;
- cerr << "*WARNING - different index file formats found"
- << ", parsing whole file(s) to get alignment counts for target region"
- << " (could be slow)" << endl;
+ // if error
+ if ( !openedOK ) {
+ cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
+ return 1;
}
- // if any input file has no index, or if input files use different index formats
- // can't use BamMultiReader to jump directly (**for now**)
- if ( hasNoIndex || hasDifferentIndexTypes ) {
-
- // read through sequentially, counting all overlapping reads
- BamAlignment al;
+ // if index data available, we can use SetRegion
+ if ( reader.IsIndexLoaded() ) {
+
+ // attempt to use SetRegion(), if failed report error
+ if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
+ cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
+ reader.Close();
+ return 1;
+ }
+
+ // everything checks out, just iterate through specified region, counting alignments
+ while ( reader.GetNextAlignmentCore(al) )
+ ++alignmentCount;
+ }
+
+ // no index data available, we have to iterate through until we
+ // find overlapping alignments
+ else {
while( reader.GetNextAlignmentCore(al) ) {
if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
- (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
+ (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
{
++alignmentCount;
}
}
}
-
- // has index file for each input file (and same format)
- else {
-
- // this is kind of a hack...?
- BamMultiReader reader;
- reader.Open(m_settings->InputFiles, true, true, hasDefaultIndex );
-
- if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
- foundError = true;
- errorStream << "Could not set BamReader region to REGION: " << m_settings->Region << endl;
- } else {
- BamAlignment al;
- while ( reader.GetNextAlignmentCore(al) )
- ++alignmentCount;
- }
- }
-
- } else {
- foundError = true;
- errorStream << "Could not parse REGION: " << m_settings->Region << endl;
- errorStream << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
+ }
+
+ // error parsing REGION string
+ else {
+ cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl;
+ cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
+ reader.Close();
+ return 1;
}
}
-
- // print errors OR results
- if ( foundError )
- cerr << errorStream.str() << endl;
- else
- cout << alignmentCount << endl;
+
+ // print results
+ cout << alignmentCount << endl;
// clean & exit
reader.Close();
- return (int)foundError;
+ return 0;
}
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 1 June 2010
+// Last modified: 31 August 2010
// ---------------------------------------------------------------------------
// Filters a single BAM file (or filters multiple BAM files and merges)
// according to some user-specified criteria.
// ***************************************************************************
+// std includes
+#include <cstdio>
#include <iostream>
+#include <sstream>
#include <string>
#include <vector>
+// BamTools includes
#include "bamtools_filter.h"
+#include "bamtools_filter_engine.h"
#include "bamtools_options.h"
+#include "bamtools_utilities.h"
#include "BamReader.h"
#include "BamMultiReader.h"
+#include "BamWriter.h"
+
+//JsonCPP includes
+#include "jsoncpp/json.h"
using namespace std;
using namespace BamTools;
+using namespace Json;
+
+namespace BamTools {
+
+// -------------------------------
+// string literal constants
+
+// property names
+const string ALIGNMENTFLAG_PROPERTY = "alignmentFlag";
+const string INSERTSIZE_PROPERTY = "insertSize";
+const string ISDUPLICATE_PROPERTY = "isDuplicate";
+const string ISFAILEDQC_PROPERTY = "isFailedQC";
+const string ISFIRSTMATE_PROPERTY = "isFirstMate";
+const string ISMAPPED_PROPERTY = "isMapped";
+const string ISMATEMAPPED_PROPERTY = "isMateMapped";
+const string ISMATEREVERSESTRAND_PROPERTY = "isMateReverseStrand";
+const string ISPAIRED_PROPERTY = "isPaired";
+const string ISPRIMARYALIGNMENT_PROPERTY = "isPrimaryAlignment";
+const string ISPROPERPAIR_PROPERTY = "isProperPair";
+const string ISREVERSESTRAND_PROPERTY = "isReverseStrand";
+const string ISSECONDMATE_PROPERTY = "isSecondMate";
+const string MAPQUALITY_PROPERTY = "mapQuality";
+const string MATEPOSITION_PROPERTY = "matePosition";
+const string MATEREFERENCE_PROPERTY = "mateReference";
+const string NAME_PROPERTY = "name";
+const string POSITION_PROPERTY = "position";
+const string QUERYBASES_PROPERTY = "queryBases";
+const string REFERENCE_PROPERTY = "reference";
+
+// boolalpha
+const string TRUE_STR = "true";
+const string FALSE_STR = "false";
+
+} // namespace BamTools
+
+// ---------------------------------------------
+// FilterToolPrivate declaration
+
+class FilterTool::FilterToolPrivate {
+
+ // ctor & dtor
+ public:
+ FilterToolPrivate(FilterTool::FilterSettings* settings);
+ ~FilterToolPrivate(void);
+
+ // 'public' interface
+ public:
+ bool Run(void);
+
+ // internal methods
+ private:
+ bool AddPropertyTokensToFilter(const string& filterName, const map<string, string>& propertyTokens);
+ bool CheckAlignment(const BamAlignment& al);
+ const string GetScriptContents(void);
+ void InitProperties(void);
+ bool ParseCommandLine(void);
+ bool ParseFilterObject(const string& filterName, const Json::Value& filterObject);
+ bool ParseScript(void);
+ bool SetupFilters(void);
+
+ // data members
+ private:
+ vector<string> m_propertyNames;
+ FilterTool::FilterSettings* m_settings;
+ RefVector m_references;
+};
// ---------------------------------------------
// FilterSettings implementation
struct FilterTool::FilterSettings {
+ // ----------------------------------
+ // IO opts
+
// flags
bool HasInputBamFilename;
bool HasOutputBamFilename;
-
+ bool HasRegion;
+ bool HasScriptFilename;
+ bool IsForceCompression;
+
// filenames
vector<string> InputFiles;
string OutputFilename;
+ string Region;
+ string ScriptFilename;
+
+ // -----------------------------------
+ // General filter opts
+
+ // flags
+ bool HasAlignmentFlagFilter;
+ bool HasInsertSizeFilter;
+ bool HasMapQualityFilter;
+ bool HasNameFilter;
+ bool HasQueryBasesFilter;
+// bool HasTagFilters;
+
+ // filters
+ string AlignmentFlagFilter;
+ string InsertSizeFilter;
+ string NameFilter;
+ string MapQualityFilter;
+ string QueryBasesFilter;
+
+// vector<string> TagFilters;
+
+ // -----------------------------------
+ // AlignmentFlag filter opts
+
+ // flags
+ bool HasIsDuplicateFilter;
+ bool HasIsFailedQCFilter;
+ bool HasIsFirstMateFilter;
+ bool HasIsMappedFilter;
+ bool HasIsMateMappedFilter;
+ bool HasIsMateReverseStrandFilter;
+ bool HasIsPairedFilter;
+ bool HasIsPrimaryAlignmentFilter;
+ bool HasIsProperPairFilter;
+ bool HasIsReverseStrandFilter;
+ bool HasIsSecondMateFilter;
+
+ // filters
+ string IsDuplicateFilter;
+ string IsFailedQCFilter;
+ string IsFirstMateFilter;
+ string IsMappedFilter;
+ string IsMateMappedFilter;
+ string IsMateReverseStrandFilter;
+ string IsPairedFilter;
+ string IsPrimaryAlignmentFilter;
+ string IsProperPairFilter;
+ string IsReverseStrandFilter;
+ string IsSecondMateFilter;
+
+ // ---------------------------------
// constructor
+
FilterSettings(void)
: HasInputBamFilename(false)
, HasOutputBamFilename(false)
+ , HasRegion(false)
+ , HasScriptFilename(false)
+ , IsForceCompression(false)
, OutputFilename(Options::StandardOut())
+ , HasAlignmentFlagFilter(false)
+ , HasInsertSizeFilter(false)
+ , HasMapQualityFilter(false)
+ , HasNameFilter(false)
+ , HasQueryBasesFilter(false)
+// , HasTagFilters(false)
+ , HasIsDuplicateFilter(false)
+ , HasIsFailedQCFilter(false)
+ , HasIsFirstMateFilter(false)
+ , HasIsMappedFilter(false)
+ , HasIsMateMappedFilter(false)
+ , HasIsMateReverseStrandFilter(false)
+ , HasIsPairedFilter(false)
+ , HasIsPrimaryAlignmentFilter(false)
+ , HasIsProperPairFilter(false)
+ , HasIsReverseStrandFilter(false)
+ , HasIsSecondMateFilter(false)
+ , IsDuplicateFilter(TRUE_STR)
+ , IsFailedQCFilter(TRUE_STR)
+ , IsFirstMateFilter(TRUE_STR)
+ , IsMappedFilter(TRUE_STR)
+ , IsMateMappedFilter(TRUE_STR)
+ , IsMateReverseStrandFilter(TRUE_STR)
+ , IsPairedFilter(TRUE_STR)
+ , IsPrimaryAlignmentFilter(TRUE_STR)
+ , IsProperPairFilter(TRUE_STR)
+ , IsReverseStrandFilter(TRUE_STR)
+ , IsSecondMateFilter(TRUE_STR)
{ }
};
FilterTool::FilterTool(void)
: AbstractTool()
, m_settings(new FilterSettings)
+ , m_impl(0)
{
// set program details
- Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", "-in <filename> [-in <filename> ... ] -out <filename> ");
+ Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", "-in <filename> [-in <filename> ... ] -out <filename> -region <REGION> [ [-script <filename] | [filterOptions] ]");
- // set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
- Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn());
- Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+ Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+ Options::AddValueOption("-region", "REGION", "only read data from this genomic region (see README for more details)", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
+ Options::AddValueOption("-script", "filename", "the filter script file (see README for more details)", "", m_settings->HasScriptFilename, m_settings->ScriptFilename, IO_Opts);
+ Options::AddOption("-forceCompression", "if results are sent to stdout (like when piping to another tool), default behavior is to leave output uncompressed. Use this flag to override and force compression", m_settings->IsForceCompression, IO_Opts);
+
+ OptionGroup* FilterOpts = Options::CreateOptionGroup("General Filters");
+ Options::AddValueOption("-alignmentFlag", "int", "keep reads with this *exact* alignment flag (for more detailed queries, see below)", "", m_settings->HasAlignmentFlagFilter, m_settings->AlignmentFlagFilter, FilterOpts);
+ Options::AddValueOption("-insertSize", "int", "keep reads with insert size that mathces pattern", "", m_settings->HasInsertSizeFilter, m_settings->InsertSizeFilter, FilterOpts);
+ Options::AddValueOption("-mapQuality", "[0-255]", "keep reads with map quality that matches pattern", "", m_settings->HasMapQualityFilter, m_settings->MapQualityFilter, FilterOpts);
+ Options::AddValueOption("-name", "string", "keep reads with name that matches pattern", "", m_settings->HasNameFilter, m_settings->NameFilter, FilterOpts);
+ Options::AddValueOption("-queryBases", "string", "keep reads with motif that mathces pattern", "", m_settings->HasQueryBasesFilter, m_settings->QueryBasesFilter, FilterOpts);
+
+// Options::AddValueOption("-tag", "TAG:VALUE", "keep reads with this key=>value pair. If multiple tags are given, reads must match all", "", m_settings->HasTagFilters, m_settings->TagFilters, FilterOpts);
+
+ OptionGroup* AlignmentFlagOpts = Options::CreateOptionGroup("Alignment Flag Filters");
+ Options::AddValueOption("-isDuplicate", "true/false", "keep only alignments that are marked as duplicate?", "", m_settings->HasIsDuplicateFilter, m_settings->IsDuplicateFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isFailedQC", "true/false", "keep only alignments that failed QC?", "", m_settings->HasIsFailedQCFilter, m_settings->IsFailedQCFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isFirstMate", "true/false", "keep only alignments marked as first mate?", "", m_settings->HasIsFirstMateFilter, m_settings->IsFirstMateFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isMapped", "true/false", "keep only alignments that were mapped?", "", m_settings->HasIsMappedFilter, m_settings->IsMappedFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isMateMapped", "true/false", "keep only alignments with mates that mapped", "", m_settings->HasIsMateMappedFilter, m_settings->IsMateMappedFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isMateReverseStrand", "true/false", "keep only alignments with mate on reverese strand?", "", m_settings->HasIsMateReverseStrandFilter, m_settings->IsMateReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isPaired", "true/false", "keep only alignments that were sequenced as paired?","", m_settings->HasIsPairedFilter, m_settings->IsPairedFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isPrimaryAlignment", "true/false", "keep only alignments marked as primary?", "", m_settings->HasIsPrimaryAlignmentFilter, m_settings->IsPrimaryAlignmentFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isProperPair", "true/false", "keep only alignments that passed PE resolution?", "", m_settings->HasIsProperPairFilter, m_settings->IsProperPairFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isReverseStrand", "true/false", "keep only alignments on reverse strand?", "", m_settings->HasIsReverseStrandFilter, m_settings->IsReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isSecondMate", "true/false", "keep only alignments marked as second mate?", "", m_settings->HasIsSecondMateFilter, m_settings->IsSecondMateFilter, AlignmentFlagOpts, TRUE_STR);
}
FilterTool::~FilterTool(void) {
delete m_settings;
m_settings = 0;
+
+ delete m_impl;
+ m_impl = 0;
}
int FilterTool::Help(void) {
// parse command line arguments
Options::Parse(argc, argv, 1);
+
+ // run internal FilterTool implementation, return success/fail
+ m_impl = new FilterToolPrivate(m_settings);
+
+ if ( m_impl->Run() ) return 0;
+ else return 1;
+}
+
+// ---------------------------------------------
+// FilterToolPrivate implementation
+
+// constructor
+FilterTool::FilterToolPrivate::FilterToolPrivate(FilterTool::FilterSettings* settings)
+ : m_settings(settings)
+{ }
+
+// destructor
+FilterTool::FilterToolPrivate::~FilterToolPrivate(void) { }
+
+bool FilterTool::FilterToolPrivate::AddPropertyTokensToFilter(const string& filterName, const map<string, string>& propertyTokens) {
+
+
+ // dummy temp values for token parsing
+ bool boolValue;
+ int32_t int32Value;
+ uint16_t uint16Value;
+ uint32_t uint32Value;
+ string stringValue;
+ PropertyFilterValue::ValueCompareType type;
+
+ // iterate over property token map
+ map<string, string>::const_iterator mapIter = propertyTokens.begin();
+ map<string, string>::const_iterator mapEnd = propertyTokens.end();
+ for ( ; mapIter != mapEnd; ++mapIter ) {
+
+ const string& propertyName = (*mapIter).first;
+ const string& token = (*mapIter).second;
+
+ // ------------------------------
+ // convert token to value & compare type
+ // then add to filter engine
+
+ // bool conversion
+ if ( propertyName == ISDUPLICATE_PROPERTY ||
+ propertyName == ISFAILEDQC_PROPERTY ||
+ propertyName == ISFIRSTMATE_PROPERTY ||
+ propertyName == ISMAPPED_PROPERTY ||
+ propertyName == ISMATEMAPPED_PROPERTY ||
+ propertyName == ISMATEREVERSESTRAND_PROPERTY ||
+ propertyName == ISPAIRED_PROPERTY ||
+ propertyName == ISPRIMARYALIGNMENT_PROPERTY ||
+ propertyName == ISPROPERPAIR_PROPERTY ||
+ propertyName == ISREVERSESTRAND_PROPERTY ||
+ propertyName == ISSECONDMATE_PROPERTY
+ )
+ {
+ FilterEngine::parseToken(token, boolValue, type);
+ FilterEngine::setProperty(filterName, propertyName, boolValue, type);
+ }
+
+ // int32_t conversion
+ else if ( propertyName == INSERTSIZE_PROPERTY ||
+ propertyName == MATEPOSITION_PROPERTY ||
+ propertyName == POSITION_PROPERTY
+ )
+ {
+ FilterEngine::parseToken(token, int32Value, type);
+ FilterEngine::setProperty(filterName, propertyName, int32Value, type);
+ }
+
+ // uint16_t conversion
+ else if ( propertyName == MAPQUALITY_PROPERTY )
+ {
+ FilterEngine::parseToken(token, uint16Value, type);
+ FilterEngine::setProperty(filterName, propertyName, uint16Value, type);
+ }
+
+ // uint32_t conversion
+ else if ( propertyName == ALIGNMENTFLAG_PROPERTY )
+ {
+ FilterEngine::parseToken(token, uint32Value, type);
+ FilterEngine::setProperty(filterName, propertyName, uint32Value, type);
+ }
+
+ // string conversion
+ else if ( propertyName == MATEREFERENCE_PROPERTY ||
+ propertyName == NAME_PROPERTY ||
+ propertyName == QUERYBASES_PROPERTY ||
+ propertyName == REFERENCE_PROPERTY
+ )
+ {
+ FilterEngine::parseToken(token, stringValue, type);
+ FilterEngine::setProperty(filterName, propertyName, stringValue, type);
+ }
+
+ // else unknown property
+ else {
+ cerr << "Unknown property: " << propertyName << "!" << endl;
+ return false;
+ }
+ }
+ return true;
+}
+
+bool FilterTool::FilterToolPrivate::CheckAlignment(const BamAlignment& al) {
+
+ bool keepAlignment = true;
+
+ // only consider properties that are actually enabled
+ // iterate over these enabled properties
+ const vector<string> enabledProperties = FilterEngine::enabledPropertyNames();
+ vector<string>::const_iterator propIter = enabledProperties.begin();
+ vector<string>::const_iterator propEnd = enabledProperties.end();
+ for ( ; propIter != propEnd; ++propIter ) {
+
+ // check alignment data field depending on propertyName
+ const string& propertyName = (*propIter);
+ if ( propertyName == ALIGNMENTFLAG_PROPERTY ) keepAlignment &= FilterEngine::check(ALIGNMENTFLAG_PROPERTY, al.AlignmentFlag);
+ else if ( propertyName == INSERTSIZE_PROPERTY ) keepAlignment &= FilterEngine::check(INSERTSIZE_PROPERTY, al.InsertSize);
+ else if ( propertyName == ISDUPLICATE_PROPERTY ) keepAlignment &= FilterEngine::check(ISDUPLICATE_PROPERTY, al.IsDuplicate());
+ else if ( propertyName == ISFAILEDQC_PROPERTY ) keepAlignment &= FilterEngine::check(ISFAILEDQC_PROPERTY, al.IsFailedQC());
+ else if ( propertyName == ISFIRSTMATE_PROPERTY ) keepAlignment &= FilterEngine::check(ISFIRSTMATE_PROPERTY, al.IsFirstMate());
+ else if ( propertyName == ISMAPPED_PROPERTY ) keepAlignment &= FilterEngine::check(ISMAPPED_PROPERTY, al.IsMapped());
+ else if ( propertyName == ISMATEMAPPED_PROPERTY ) keepAlignment &= FilterEngine::check(ISMATEMAPPED_PROPERTY, al.IsMateMapped());
+ else if ( propertyName == ISMATEREVERSESTRAND_PROPERTY ) keepAlignment &= FilterEngine::check(ISMATEREVERSESTRAND_PROPERTY, al.IsMateReverseStrand());
+ else if ( propertyName == ISPAIRED_PROPERTY ) keepAlignment &= FilterEngine::check(ISPAIRED_PROPERTY, al.IsPaired());
+ else if ( propertyName == ISPRIMARYALIGNMENT_PROPERTY ) keepAlignment &= FilterEngine::check(ISPRIMARYALIGNMENT_PROPERTY, al.IsPrimaryAlignment());
+ else if ( propertyName == ISPROPERPAIR_PROPERTY ) keepAlignment &= FilterEngine::check(ISPROPERPAIR_PROPERTY, al.IsProperPair());
+ else if ( propertyName == ISREVERSESTRAND_PROPERTY ) keepAlignment &= FilterEngine::check(ISREVERSESTRAND_PROPERTY, al.IsReverseStrand());
+ else if ( propertyName == ISSECONDMATE_PROPERTY ) keepAlignment &= FilterEngine::check(ISSECONDMATE_PROPERTY, al.IsSecondMate());
+ else if ( propertyName == MAPQUALITY_PROPERTY ) keepAlignment &= FilterEngine::check(MAPQUALITY_PROPERTY, al.MapQuality);
+ else if ( propertyName == MATEPOSITION_PROPERTY ) keepAlignment &= ( al.IsPaired() && al.IsMateMapped() && FilterEngine::check(MATEPOSITION_PROPERTY, al.MateRefID) );
+ else if ( propertyName == MATEREFERENCE_PROPERTY ) {
+ if ( !al.IsPaired() || !al.IsMateMapped() ) return false;
+ BAMTOOLS_ASSERT_MESSAGE( (al.MateRefID>=0 && (al.MateRefID<(int)m_references.size())), "Invalid MateRefID");
+ const string& refName = m_references.at(al.MateRefID).RefName;
+ keepAlignment &= FilterEngine::check(MATEREFERENCE_PROPERTY, refName);
+ }
+ else if ( propertyName == NAME_PROPERTY ) keepAlignment &= FilterEngine::check(NAME_PROPERTY, al.Name);
+ else if ( propertyName == POSITION_PROPERTY ) keepAlignment &= FilterEngine::check(POSITION_PROPERTY, al.Position);
+ else if ( propertyName == QUERYBASES_PROPERTY ) keepAlignment &= FilterEngine::check(QUERYBASES_PROPERTY, al.QueryBases);
+ else if ( propertyName == REFERENCE_PROPERTY ) {
+ BAMTOOLS_ASSERT_MESSAGE( (al.RefID>=0 && (al.RefID<(int)m_references.size())), "Invalid RefID");
+ const string& refName = m_references.at(al.RefID).RefName;
+ keepAlignment &= FilterEngine::check(REFERENCE_PROPERTY, refName);
+ }
+ else BAMTOOLS_ASSERT_MESSAGE( false, "Unknown property");
+
+ // if alignment fails at ANY point, just quit and return false
+ if ( !keepAlignment ) return false;
+ }
+ // return success (should still be true at this point)
+ return keepAlignment;
+}
+
+const string FilterTool::FilterToolPrivate::GetScriptContents(void) {
+
+ // open script for reading
+ FILE* inFile = fopen(m_settings->ScriptFilename.c_str(), "rb");
+ if ( !inFile ) {
+ cerr << "FilterTool error: Could not open script: " << m_settings->ScriptFilename << " for reading" << endl;
+ return false;
+ }
+
+ // read in entire script contents
+ char buffer[1024];
+ ostringstream docStream("");
+ while ( true ) {
+
+ // peek ahead, make sure there is data available
+ char ch = fgetc(inFile);
+ ungetc(ch, inFile);
+ if( feof(inFile) ) break;
+
+ // read next block of data
+ if ( fgets(buffer, 1024, inFile) == 0 ) {
+ cerr << "FilterTool error : could not read from script" << endl;
+ return false;
+ }
+
+ docStream << buffer;
+ }
+
+ // close script file
+ fclose(inFile);
+
+ // import buffer contents to document, return
+ string document = docStream.str();
+ return document;
+}
+
+void FilterTool::FilterToolPrivate::InitProperties(void) {
+
+ // store property names in vector
+ m_propertyNames.push_back(ALIGNMENTFLAG_PROPERTY);
+ m_propertyNames.push_back(INSERTSIZE_PROPERTY);
+ m_propertyNames.push_back(ISDUPLICATE_PROPERTY);
+ m_propertyNames.push_back(ISFAILEDQC_PROPERTY);
+ m_propertyNames.push_back(ISFIRSTMATE_PROPERTY);
+ m_propertyNames.push_back(ISMAPPED_PROPERTY);
+ m_propertyNames.push_back(ISMATEMAPPED_PROPERTY);
+ m_propertyNames.push_back(ISMATEREVERSESTRAND_PROPERTY);
+ m_propertyNames.push_back(ISPAIRED_PROPERTY);
+ m_propertyNames.push_back(ISPRIMARYALIGNMENT_PROPERTY);
+ m_propertyNames.push_back(ISPROPERPAIR_PROPERTY);
+ m_propertyNames.push_back(ISREVERSESTRAND_PROPERTY);
+ m_propertyNames.push_back(ISSECONDMATE_PROPERTY);
+ m_propertyNames.push_back(MAPQUALITY_PROPERTY);
+ m_propertyNames.push_back(MATEPOSITION_PROPERTY);
+ m_propertyNames.push_back(MATEREFERENCE_PROPERTY);
+ m_propertyNames.push_back(NAME_PROPERTY);
+ m_propertyNames.push_back(POSITION_PROPERTY);
+ m_propertyNames.push_back(QUERYBASES_PROPERTY);
+ m_propertyNames.push_back(REFERENCE_PROPERTY);
+
+ // add vector contents to FilterEngine
+ vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
+ vector<string>::const_iterator propertyNameEnd = m_propertyNames.end();
+ for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter )
+ FilterEngine::addProperty((*propertyNameIter));
+}
+
+bool FilterTool::FilterToolPrivate::ParseCommandLine(void) {
+
+ // add a rule set to filter engine
+ const string CMD = "COMMAND_LINE";
+ FilterEngine::addFilter(CMD);
+
+ // map property names to command line args
+ map<string, string> propertyTokens;
+ if ( m_settings->HasAlignmentFlagFilter ) propertyTokens.insert( make_pair(ALIGNMENTFLAG_PROPERTY, m_settings->AlignmentFlagFilter) );
+ if ( m_settings->HasInsertSizeFilter ) propertyTokens.insert( make_pair(INSERTSIZE_PROPERTY, m_settings->InsertSizeFilter) );
+ if ( m_settings->HasIsDuplicateFilter ) propertyTokens.insert( make_pair(ISDUPLICATE_PROPERTY, m_settings->IsDuplicateFilter) );
+ if ( m_settings->HasIsFailedQCFilter ) propertyTokens.insert( make_pair(ISFAILEDQC_PROPERTY, m_settings->IsFailedQCFilter) );
+ if ( m_settings->HasIsFirstMateFilter ) propertyTokens.insert( make_pair(ISFIRSTMATE_PROPERTY, m_settings->IsFirstMateFilter) );
+ if ( m_settings->HasIsMappedFilter ) propertyTokens.insert( make_pair(ISMAPPED_PROPERTY, m_settings->IsMappedFilter) );
+ if ( m_settings->HasIsMateMappedFilter ) propertyTokens.insert( make_pair(ISMATEMAPPED_PROPERTY, m_settings->IsMateMappedFilter) );
+ if ( m_settings->HasIsMateReverseStrandFilter ) propertyTokens.insert( make_pair(ISMATEREVERSESTRAND_PROPERTY, m_settings->IsMateReverseStrandFilter) );
+ if ( m_settings->HasIsPairedFilter ) propertyTokens.insert( make_pair(ISPAIRED_PROPERTY, m_settings->IsPairedFilter) );
+ if ( m_settings->HasIsPrimaryAlignmentFilter ) propertyTokens.insert( make_pair(ISPRIMARYALIGNMENT_PROPERTY, m_settings->IsPrimaryAlignmentFilter) );
+ if ( m_settings->HasIsProperPairFilter ) propertyTokens.insert( make_pair(ISPROPERPAIR_PROPERTY, m_settings->IsProperPairFilter) );
+ if ( m_settings->HasIsReverseStrandFilter ) propertyTokens.insert( make_pair(ISREVERSESTRAND_PROPERTY, m_settings->IsReverseStrandFilter) );
+ if ( m_settings->HasIsSecondMateFilter ) propertyTokens.insert( make_pair(ISSECONDMATE_PROPERTY, m_settings->IsSecondMateFilter) );
+ if ( m_settings->HasMapQualityFilter ) propertyTokens.insert( make_pair(MAPQUALITY_PROPERTY, m_settings->MapQualityFilter) );
+ if ( m_settings->HasNameFilter ) propertyTokens.insert( make_pair(NAME_PROPERTY, m_settings->NameFilter) );
+ if ( m_settings->HasQueryBasesFilter ) propertyTokens.insert( make_pair(QUERYBASES_PROPERTY, m_settings->QueryBasesFilter) );
+
+ // send add these properties to filter set "COMMAND_LINE"
+ return AddPropertyTokensToFilter(CMD, propertyTokens);
+}
+
+bool FilterTool::FilterToolPrivate::ParseFilterObject(const string& filterName, const Json::Value& filterObject) {
+
+ // filter object parsing variables
+ Json::Value null(Json::nullValue);
+ Json::Value propertyValue;
+
+ // store results
+ map<string, string> propertyTokens;
+
+ // iterate over known properties
+ vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
+ vector<string>::const_iterator propertyNameEnd = m_propertyNames.end();
+ for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter ) {
+ const string& propertyName = (*propertyNameIter);
+
+ // if property defined in filter, add to token list
+ propertyValue = filterObject.get(propertyName, null);
+ if ( propertyValue != null )
+ propertyTokens.insert( make_pair(propertyName, propertyValue.asString()) );
+ }
+
+ // add this filter to engin
+ FilterEngine::addFilter(filterName);
+
+ // add token list to this filter
+ return AddPropertyTokensToFilter(filterName, propertyTokens);
+}
+
+bool FilterTool::FilterToolPrivate::ParseScript(void) {
+
+ // read in script contents from file
+ const string document = GetScriptContents();
+
+ // set up JsonCPP reader and attempt to parse script
+ Json::Value root;
+ Json::Reader reader;
+ if ( !reader.parse(document, root) ) {
+ // use built-in error reporting mechanism to alert user what was wrong with the script
+ cerr << "Failed to parse configuration\n" << reader.getFormatedErrorMessages();
+ return false;
+ }
+
+ // initialize return status
+ bool success = true;
+
+ // see if root object contains multiple filters
+ const Json::Value filters = root["filters"];
+ if ( !filters.isNull() ) {
+
+ // iterate over any filters found
+ int filterIndex = 0;
+ Json::Value::const_iterator filtersIter = filters.begin();
+ Json::Value::const_iterator filtersEnd = filters.end();
+ for ( ; filtersIter != filtersEnd; ++filtersIter, ++filterIndex ) {
+ Json::Value filter = (*filtersIter);
+
+ // convert filter index to string
+ string filterName;
+
+ // if id tag supplied
+ const Json::Value id = filter["id"];
+ if ( !id.isNull() ) {
+ filterName = id.asString();
+ }
+
+ // use array index
+ else {
+ stringstream convert;
+ convert << filterIndex;
+ filterName = convert.str();
+ }
+
+ // create & parse filter
+ success &= ParseFilterObject(filterName, filter);
+ }
+
+ // see if user defined "rule" for these filters
+ const Json::Value rule = root["rule"];
+ if ( !rule.isNull() ) {
+ cout << "found rule: " << rule.asString() << endl;
+ } else {
+ cout << "no rule found!" << endl;
+ }
+
+ return success;
+ }
+
+ // otherwise, root is the only filter (just contains properties)
+ // create & parse filter named "ROOT"
+ else success = ParseFilterObject("ROOT", root);
+
+ // return success/failure
+ return success;
+}
+
+
+bool FilterTool::FilterToolPrivate::Run(void) {
+
// set to default input if none provided
if ( !m_settings->HasInputBamFilename )
m_settings->InputFiles.push_back(Options::StandardIn());
- // open files
+ // initialize defined properties & user-specified filters
+ // quit if failed
+ if ( !SetupFilters() ) return 1;
+
+ // open reader without index
BamMultiReader reader;
- reader.Open(m_settings->InputFiles, false);
-
- // do filtering
+ reader.Open(m_settings->InputFiles, false, true);
+ const string headerText = reader.GetHeaderText();
+ m_references = reader.GetReferenceData();
+ // open writer
+ BamWriter writer;
+ bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && !m_settings->IsForceCompression );
+ writer.Open(m_settings->OutputFilename, headerText, m_references, writeUncompressed);
+
+ BamAlignment al;
+
+ // if no region specified, filter entire file
+ if ( !m_settings->HasRegion ) {
+ while ( reader.GetNextAlignment(al) ) {
+ if ( CheckAlignment(al) )
+ writer.SaveAlignment(al);
+ }
+ }
+
+ // otherwise attempt to use region as constraint
+ else {
+
+ // if region string parses OK
+ BamRegion region;
+ if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
+
+ // attempt to re-open reader with index files
+ reader.Close();
+ bool openedOK = reader.Open(m_settings->InputFiles, true, true );
+
+ // if error
+ if ( !openedOK ) {
+ cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
+ return 1;
+ }
+
+ // if index data available, we can use SetRegion
+ if ( reader.IsIndexLoaded() ) {
+
+ // attempt to use SetRegion(), if failed report error
+ if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
+ cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
+ reader.Close();
+ return 1;
+ }
+
+ // everything checks out, just iterate through specified region, filtering alignments
+ while ( reader.GetNextAlignmentCore(al) )
+ if ( CheckAlignment(al) )
+ writer.SaveAlignment(al);
+ }
+
+ // no index data available, we have to iterate through until we
+ // find overlapping alignments
+ else {
+ while( reader.GetNextAlignmentCore(al) ) {
+ if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
+ (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
+ {
+ if ( CheckAlignment(al) )
+ writer.SaveAlignment(al);
+ }
+ }
+ }
+ }
+
+ // error parsing REGION string
+ else {
+ cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl;
+ cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
+ reader.Close();
+ return 1;
+ }
+ }
+
// clean up & exit
reader.Close();
+ writer.Close();
return 0;
-}
\ No newline at end of file
+}
+
+bool FilterTool::FilterToolPrivate::SetupFilters(void) {
+
+ // add known properties to FilterEngine
+ InitProperties();
+
+ // parse script for filter rules, if given
+ if ( m_settings->HasScriptFilename ) return ParseScript();
+
+ // otherwise check command line for filters
+ else return ParseCommandLine();
+}
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
+// Last modified: 28 August 2010
// ---------------------------------------------------------------------------
// Filters a single BAM file (or filters multiple BAM files and merges)
// according to some user-specified criteria.
private:
struct FilterSettings;
FilterSettings* m_settings;
+
+ struct FilterToolPrivate;
+ FilterToolPrivate* m_impl;
};
} // namespace BamTools
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 7 July 2010
+// Last modified: 2 September 2010
// ---------------------------------------------------------------------------
// Creates a BAM index (".bai") file for the provided BAM file.
// ***************************************************************************
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
- Options::AddOption("-bti", "use (non-standard) BamTools indexing scheme", m_settings->IsUsingBamtoolsIndex, IO_Opts);
+ Options::AddOption("-bti", "create (non-standard) BamTools index file", m_settings->IsUsingBamtoolsIndex, IO_Opts);
}
IndexTool::~IndexTool(void) {
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
+// Last modified: 7 September 2010
// ---------------------------------------------------------------------------
// Merges multiple BAM files into one.
-//
-// ** Provide selectable region? eg chr2:10000..20000
-//
// ***************************************************************************
#include <iostream>
// flags
bool HasInputBamFilename;
bool HasOutputBamFilename;
-// bool HasRegion;
+ bool IsForceCompression;
+ bool HasRegion;
// filenames
vector<string> InputFiles;
// other parameters
string OutputFilename;
-// string Region;
+ string Region;
// constructor
MergeSettings(void)
: HasInputBamFilename(false)
, HasOutputBamFilename(false)
-// , HasRegion(false)
+ , IsForceCompression(false)
+ , HasRegion(false)
, OutputFilename(Options::StandardOut())
{ }
};
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts);
Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts);
+ Options::AddOption("-forceCompression", "if results are sent to stdout (like when piping to another tool), default behavior is to leave output uncompressed. Use this flag to override and force compression", m_settings->IsForceCompression, IO_Opts);
-// OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
-// Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
+ OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
+ Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
}
MergeTool::~MergeTool(void) {
Options::Parse(argc, argv, 1);
// set to default input if none provided
- if ( !m_settings->HasInputBamFilename ) m_settings->InputFiles.push_back(Options::StandardIn());
+ if ( !m_settings->HasInputBamFilename )
+ m_settings->InputFiles.push_back(Options::StandardIn());
- // opens the BAM files without checking for indexes
+ // opens the BAM files (by default without checking for indexes)
BamMultiReader reader;
- reader.Open(m_settings->InputFiles, false, true);
-
+ if ( !reader.Open(m_settings->InputFiles, false, true) ) {
+ cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
+ return 1;
+ }
+
// retrieve header & reference dictionary info
std::string mergedHeader = reader.GetHeaderText();
RefVector references = reader.GetReferenceData();
- // open BamWriter
+ // open writer
BamWriter writer;
- writer.Open(m_settings->OutputFilename, mergedHeader, references);
+ bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && !m_settings->IsForceCompression );
+ if ( !writer.Open(m_settings->OutputFilename, mergedHeader, references, writeUncompressed) ) {
+ cerr << "ERROR: Could not open BAM file " << m_settings->OutputFilename << " for writing... Aborting." << endl;
+ reader.Close();
+ return 1;
+ }
+
+ // if no region specified, store entire contents of file(s)
+ if ( !m_settings->HasRegion ) {
+ BamAlignment al;
+ while ( reader.GetNextAlignmentCore(al) )
+ writer.SaveAlignment(al);
+ }
+
+ // otherwise attempt to use region as constraint
+ else {
+
+ // if region string parses OK
+ BamRegion region;
+ if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
- // store alignments to output file
- BamAlignment bAlignment;
- while (reader.GetNextAlignmentCore(bAlignment)) {
- writer.SaveAlignment(bAlignment);
+ // attempt to re-open reader with index files
+ reader.Close();
+ bool openedOK = reader.Open(m_settings->InputFiles, true, true );
+
+ // if error
+ if ( !openedOK ) {
+ cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
+ return 1;
+ }
+
+ // if index data available, we can use SetRegion
+ if ( reader.IsIndexLoaded() ) {
+
+ // attempt to use SetRegion(), if failed report error
+ if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
+ cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
+ reader.Close();
+ return 1;
+ }
+
+ // everything checks out, just iterate through specified region, storing alignments
+ BamAlignment al;
+ while ( reader.GetNextAlignmentCore(al) )
+ writer.SaveAlignment(al);
+ }
+
+ // no index data available, we have to iterate through until we
+ // find overlapping alignments
+ else {
+ BamAlignment al;
+ while ( reader.GetNextAlignmentCore(al) ) {
+ if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
+ (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
+ {
+ writer.SaveAlignment(al);
+ }
+ }
+ }
+ }
+
+ // error parsing REGION string
+ else {
+ cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl;
+ cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
+ reader.Close();
+ writer.Close();
+ return 1;
+ }
}
// clean & exit
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 20 July 2010 (DB)
+// Last modified: 3 September 2010 (DB)
// ---------------------------------------------------------------------------
// Grab a random subset of alignments.
// ***************************************************************************
namespace BamTools {
- // define constants
- const unsigned int RANDOM_MAX_ALIGNMENT_COUNT = 10000;
+// define constants
+const unsigned int RANDOM_MAX_ALIGNMENT_COUNT = 10000;
+
+// utility methods for RandomTool
+const int getRandomInt(const int& lowerBound, const int& upperBound) {
+ const int range = (upperBound - lowerBound) + 1;
+ return ( lowerBound + (int)(range * (double)rand()/((double)RAND_MAX + 1)) );
+}
} // namespace BamTools
bool HasInput;
bool HasOutput;
bool HasRegion;
+ bool IsForceCompression;
// parameters
unsigned int AlignmentCount;
, HasInput(false)
, HasOutput(false)
, HasRegion(false)
+ , IsForceCompression(false)
, AlignmentCount(RANDOM_MAX_ALIGNMENT_COUNT)
+ , OutputFilename(Options::StandardOut())
{ }
};
, m_settings(new RandomSettings)
{
// set program details
- Options::SetProgramInfo("bamtools random", "grab a random subset of alignments", "[-in <filename> -in <filename> ...] [-out <filename>] [-region <REGION>]");
+ Options::SetProgramInfo("bamtools random", "grab a random subset of alignments", "[-in <filename> -in <filename> ...] [-out <filename>] [-forceCompression] [-n] [-region <REGION>]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+ Options::AddOption("-forceCompression", "if results are sent to stdout (like when piping to another tool), default behavior is to leave output uncompressed. Use this flag to override and force compression", m_settings->IsForceCompression, IO_Opts);
OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
- Options::AddValueOption("-n", "count", "number of alignments to grab. Note - no duplicate checking is performed (currently)", "", m_settings->HasAlignmentCount, m_settings->AlignmentCount, FilterOpts, RANDOM_MAX_ALIGNMENT_COUNT);
+ Options::AddValueOption("-n", "count", "number of alignments to grab. Note - no duplicate checking is performed", "", m_settings->HasAlignmentCount, m_settings->AlignmentCount, FilterOpts, RANDOM_MAX_ALIGNMENT_COUNT);
Options::AddValueOption("-region", "REGION", "limit source of random alignment subset to a particular genomic region. Index file is recommended for better performance, and is read automatically if it exists as <filename>.bai or <filename>.bti. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
}
int RandomTool::Run(int argc, char* argv[]) {
- // TODO: Handle BAM input WITHOUT index files.
-
// parse command line arguments
Options::Parse(argc, argv, 1);
- // set to default input if none provided
+ // set to default stdin if no input files provided
if ( !m_settings->HasInput )
m_settings->InputFiles.push_back(Options::StandardIn());
- // open our BAM reader
+ // open our reader
BamMultiReader reader;
- reader.Open(m_settings->InputFiles);
- string headerText = reader.GetHeaderText();
- RefVector references = reader.GetReferenceData();
-
- // check that reference data is available, used for generating random jumps
- if ( references.empty() ) {
- cerr << "No reference data available... quitting." << endl;
+ if ( !reader.Open(m_settings->InputFiles) ) {
+ cerr << "ERROR: Could not open input BAM file(s)." << endl;
+ return 1;
+ }
+
+ // make sure index data is available
+ if ( !reader.IsIndexLoaded() ) {
+ cerr << "ERROR: Could not load index data for all input BAM file(s)." << endl;
+ cerr << "\'bamtools random\' requires valid index files to provide efficient performance." << endl;
reader.Close();
return 1;
+
}
-
- // see if user specified a REGION
- BamRegion region;
- if ( m_settings->HasRegion ) {
- if ( Utilities::ParseRegionString(m_settings->Region, reader, region) )
- reader.SetRegion(region);
+
+ // get BamReader metadata
+ const string headerText = reader.GetHeaderText();
+ const RefVector references = reader.GetReferenceData();
+ if ( references.empty() ) {
+ cerr << "ERROR: No reference data available - required to perform random access throughtout input file(s)." << endl;
+ reader.Close();
+ return 1;
}
- // open out BAM writer
+ // open our writer
BamWriter writer;
- writer.Open(m_settings->OutputFilename, headerText, references);
-
+ bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && !m_settings->IsForceCompression );
+ if ( !writer.Open(m_settings->OutputFilename, headerText, references, writeUncompressed) ) {
+ cerr << "ERROR: Could not open BamWriter." << endl;
+ reader.Close();
+ return 1;
+ }
+
+ // if user specified a REGION constraint, attempt to parse REGION string
+ BamRegion region;
+ if ( m_settings->HasRegion && !Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
+ cerr << "ERROR: Could not parse REGION: " << m_settings->Region << endl;
+ cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
+ reader.Close();
+ writer.Close();
+ return 1;
+ }
+
// seed our random number generator
- srand (time(NULL) );
+ srand( time(NULL) );
// grab random alignments
BamAlignment al;
int randomRefId = 0;
int randomPosition = 0;
- // use REGION constraints to generate random refId & position
+ // use REGION constraints to select random refId & position
if ( m_settings->HasRegion ) {
- int lowestRefId = region.LeftRefID;
- int highestRefId = region.RightRefID;
- int rangeRefId = (highestRefId - lowestRefId) + 1;
- randomRefId = lowestRefId + (int)(rangeRefId * (double)(rand()/((double)RAND_MAX + 1)));
+ // select a random refId
+ randomRefId = getRandomInt(region.LeftRefID, region.RightRefID);
- int lowestPosition = ( (randomRefId == region.LeftRefID) ? region.LeftPosition : 0 );
- int highestPosition = ( (randomRefId == region.RightRefID) ? region.RightPosition : references.at(randomRefId).RefLength - 1 );
- int rangePosition = (highestPosition - lowestPosition) + 1;
- randomPosition = lowestPosition + (int)(rangePosition * (double)(rand()/((double)RAND_MAX + 1)));
+ // select a random position based on randomRefId
+ const int lowerBoundPosition = ( (randomRefId == region.LeftRefID) ? region.LeftPosition : 0 );
+ const int upperBoundPosition = ( (randomRefId == region.RightRefID) ? region.RightPosition : (references.at(randomRefId).RefLength - 1) );
+ randomPosition = getRandomInt(lowerBoundPosition, upperBoundPosition);
}
- // otherwise generate 'normal' random refId & position
+ // otherwise select from all possible random refId & position
else {
- // generate random refId
- int lowestRefId = 0;
- int highestRefId = references.size() - 1;
- int rangeRefId = (highestRefId - lowestRefId) + 1;
- randomRefId = lowestRefId + (int)(rangeRefId * (double)(rand()/((double)RAND_MAX + 1)));
+ // select random refId
+ randomRefId = getRandomInt(0, (int)references.size() - 1);
- // generate random position
- int lowestPosition = 0;
- int highestPosition = references.at(randomRefId).RefLength - 1;
- int rangePosition = (highestPosition - lowestPosition) + 1;
- randomPosition = lowestPosition + (int)(rangePosition * (double)(rand()/((double)RAND_MAX + 1)));
+ // select random position based on randomRefId
+ const int lowerBoundPosition = 0;
+ const int upperBoundPosition = references.at(randomRefId).RefLength - 1;
+ randomPosition = getRandomInt(lowerBoundPosition, upperBoundPosition);
}
- // if jump & read successful, save alignment
+ // if jump & read successful, save first alignment that overlaps random refId & position
if ( reader.Jump(randomRefId, randomPosition) ) {
while ( reader.GetNextAlignmentCore(al) ) {
if ( al.RefID == randomRefId && al.Position >= randomPosition ) {
}
}
- // close reader & writer
+ // cleanup & exit
reader.Close();
writer.Close();
return 0;
# define our source and object files
# ----------------------------------
SOURCES = bamtools_fasta.cpp \
+ bamtools_filter_engine.cpp \
bamtools_options.cpp \
bamtools_pileup.cpp \
bamtools_utilities.cpp
--- /dev/null
+// ***************************************************************************
+// bamtools_filter_engine.cpp (c) 2010 Derek Barnett, Erik Garrison
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 30 August 2010
+// ---------------------------------------------------------------------------
+//
+// ***************************************************************************
+
+#include <iostream>
+#include "bamtools_filter_engine.h"
+#include "BamAux.h"
+using namespace std;
+using namespace BamTools;
+
+// ---------------------------------------------------------
+// FilterValue implementation
+
+// checks a string query against filter (value, compare type)
+bool PropertyFilterValue::check(const string& query) const {
+
+ // ensure filter value & query are same type
+ if ( !Value.is_type<string>() ) {
+ cerr << "Cannot compare different types!" << endl;
+ return false;
+ }
+
+ // localize string version of our filter value
+ const string& valueString = Value.get<string>();
+
+ // string matching based on our filter type
+ switch ( Type ) {
+ case ( PropertyFilterValue::CONTAINS) : return ( query.find(valueString) != string::npos );
+ case ( PropertyFilterValue::ENDS_WITH) : return ( query.find(valueString) == (query.length() - valueString.length()) );
+ case ( PropertyFilterValue::EXACT) : return ( query == valueString );
+ case ( PropertyFilterValue::GREATER_THAN) : return ( query > valueString );
+ case ( PropertyFilterValue::GREATER_THAN_EQUAL) : return ( query >= valueString );
+ case ( PropertyFilterValue::LESS_THAN) : return ( query < valueString );
+ case ( PropertyFilterValue::LESS_THAN_EQUAL) : return ( query <= valueString );
+ case ( PropertyFilterValue::NOT) : return ( query != valueString );
+ case ( PropertyFilterValue::STARTS_WITH) : return ( query.find(valueString) == 0 );
+ default : BAMTOOLS_ASSERT_UNREACHABLE;
+ }
+ return false;
+}
+
+// ---------------------------------------------------------
+// FilterEngine implementation
+
+// static FilterEngine data members
+FilterMap FilterEngine::m_filters;
+vector<Property> FilterEngine::m_properties;
+
+// creates a new filter set, returns true if created, false if error or already exists
+bool FilterEngine::addFilter(const string& filterName) {
+ return (m_filters.insert(make_pair(filterName, PropertyFilter()))).second;
+}
+
+// return list of current filter names
+const vector<string> FilterEngine::filterNames(void) {
+ vector<string> names;
+ names.reserve(m_filters.size());
+ FilterMap::const_iterator mapIter = m_filters.begin();
+ FilterMap::const_iterator mapEnd = m_filters.end();
+ for ( ; mapIter != mapEnd; ++mapIter )
+ names.push_back( (*mapIter).first );
+ return names;
+}
+
+// add a new known property (& type) to engine
+bool FilterEngine::addProperty(const string& propertyName) {
+ const vector<string> propertyNames = allPropertyNames();
+ bool found = binary_search( propertyNames.begin(), propertyNames.end(), propertyName );
+ if ( found ) return false;
+ m_properties.push_back( Property(propertyName) );
+ sort( m_properties.begin(), m_properties.end() );
+ return true;
+}
+
+
+// returns list of all properties known by FilterEngine ( any created using addProperty() )
+const vector<string> FilterEngine::allPropertyNames(void) {
+ vector<string> names;
+ names.reserve(m_properties.size());
+ vector<Property>::const_iterator propIter = m_properties.begin();
+ vector<Property>::const_iterator propEnd = m_properties.end();
+ for ( ; propIter != propEnd; ++propIter )
+ names.push_back( (*propIter).Name );
+ return names;
+}
+
+// returns list of property names that are 'enabled' ( only those touched by setProperty() )
+const vector<string> FilterEngine::enabledPropertyNames(void) {
+ vector<string> names;
+ names.reserve(m_properties.size());
+ vector<Property>::const_iterator propIter = m_properties.begin();
+ vector<Property>::const_iterator propEnd = m_properties.end();
+ for ( ; propIter != propEnd; ++propIter )
+ if ( (*propIter).IsEnabled ) names.push_back( (*propIter).Name );
+ return names;
+}
--- /dev/null
+// ***************************************************************************
+// bamtools_filter_engine.h (c) 2010 Derek Barnett, Erik Garrison
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 30 August 2010
+// ---------------------------------------------------------------------------
+//
+// ***************************************************************************
+
+#ifndef BAMTOOLS_FILTER_ENGINE_H
+#define BAMTOOLS_FILTER_ENGINE_H
+
+#include <algorithm>
+#include <map>
+#include <sstream>
+#include <string>
+#include <utility>
+#include <vector>
+#include "bamtools_utilities.h"
+#include "bamtools_variant.h"
+
+namespace BamTools {
+
+struct PropertyFilterValue {
+
+ // define valid ValueCompareTypes
+ enum ValueCompareType { CONTAINS = 0
+ , ENDS_WITH
+ , EXACT
+ , GREATER_THAN
+ , GREATER_THAN_EQUAL
+ , LESS_THAN
+ , LESS_THAN_EQUAL
+ , NOT
+ , STARTS_WITH
+ };
+
+ // ctor
+ PropertyFilterValue(const Variant& value = Variant(),
+ const ValueCompareType& type = PropertyFilterValue::EXACT)
+ : Value(value)
+ , Type(type)
+ { }
+
+ // filter check methods
+ template<typename T>
+ bool check(const T& query) const;
+ bool check(const std::string& query) const;
+
+ // data members
+ Variant Value;
+ ValueCompareType Type;
+};
+
+inline
+const std::string toString(const PropertyFilterValue::ValueCompareType& type) {
+
+ switch ( type ) {
+ case ( PropertyFilterValue::CONTAINS ) : return std::string( "CONTAINS");
+ case ( PropertyFilterValue::ENDS_WITH ) : return std::string( "ENDS_WITH");
+ case ( PropertyFilterValue::EXACT ) : return std::string( "EXACT");
+ case ( PropertyFilterValue::GREATER_THAN ) : return std::string( "GREATER_THAN");
+ case ( PropertyFilterValue::GREATER_THAN_EQUAL ) : return std::string( "GREATER_THAN_EQUAL");
+ case ( PropertyFilterValue::LESS_THAN ) : return std::string( "LESS_THAN");
+ case ( PropertyFilterValue::LESS_THAN_EQUAL ) : return std::string( "LESS_THAN_EQUAL");
+ case ( PropertyFilterValue::NOT ) : return std::string( "NOT");
+ case ( PropertyFilterValue::STARTS_WITH ) : return std::string( "STARTS_WITH");
+ default : BAMTOOLS_ASSERT_UNREACHABLE;
+ }
+ return std::string();
+}
+
+// property name => property filter value
+// ('name' => ('SSR', STARTS_WITH), 'mapQuality' => (50, GREATER_THAN_EQUAL), etc...)
+typedef std::map<std::string, PropertyFilterValue> PropertyMap;
+
+struct PropertyFilter {
+
+ // will be used more later
+ // if we implement a compound 'rules' system - i.e. "(filter1 AND filter2) OR filter 3"
+ enum FilterCompareType { AND = 0
+ , EXACT
+ , NOT
+ , OR
+ };
+
+ // data members
+ PropertyMap Properties;
+ FilterCompareType Type;
+
+ // ctor
+ PropertyFilter(void) : Type( PropertyFilter::EXACT ) { }
+
+ // filter check methods
+ template<typename T>
+ bool check(const std::string& propertyName, const T& query) const;
+};
+
+// filter name => properties
+// ('filter1' => properties1, 'filter2' => properties2, etc...)
+typedef std::map<std::string, PropertyFilter> FilterMap;
+
+// used to store properties known to engine & keep track of enabled state
+struct Property {
+ std::string Name;
+ bool IsEnabled;
+ Property(const std::string& name, bool isEnabled = false)
+ : Name(name)
+ , IsEnabled(isEnabled)
+ { }
+};
+
+inline bool operator< (const Property& lhs, const Property& rhs) { return lhs.Name < rhs.Name; }
+inline bool operator== (const Property& lhs, const Property& rhs) { return lhs.Name == rhs.Name; }
+
+class FilterEngine {
+
+ // 'filter set' methods
+ public:
+ // creates a new filter set, returns true if created, false if error or already exists
+ static bool addFilter(const std::string& filterName);
+
+ // return list of current filter names
+ static const std::vector<std::string> filterNames(void);
+
+ // 'property' methods
+ public:
+
+ // add a new known property (& type) to engine
+ static bool addProperty(const std::string& propertyName);
+
+ // sets property filter (value, type) for propertyName, on a particular filter set
+ // setProperty("filter1", "mapQuality", 50, GREATER_THAN_EQUAL)
+ template<typename T>
+ static bool setProperty(const std::string& filterName,
+ const std::string& propertyName,
+ const T& value,
+ const PropertyFilterValue::ValueCompareType& type = PropertyFilterValue::EXACT);
+
+ // returns list of all properties known by FilterEngine ( any created using addProperty() )
+ static const std::vector<std::string> allPropertyNames(void);
+
+ // returns list of property names that are 'enabled' ( only those touched by setProperty() )
+ static const std::vector<std::string> enabledPropertyNames(void);
+
+ // token parsing (for property filter generation)
+ public:
+ template<typename T>
+ static bool parseToken(const std::string& token, T& value, PropertyFilterValue::ValueCompareType& type);
+
+ // query evaluation
+ public:
+ // returns true if query passes all filters on 'propertyName'
+ template<typename T>
+ static bool check(const std::string& propertyName, const T& query);
+
+ // data members
+ private:
+ // all 'filter sets'
+ static FilterMap m_filters;
+
+ // all known properties
+ static std::vector<Property> m_properties;
+
+ // token-parsing constants
+ static const int NOT_CHAR = (int)'!';
+ static const int EQUAL_CHAR = (int)'=';
+ static const int GREATER_THAN_CHAR = (int)'>';
+ static const int LESS_THAN_CHAR = (int)'<';
+ static const int WILDCARD_CHAR = (int)'*';
+};
+
+// -------------------------------------------------------------------
+// template methods
+
+// checks a query against a filter (value, compare type)
+template<typename T>
+bool PropertyFilterValue::check(const T& query) const {
+
+ // ensure filter value & query are same type
+ if ( !Value.is_type<T>() ) {
+ std::cerr << "Cannot compare different types!" << std::endl;
+ return false;
+ }
+
+ // string matching
+ if ( Value.is_type<std::string>() ) {
+ std::cerr << "Cannot compare different types - query is a string!" << std::endl;
+ return false;
+ }
+
+ // numeric matching based on our filter type
+ switch ( Type ) {
+ case ( PropertyFilterValue::EXACT) : return ( query == Value.get<T>() );
+ case ( PropertyFilterValue::GREATER_THAN) : return ( query > Value.get<T>() );
+ case ( PropertyFilterValue::GREATER_THAN_EQUAL) : return ( query >= Value.get<T>() );
+ case ( PropertyFilterValue::LESS_THAN) : return ( query < Value.get<T>() );
+ case ( PropertyFilterValue::LESS_THAN_EQUAL) : return ( query <= Value.get<T>() );
+ case ( PropertyFilterValue::NOT) : return ( query != Value.get<T>() );
+ default : BAMTOOLS_ASSERT_UNREACHABLE;
+ }
+ return false;
+}
+
+template<typename T>
+bool PropertyFilter::check(const std::string& propertyName, const T& query) const {
+
+ // if propertyName found for this filter,
+ PropertyMap::const_iterator propIter = Properties.find(propertyName);
+ if ( propIter != Properties.end() ) {
+ const PropertyFilterValue& filterValue = (*propIter).second;
+
+ // check
+ switch ( Type ) {
+ case ( PropertyFilter::EXACT ) : return filterValue.check(query);
+ case ( PropertyFilter::NOT ) : return !filterValue.check(query);
+ case ( PropertyFilter::AND ) :
+ case ( PropertyFilter::OR ) : BAMTOOLS_ASSERT_MESSAGE(false, "Cannot use a binary compare operator on 1 value");
+ default : BAMTOOLS_ASSERT_UNREACHABLE;
+ }
+ return false; // unreachable
+ }
+
+ // property unknown to this filter
+ else return true;
+}
+
+template<typename T>
+bool FilterEngine::parseToken(const std::string& token, T& value, PropertyFilterValue::ValueCompareType& type) {
+
+ // skip if token is empty
+ if ( token.empty() ) return false;
+
+ // will store token after special chars are removed
+ std::string strippedToken;
+
+ // if only single character
+ if ( token.length() == 1 ) {
+ strippedToken = token;
+ type = PropertyFilterValue::EXACT;
+ }
+
+ // more than one character, check for special chars
+ else {
+ const int firstChar = (int)token.at(0);
+
+ switch ( (int)firstChar ) {
+
+ case ( (int)FilterEngine::NOT_CHAR ) :
+
+ strippedToken = token.substr(1);
+ type = PropertyFilterValue::NOT;
+
+ break;
+
+ case ( (int)FilterEngine::GREATER_THAN_CHAR ) :
+
+ // check for '>=' case
+ if ( token.at(1) == FilterEngine::EQUAL_CHAR ) {
+ if ( token.length() == 2 ) return false;
+ strippedToken = token.substr(2);
+ type = PropertyFilterValue::GREATER_THAN_EQUAL;
+ }
+
+ // otherwise only '>'
+ else {
+ strippedToken = token.substr(1);
+ type = PropertyFilterValue::GREATER_THAN;
+ }
+
+ break;
+
+ case ( (int)FilterEngine::LESS_THAN_CHAR ) :
+
+ // check for '<=' case
+ if ( token.at(1) == FilterEngine::EQUAL_CHAR ) {
+ if ( token.length() == 2 ) return false;
+ strippedToken = token.substr(2);
+ type = PropertyFilterValue::LESS_THAN_EQUAL;
+ }
+
+ // otherwise only '<'
+ else {
+ strippedToken = token.substr(1);
+ type = PropertyFilterValue::LESS_THAN;
+ }
+
+ break;
+
+ case ( (int)FilterEngine::WILDCARD_CHAR ) :
+
+ // check for *str* case (CONTAINS)
+ if ( token.at( token.length() - 1 ) == FilterEngine::WILDCARD_CHAR ) {
+ if ( token.length() == 2 ) return false;
+ strippedToken = token.substr(1, token.length() - 2);
+ type = PropertyFilterValue::CONTAINS;
+ }
+
+ // otherwise *str case (ENDS_WITH)
+ else {
+ strippedToken = token.substr(1);
+ type = PropertyFilterValue::ENDS_WITH;
+ }
+
+ break;
+
+
+ default :
+
+ // check for str* case (STARTS_WITH)
+ if ( token.at( token.length() - 1 ) == FilterEngine::WILDCARD_CHAR ) {
+ if ( token.length() == 2 ) return false;
+ strippedToken = token.substr(0, token.length() - 1);
+ type = PropertyFilterValue::STARTS_WITH;
+ }
+
+ // otherwise EXACT
+ else {
+ strippedToken = token;
+ type = PropertyFilterValue::EXACT;
+ }
+
+ break;
+ }
+ }
+
+ // convert stripped token to value
+ std::stringstream stream(strippedToken);
+ if ( strippedToken == "true" || strippedToken == "false" )
+ stream >> std::boolalpha >> value;
+ else
+ stream >> value;
+
+ // check for valid CompareType on type T
+ Variant variantCheck = value;
+
+ // if T is not string AND CompareType is for string values, return false
+ if ( !variantCheck.is_type<std::string>() ) {
+ if ( type == PropertyFilterValue::CONTAINS ||
+ type == PropertyFilterValue::ENDS_WITH ||
+ type == PropertyFilterValue::STARTS_WITH )
+
+ return false;
+ }
+
+ // return success
+ return true;
+}
+
+// sets property filter (value, type) for propertyName, on a particular filter set
+// setProperty("filter1", "mapQuality", 50, GREATER_THAN_EQUAL)
+template<typename T>
+bool FilterEngine::setProperty(const std::string& filterName,
+ const std::string& propertyName,
+ const T& value,
+ const PropertyFilterValue::ValueCompareType& type)
+{
+ // lookup filter by name, return false if not found
+ FilterMap::iterator filterIter = m_filters.find(filterName);
+ if ( filterIter == m_filters.end() ) return false;
+
+ // lookup property for filter, add new PropertyFilterValue if not found, modify if already exists
+ PropertyFilter& filter = (*filterIter).second;
+ PropertyMap::iterator propertyIter = filter.Properties.find(propertyName);
+
+ bool success;
+
+ // property not found for this filter, create new entry
+ if ( propertyIter == filter.Properties.end() )
+ success = (filter.Properties.insert(std::make_pair(propertyName, PropertyFilterValue(value, type)))).second;
+
+ // property already exists, modify
+ else {
+ PropertyFilterValue& filterValue = (*propertyIter).second;
+ filterValue.Value = value;
+ filterValue.Type = type;
+ success = true;
+ }
+
+ // if error so far, return false
+ if ( !success ) return false;
+
+ // --------------------------------------------
+ // otherwise, set Property.IsEnabled to true
+
+ // lookup property
+ std::vector<Property>::iterator knownPropertyIter = std::find( m_properties.begin(), m_properties.end(), propertyName);
+
+ // if not found, create a new (enabled) entry (& re-sort list)
+ if ( knownPropertyIter == m_properties.end() ) {
+ m_properties.push_back( Property(propertyName, true) );
+ std::sort( m_properties.begin(), m_properties.end() );
+ }
+
+ // property already known, set as enabled
+ else
+ (*knownPropertyIter).IsEnabled = true;
+
+ // return success
+ return true;
+}
+
+// returns false if query does not pass any filters on 'propertyName'
+// returns true if property unknown (i.e. nothing has been set for this property... so query is considered to pass filter)
+template<typename T>
+bool FilterEngine::check(const std::string& propertyName, const T& query) {
+
+ // check enabled properties list
+ // return true if no properties enabled at all OR if property is unknown to FilterEngine
+ const std::vector<std::string> enabledProperties = enabledPropertyNames();
+ if ( enabledProperties.empty() ) return true;
+ const bool found = std::binary_search( enabledProperties.begin(), enabledProperties.end(), propertyName );
+ if ( !found ) return true;
+
+ // iterate over all filters in FilterEngine
+ FilterMap::const_iterator filterIter = m_filters.begin();
+ FilterMap::const_iterator filterEnd = m_filters.end();
+ for ( ; filterIter != filterEnd; ++filterIter ) {
+
+ // check query against this filter
+ const PropertyFilter& filter = (*filterIter).second;
+ if ( filter.check(propertyName, query) ) return true;
+ }
+
+ // query passes none of the filters with current property enabled
+ return false;
+}
+
+} // namespace BamTools
+
+#endif // BAMTOOLS_FILTER_ENGINE_H
\ No newline at end of file
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
+// Last modified: 7 September 2010
// ---------------------------------------------------------------------------
// Parses command line arguments and creates a help menu
// ---------------------------------------------------------------------------
// The Mosaik suite's command line parser class: COptions
// (c) 2006 - 2009 Michael Str�mberg
// Marth Lab, Department of Biology, Boston College
-// Dual licenced under the GNU General Public License 2.0+ license or as
-// a commercial license with the Marth Lab.
+// Re-licensed under MIT License with author's permission.
//
// * Modified slightly to fit BamTools, otherwise code is same.
// * (BamTools namespace, added stdin/stdout) (DB)
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 1 June 2010
+// Last modified: 7 September 2010
// ---------------------------------------------------------------------------
// Parses command line arguments and creates a help menu
// ---------------------------------------------------------------------------
// The Mosaik suite's command line parser class: COptions
// (c) 2006 - 2009 Michael Str�mberg
// Marth Lab, Department of Biology, Boston College
-// Dual licenced under the GNU General Public License 2.0+ license or as
-// a commercial license with the Marth Lab.
+// Re-licensed under MIT License with author's permission.
//
-// * Modified to fit BamTools code-style, otherwise code is same. (DB)
+// * Modified slightly to fit BamTools, otherwise code is same.
+// * (BamTools namespace, added stdin/stdout) (DB)
// ***************************************************************************
#ifndef BAMTOOLS_OPTIONS_H
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
+// Last modified: 3 September 2010
// ---------------------------------------------------------------------------
// Provides general utilities used by BamTools sub-tools.
// ***************************************************************************
#include <cstdlib>
-#include <sys/stat.h>
+#include <fstream>
+#include <iostream>
#include "bamtools_utilities.h"
#include "BamReader.h"
#include "BamMultiReader.h"
-
using namespace std;
using namespace BamTools;
+// check if a file exists
+bool Utilities::FileExists(const std::string& filename) {
+ ifstream f(filename.c_str(), ifstream::in);
+ return !f.fail();
+}
+
// Parses a region string, does validation (valid ID's, positions), stores in Region struct
// Returns success (true/false)
bool Utilities::ParseRegionString(const std::string& regionString, const BamReader& reader, BamRegion& region) {
return true;
}
-
-bool Utilities::FileExists(const std::string& filename) {
-
- struct stat fileInfo;
- return stat(filename.c_str(), &fileInfo) == 0;
-
-}
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
+// Last modified: 30 August 2010
// ---------------------------------------------------------------------------
// Provides general utilities used by BamTools sub-tools.
// ***************************************************************************
#ifndef BAMTOOLS_UTILITIES_H
#define BAMTOOLS_UTILITIES_H
+#include <cassert>
+#include <stdexcept>
#include <string>
#include "BamAux.h"
+#define BAMTOOLS_ASSERT_UNREACHABLE assert( false )
+#define BAMTOOLS_ASSERT_MESSAGE( condition, message ) if (!( condition )) throw std::runtime_error( message );
+
namespace BamTools {
class BamReader;
class Utilities {
- public:
+ public:
+ // check if a file exists
+ static bool FileExists(const std::string& fname);
+
// Parses a region string, uses reader to do validation (valid ID's, positions), stores in Region struct
// Returns success (true/false)
static bool ParseRegionString(const std::string& regionString, const BamReader& reader, BamRegion& region);
// Same as above, but accepts a BamMultiReader
static bool ParseRegionString(const std::string& regionString, const BamMultiReader& reader, BamRegion& region);
- // check if a file exists
- static bool FileExists(const std::string& fname);
+
};
} // namespace BamTools
class Variant {
public:
- Variant(void) : data (NULL) { }
+ Variant(void) : data(NULL) { }
Variant(const Variant& other) {
- if(other.data != NULL)
+ if ( other.data != NULL )
other.data->AddRef();
data = other.data;
}
~Variant(void) {
- if(data != NULL) data->Release();
+ if ( data != NULL )
+ data->Release();
}
// NOTE: This code takes care of self-assignment.
// DO NOT CHANGE THE ORDER of the statements.
- Variant& operator=(const Variant& rhs) {
- if(rhs.data != NULL)
+ Variant& operator= (const Variant& rhs) {
+ if ( rhs.data != NULL )
rhs.data->AddRef();
- if(data != NULL)
+ if ( data != NULL )
data->Release();
data = rhs.data;
- return * this;
+ return *this;
}
// This member template constructor allows you to
// instance a variant_t object with a value of any type.
template<typename T>
- Variant(T v)
- : data(new Impl<T>(v))
+ Variant(T v)
+ : data(new Impl<T>(v))
{
data->AddRef();
}
private:
struct ImplBase {
- ImplBase() : refs(0) {}
- virtual ~ImplBase() {}
+ ImplBase() : refs(0) { }
+ virtual ~ImplBase(void) { }
- void AddRef(void) { refs ++; }
+ void AddRef(void) { ++refs; }
void Release(void) {
--refs;
- if(refs == 0) delete this;
+ if ( refs == 0 ) delete this;
}
size_t refs;
template<typename T>
struct Impl : ImplBase {
- Impl(T v) : data (v) { }
+ Impl(T v) : data(v) { }
~Impl(void) { }
T data;
};
static Impl<T>* CastFromBase(ImplBase* v) {
// This upcast will fail if T is other than the T used
// with the constructor of variant_t.
- Impl<T>* p = dynamic_cast<Impl<T>*> (v);
- if (p == NULL)
- throw std::invalid_argument(typeid(T).name()+std::string(" is not a valid type"));
+ Impl<T>* p = dynamic_cast< Impl<T>* > (v);
+ if ( p == NULL )
+ throw std::invalid_argument( typeid(T).name() + std::string(" is not a valid type") );
return p;
}
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