X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2Finternal%2FBamReader_p.h;h=2f670d59d94d829aead92868f0ed8c7a13e2cec3;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=ed3940a504ba50e2678b2d5e5b9214b42b0c66a4;hpb=94193d06ce788ba7df8b7bd856a983d1e98daac6;p=bamtools.git

diff --git a/src/api/internal/BamReader_p.h b/src/api/internal/BamReader_p.h
index ed3940a..2f670d5 100644
--- a/src/api/internal/BamReader_p.h
+++ b/src/api/internal/BamReader_p.h
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // BamReader_p.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 19 November 2010 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides the basic functionality for reading BAM files
 // ***************************************************************************
@@ -21,112 +20,97 @@
 //
 // We mean it.
 
-#include <api/BamAlignment.h>
-#include <api/BamIndex.h>
-#include <api/BGZF.h>
+#include "api/BamAlignment.h"
+#include "api/BamIndex.h"
+#include "api/BamReader.h"
+#include "api/SamHeader.h"
+#include "api/internal/BamHeader_p.h"
+#include "api/internal/BamRandomAccessController_p.h"
+#include "api/internal/BgzfStream_p.h"
 #include <string>
 
 namespace BamTools {
-
-class BamReader;
-
 namespace Internal {
 
 class BamReaderPrivate {
 
-    // enums
-    public: enum RegionState { BEFORE_REGION = 0
-                             , WITHIN_REGION
-                             , AFTER_REGION
-                             };
-
     // ctor & dtor
     public:
         BamReaderPrivate(BamReader* parent);
         ~BamReaderPrivate(void);
 
-    // 'public' interface to BamReader
+    // BamReader interface
     public:
 
         // file operations
-        void Close(void);
-        bool Open(const std::string& filename,
-                  const std::string& indexFilename,
-                  const bool lookForIndex,
-                  const bool preferStandardIndex);
+        bool Close(void);
+        const std::string Filename(void) const;
+        bool IsOpen(void) const;
+        bool Open(const std::string& filename);
         bool Rewind(void);
         bool SetRegion(const BamRegion& region);
 
         // access alignment data
-        bool GetNextAlignment(BamAlignment& bAlignment);
-        bool GetNextAlignmentCore(BamAlignment& bAlignment);
+        bool GetNextAlignment(BamAlignment& alignment);
+        bool GetNextAlignmentCore(BamAlignment& alignment);
 
         // access auxiliary data
-        const std::string GetHeaderText(void) const;
+        std::string GetHeaderText(void) const;
+        SamHeader GetSamHeader(void) const;
+        int GetReferenceCount(void) const;
+        const RefVector& GetReferenceData(void) const;
         int GetReferenceID(const std::string& refName) const;
 
         // index operations
-        bool CreateIndex(bool useStandardIndex);
-        void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);
-
-    // 'internal' methods
+        bool CreateIndex(const BamIndex::IndexType& type);
+        bool HasIndex(void) const;
+        bool LocateIndex(const BamIndex::IndexType& preferredType);
+        bool OpenIndex(const std::string& indexFilename);
+        void SetIndex(BamIndex* index);
+        void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
+
+        // error handling
+        std::string GetErrorString(void) const;
+        void SetErrorString(const std::string& where, const std::string& what);
+
+    // internal methods, but available as a BamReaderPrivate 'interface'
+    //
+    // these methods should only be used by BamTools::Internal classes
+    // (currently only used by the BamIndex subclasses)
     public:
-
-        // ---------------------------------------
-        // reading alignments and auxiliary data
-
-        // adjusts requested region if necessary (depending on where data actually begins)
-        void AdjustRegion(BamRegion& region);
-        // checks to see if alignment overlaps current region
-        RegionState IsOverlap(BamAlignment& bAlignment);
         // retrieves header text from BAM file
         void LoadHeaderData(void);
         // retrieves BAM alignment under file pointer
-        bool LoadNextAlignment(BamAlignment& bAlignment);
+        // (does no overlap checking or character data parsing)
+        bool LoadNextAlignment(BamAlignment& alignment);
         // builds reference data structure from BAM file
-        void LoadReferenceData(void);
-        // mark references with 'HasAlignments' status
-        void MarkReferences(void);
-
-        // ---------------------------------
-        // index file handling
-
-        // clear out inernal index data structure
-        void ClearIndex(void);
-        // loads index from BAM index file
-        bool LoadIndex(const bool lookForIndex, const bool preferStandardIndex);
+        bool LoadReferenceData(void);
+        // seek reader to file position
+        bool Seek(const int64_t& position);
+        // return reader's file position
+        int64_t Tell(void) const;
 
     // data members
     public:
 
-        // general file data
-        BgzfData  mBGZF;
-        std::string HeaderText;
-        BamIndex* Index;
-        RefVector References;
-        bool      HasIndex;
-        int64_t   AlignmentsBeginOffset;
-        std::string    Filename;
-        std::string    IndexFilename;
-
-        //	Internal::BamHeader* m_header;
-
-        // index caching mode
-        BamIndex::BamIndexCacheMode IndexCacheMode;
+        // general BAM file data
+        int64_t     m_alignmentsBeginOffset;
+        std::string m_filename;
+        RefVector   m_references;
 
         // system data
-        bool IsBigEndian;
-
-        // user-specified region values
-        BamRegion Region;
-        bool HasAlignmentsInRegion;
+        bool m_isBigEndian;
 
         // parent BamReader
-        BamReader* Parent;
+        BamReader* m_parent;
+
+        // BamReaderPrivate components
+        BamHeader m_header;
+        BamRandomAccessController m_randomAccessController;
+        BgzfStream m_stream;
 
-        // BAM character constants
-        const char* DNA_LOOKUP;
-        const char* CIGAR_LOOKUP;
+        // error handling
+        std::string m_errorString;
 };
 
 } // namespace Internal