Organized api/internal into subdirs

[bamtools.git] / src / api / internal / BamIndexFactory_p.cpp

diff --git a/src/api/internal/BamIndexFactory_p.cpp b/src/api/internal/BamIndexFactory_p.cpp
deleted file mode 100644 (file)
index 2cf871f..0000000
--- a/src/api/internal/BamIndexFactory_p.cpp
+++ /dev/null
@@ -1,112 +0,0 @@
-// ***************************************************************************
-// BamIndexFactory_p.cpp (c) 2011 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides interface for generating BamIndex implementations
-// ***************************************************************************
-
-#include "api/BamAux.h"
-#include "api/internal/BamIndexFactory_p.h"
-#include "api/internal/BamStandardIndex_p.h"
-#include "api/internal/BamToolsIndex_p.h"
-using namespace BamTools;
-using namespace BamTools::Internal;
-using namespace std;
-
-// generates index filename from BAM filename (depending on requested type)
-// if type is unknown, returns empty string
-const string BamIndexFactory::CreateIndexFilename(const string& bamFilename,
-                                                  const BamIndex::IndexType& type)
-{
-    switch ( type ) {
-        case ( BamIndex::STANDARD ) : return ( bamFilename + BamStandardIndex::Extension() );
-        case ( BamIndex::BAMTOOLS ) : return ( bamFilename + BamToolsIndex::Extension() );
-        default :
-            return string();
-    }
-}
-
-// creates a new BamIndex object, depending on extension of @indexFilename
-BamIndex* BamIndexFactory::CreateIndexFromFilename(const string& indexFilename, BamReaderPrivate* reader) {
-
-    // if file doesn't exist, return null index
-    if ( !BamTools::FileExists(indexFilename) )
-        return 0;
-
-    // get file extension from index filename, including dot (".EXT")
-    // if can't get file extension, return null index
-    const string extension = FileExtension(indexFilename);
-    if ( extension.empty() )
-        return 0;
-
-    // create index based on extension
-    if      ( extension == BamStandardIndex::Extension() ) return new BamStandardIndex(reader);
-    else if ( extension == BamToolsIndex::Extension()    ) return new BamToolsIndex(reader);
-    else
-        return 0;
-}
-
-// creates a new BamIndex, object of requested @type
-BamIndex* BamIndexFactory::CreateIndexOfType(const BamIndex::IndexType& type,
-                                             BamReaderPrivate* reader)
-{
-    switch ( type ) {
-        case ( BamIndex::STANDARD ) : return new BamStandardIndex(reader);
-        case ( BamIndex::BAMTOOLS ) : return new BamToolsIndex(reader);
-        default :
-            return 0;
-    }
-}
-
-// retrieves file extension (including '.')
-const string BamIndexFactory::FileExtension(const string& filename) {
-
-    // if filename cannot contain valid path + extension, return empty string
-    if ( filename.empty() || filename.length() <= 4 )
-        return string();
-
-    // look for last dot in filename
-    const size_t lastDotPosition = filename.find_last_of('.');
-
-    // if none found, return empty string
-    if ( lastDotPosition == string::npos )
-        return string();
-
-    // return substring from last dot position
-    return filename.substr(lastDotPosition);
-}
-
-// returns name of existing index file that corresponds to @bamFilename
-// will defer to @preferredType if possible, if not will attempt to load any supported type
-// returns empty string if not found
-const string BamIndexFactory::FindIndexFilename(const string& bamFilename,
-                                                const BamIndex::IndexType& preferredType)
-{
-    // skip if BAM filename provided is empty
-    if ( bamFilename.empty() )
-        return string();
-
-    // try to find index of preferred type first
-    // return index filename if found
-    string indexFilename = CreateIndexFilename(bamFilename, preferredType);
-    if ( !indexFilename.empty() && BamTools::FileExists(indexFilename) )
-        return indexFilename;
-
-    // couldn't find preferred type, try the other supported types
-    // return index filename if found
-    if ( preferredType != BamIndex::STANDARD ) {
-        indexFilename = CreateIndexFilename(bamFilename, BamIndex::STANDARD);
-        if ( !indexFilename.empty() && BamTools::FileExists(indexFilename) )
-            return indexFilename;
-    }
-    if ( preferredType != BamIndex::BAMTOOLS ) {
-        indexFilename = CreateIndexFilename(bamFilename, BamIndex::BAMTOOLS);
-        if ( !indexFilename.empty() && BamTools::FileExists(indexFilename) )
-            return indexFilename;
-    }
-
-    // otherwise couldn't find any index matching this filename
-    return string();
-}