src/api/internal/BamIndexFactory_p.h

   1 // ***************************************************************************
   2 // BamIndexFactory_p.h (c) 2011 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 5 April 2011 (DB)
   7 // ---------------------------------------------------------------------------
   8 // Provides interface for generating BamIndex implementations
   9 // ***************************************************************************
  10
  11 #ifndef BAMINDEX_FACTORY_P_H
  12 #define BAMINDEX_FACTORY_P_H
  13
  14 #include <api/BamIndex.h>
  15 #include <string>
  16
  17 namespace BamTools {
  18 namespace Internal {
  19
  20 class BamIndexFactory {
  21
  22     // static interface methods
  23     public:
  24         // creates a new BamIndex object, depending on extension of @indexFilename
  25         static BamIndex* CreateIndexFromFilename(const std::string& indexFilename,
  26                                                  BamReaderPrivate* reader);
  27         // creates a new BamIndex object, of requested @type
  28         static BamIndex* CreateIndexOfType(const BamIndex::IndexType& type,
  29                                            BamReaderPrivate* reader);
  30         // returns name of existing index file that corresponds to @bamFilename
  31         // will defer to @preferredType if possible
  32         // if @preferredType not found, will attempt to load any supported index type
  33         // returns empty string if no index file (of any type) is found
  34         static const std::string FindIndexFilename(const std::string& bamFilename,
  35                                                    const BamIndex::IndexType& preferredType);
  36
  37     // internal methods
  38     public:
  39         // generates index filename from BAM filename (depending on requested type)
  40         // if type is unknown, returns empty string
  41         static const std::string CreateIndexFilename(const std::string& bamFilename,
  42                                                      const BamIndex::IndexType& type);
  43         // retrieves file extension (including '.')
  44         static const std::string FileExtension(const std::string& filename);
  45 };
  46
  47 } // namespace Internal
  48 } // namespace BamTools
  49
  50 #endif // BAMINDEX_FACTORY_P_H