src/api/internal/BamIndexFactory_p.h

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