src/api/SamSequence.h

   1 // ***************************************************************************
   2 // SamSequence.h (c) 2010 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 23 December 2010 (DB)
   7 // ---------------------------------------------------------------------------
   8 // Provides functionality for querying/manipulating sequence data
   9 // **************************************************************************
  10
  11 #ifndef SAM_SEQUENCE_H
  12 #define SAM_SEQUENCE_H
  13
  14 #include <api/api_global.h>
  15 #include <string>
  16
  17 namespace BamTools {
  18
  19 class API_EXPORT SamSequence {
  20
  21     // ctor & dtor
  22     public:
  23         SamSequence(const std::string& name = "");
  24         ~SamSequence(void);
  25
  26     // public methods
  27     public:
  28
  29         // clear all contents
  30         void Clear(void);
  31
  32         // convenience methods to check if SamSequence contains these values:
  33         bool HasName(void) const;
  34         bool HasLength(void) const;
  35         bool HasAssemblyID(void) const;
  36         bool HasChecksum(void) const;
  37         bool HasURI(void) const;
  38         bool HasSpecies(void) const;
  39
  40     // data members
  41     public:
  42         std::string Name;       // SN:<Name>
  43         std::string Length;     // LN:<Length>
  44         std::string AssemblyID; // AS:<AssemblyID>
  45         std::string Checksum;   // M5:<Checksum>
  46         std::string URI;        // UR:<URI>
  47         std::string Species;    // SP:<Species>
  48 };
  49
  50 // ---------------------------------------------------
  51 // comparison operators
  52
  53 // for equality: compare Name, Length, & Checksum (if it exists for both)
  54 inline bool operator==(const SamSequence& lhs, const SamSequence& rhs) {
  55     if ( lhs.Name   != rhs.Name   ) return false;
  56     if ( lhs.Length != rhs.Length ) return false;
  57     if ( lhs.HasChecksum() && rhs.HasChecksum() )
  58         return (lhs.Checksum == rhs.Checksum);
  59     else return true;
  60 }
  61
  62 } // namespace BamTools
  63
  64 #endif // SAM_SEQUENCE_H