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(const SamSequence& other);
  25         ~SamSequence(void);
  26
  27     // public methods
  28     public:
  29
  30         // clear all contents
  31         void Clear(void);
  32
  33         // convenience methods to check if SamSequence contains these values:
  34         bool HasName(void) const;
  35         bool HasLength(void) const;
  36         bool HasAssemblyID(void) const;
  37         bool HasChecksum(void) const;
  38         bool HasURI(void) const;
  39         bool HasSpecies(void) const;
  40
  41     // data members
  42     public:
  43         std::string Name;       // SN:<Name>
  44         std::string Length;     // LN:<Length>
  45         std::string AssemblyID; // AS:<AssemblyID>
  46         std::string Checksum;   // M5:<Checksum>
  47         std::string URI;        // UR:<URI>
  48         std::string Species;    // SP:<Species>
  49 };
  50
  51 // ---------------------------------------------------
  52 // comparison operators
  53
  54 // for equality: compare Name, Length, & Checksum (if it exists for both)
  55 inline bool operator==(const SamSequence& lhs, const SamSequence& rhs) {
  56     if ( lhs.Name   != rhs.Name   ) return false;
  57     if ( lhs.Length != rhs.Length ) return false;
  58     if ( lhs.HasChecksum() && rhs.HasChecksum() )
  59         return (lhs.Checksum == rhs.Checksum);
  60     else return true;
  61 }
  62
  63 } // namespace BamTools
  64
  65 #endif // SAM_SEQUENCE_H