src/api/SamSequence.cpp

   1 // ***************************************************************************
   2 // SamSequence.cpp (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 #include <api/SamSequence.h>
  12 using namespace BamTools;
  13 using namespace std;
  14
  15 // ctor
  16 SamSequence::SamSequence(const string& name)
  17     : Name(name)
  18     , Length("")
  19     , AssemblyID("")
  20     , Checksum("")
  21     , URI("")
  22     , Species("")
  23 { }
  24
  25 // copy ctor
  26 SamSequence::SamSequence(const SamSequence& other)
  27     : Name(other.Name)
  28     , Length(other.Length)
  29     , AssemblyID(other.AssemblyID)
  30     , Checksum(other.Checksum)
  31     , URI(other.URI)
  32     , Species(other.Species)
  33 { }
  34
  35 // dtor
  36 SamSequence::~SamSequence(void) {
  37     Clear();
  38 }
  39
  40 // clear all contents
  41 void SamSequence::Clear(void) {
  42     Name.clear();
  43     Length.clear();
  44     AssemblyID.clear();
  45     Checksum.clear();
  46     URI.clear();
  47     Species.clear();
  48 }
  49
  50 // convenience methods to check if SamSequence contains these values:
  51 bool SamSequence::HasName(void) const       { return (!Name.empty());       }
  52 bool SamSequence::HasLength(void) const     { return (!Length.empty());     }
  53 bool SamSequence::HasAssemblyID(void) const { return (!AssemblyID.empty()); }
  54 bool SamSequence::HasChecksum(void) const   { return (!Checksum.empty());   }
  55 bool SamSequence::HasURI(void) const        { return (!URI.empty());        }
  56 bool SamSequence::HasSpecies(void) const    { return (!Species.empty());    }