src/api/SamReadGroup.cpp

   1 // ***************************************************************************
   2 // SamReadGroup.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 read group data
   9 // **************************************************************************
  10
  11 #include <api/SamReadGroup.h>
  12 using namespace BamTools;
  13 using namespace std;
  14
  15 // default ctor
  16 SamReadGroup::SamReadGroup(void)
  17     : ID("")
  18     , Sample("")
  19     , Library("")
  20     , Description("")
  21     , PlatformUnit("")
  22     , PredictedInsertSize("")
  23     , SequencingCenter("")
  24     , ProductionDate("")
  25     , SequencingTechnology("")
  26 { }
  27
  28 // ctor with provided ID
  29 SamReadGroup::SamReadGroup(const string& id)
  30     : ID(id)
  31     , Sample("")
  32     , Library("")
  33     , Description("")
  34     , PlatformUnit("")
  35     , PredictedInsertSize("")
  36     , SequencingCenter("")
  37     , ProductionDate("")
  38     , SequencingTechnology("")
  39 { }
  40
  41 // copy ctor
  42 SamReadGroup::SamReadGroup(const SamReadGroup& other)
  43     : ID(other.ID)
  44     , Sample(other.Sample)
  45     , Library(other.Library)
  46     , Description(other.Description)
  47     , PlatformUnit(other.PlatformUnit)
  48     , PredictedInsertSize(other.PredictedInsertSize)
  49     , SequencingCenter(other.SequencingCenter)
  50     , ProductionDate(other.ProductionDate)
  51     , SequencingTechnology(other.SequencingTechnology)
  52 { }
  53
  54 // dtor
  55 SamReadGroup::~SamReadGroup(void) {
  56     Clear();
  57 }
  58
  59 // clear all contents
  60 void SamReadGroup::Clear(void) {
  61     ID.clear();
  62     Sample.clear();
  63     Library.clear();
  64     Description.clear();
  65     PlatformUnit.clear();
  66     PredictedInsertSize.clear();
  67     SequencingCenter.clear();
  68     ProductionDate.clear();
  69     SequencingTechnology.clear();
  70 }
  71
  72 // convenience methods to check if SamReadGroup contains these values:
  73 bool SamReadGroup::HasID(void) const                   { return (!ID.empty());                   }
  74 bool SamReadGroup::HasSample(void) const               { return (!Sample.empty());               }
  75 bool SamReadGroup::HasLibrary(void) const              { return (!Library.empty());              }
  76 bool SamReadGroup::HasDescription(void) const          { return (!Description.empty());          }
  77 bool SamReadGroup::HasPlatformUnit(void) const         { return (!PlatformUnit.empty());         }
  78 bool SamReadGroup::HasPredictedInsertSize(void) const  { return (!PredictedInsertSize.empty());  }
  79 bool SamReadGroup::HasSequencingCenter(void) const     { return (!SequencingCenter.empty());     }
  80 bool SamReadGroup::HasProductionDate(void) const       { return (!ProductionDate.empty());       }
  81 bool SamReadGroup::HasSequencingTechnology(void) const { return (!SequencingTechnology.empty()); }