src/api/SamProgram.cpp

   1 // ***************************************************************************
   2 // SamProgram.cpp (c) 2011 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // ---------------------------------------------------------------------------
   5 // Last modified: 10 October 2011 (DB)
   6 // ---------------------------------------------------------------------------
   7 // Provides direct read/write access to the SAM header program records.
   8 // ***************************************************************************
   9
  10 #include "api/SamProgram.h"
  11 using namespace BamTools;
  12 using namespace std;
  13
  14 /*! \struct BamTools::SamProgram
  15     \brief Represents a SAM program record.
  16
  17     Provides direct read/write access to the SAM header program records.
  18
  19     \sa \samSpecURL
  20 */
  21 /*! \var SamProgram::CommandLine
  22     \brief corresponds to \@PG CL:\<CommandLine\>
  23 */
  24 /*! \var SamProgram::ID
  25     \brief corresponds to \@PG ID:\<ID\>
  26
  27     Required for valid SAM header.
  28 */
  29 /*! \var SamProgram::Name
  30     \brief corresponds to \@PG PN:\<Name\>
  31 */
  32 /*! \var SamProgram::PreviousProgramID
  33     \brief corresponds to \@PG PP:\<PreviousProgramID\>
  34 */
  35 /*! \var SamProgram::Version
  36     \brief corresponds to \@PG VN:\<Version\>
  37 */
  38 /*! \var SamProgram::NextProgramID
  39     \internal
  40     Holds ID of the "next" program record in a SamProgramChain
  41 */
  42
  43 /*! \fn SamProgram::SamProgram(void)
  44     \brief default constructor
  45 */
  46 SamProgram::SamProgram(void)
  47     : CommandLine("")
  48     , ID("")
  49     , Name("")
  50     , PreviousProgramID("")
  51     , Version("")
  52     , NextProgramID("")
  53 { }
  54
  55 /*! \fn SamProgram::SamProgram(const std::string& id)
  56     \brief constructs program record with \a id
  57
  58     \param id desired program record ID
  59 */
  60 SamProgram::SamProgram(const std::string& id)
  61     : CommandLine("")
  62     , ID(id)
  63     , Name("")
  64     , PreviousProgramID("")
  65     , Version("")
  66     , NextProgramID("")
  67 { }
  68
  69 /*! \fn SamProgram::SamProgram(const SamProgram& other)
  70     \brief copy constructor
  71 */
  72 SamProgram::SamProgram(const SamProgram& other)
  73     : CommandLine(other.CommandLine)
  74     , ID(other.ID)
  75     , Name(other.Name)
  76     , PreviousProgramID(other.PreviousProgramID)
  77     , Version(other.Version)
  78     , NextProgramID(other.NextProgramID)
  79 { }
  80
  81 /*! \fn SamProgram::~SamProgram(void)
  82     \brief destructor
  83 */
  84 SamProgram::~SamProgram(void) { }
  85
  86 /*! \fn void SamProgram::Clear(void)
  87     \brief Clears all data fields.
  88 */
  89 void SamProgram::Clear(void) {
  90     CommandLine.clear();
  91     ID.clear();
  92     Name.clear();
  93     PreviousProgramID.clear();
  94     Version.clear();
  95     NextProgramID.clear();
  96 }
  97
  98 /*! \fn bool SamProgram::HasCommandLine(void) const
  99     \brief Returns \c true if program record contains \@PG: CL:\<CommandLine\>
 100 */
 101 bool SamProgram::HasCommandLine(void) const {
 102     return (!CommandLine.empty());
 103 }
 104
 105 /*! \fn bool SamProgram::HasID(void) const
 106     \brief Returns \c true if program record contains \@PG: ID:\<ID\>
 107 */
 108 bool SamProgram::HasID(void) const {
 109     return (!ID.empty());
 110 }
 111
 112 /*! \fn bool SamProgram::HasName(void) const
 113     \brief Returns \c true if program record contains \@PG: PN:\<Name\>
 114 */
 115 bool SamProgram::HasName(void) const {
 116     return (!Name.empty());
 117 }
 118
 119 /*! \fn bool SamProgram::HasNextProgramID(void) const
 120     \internal
 121     \return true if program has a "next" record in a SamProgramChain
 122 */
 123 bool SamProgram::HasNextProgramID(void) const {
 124     return (!NextProgramID.empty());
 125 }
 126
 127 /*! \fn bool SamProgram::HasPreviousProgramID(void) const
 128     \brief Returns \c true if program record contains \@PG: PP:\<PreviousProgramID\>
 129 */
 130 bool SamProgram::HasPreviousProgramID(void) const {
 131     return (!PreviousProgramID.empty());
 132 }
 133
 134 /*! \fn bool SamProgram::HasVersion(void) const
 135     \brief Returns \c true if program record contains \@PG: VN:\<Version\>
 136 */
 137 bool SamProgram::HasVersion(void) const {
 138     return (!Version.empty());
 139 }