src/api/SamProgram.cpp

   1 // ***************************************************************************
   2 // SamProgram.cpp (c) 2011 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 19 April 2011 (DB)
   7 // ---------------------------------------------------------------------------
   8 // Provides direct read/write access to the SAM header program records.
   9 // ***************************************************************************
  10
  11 #include <api/SamProgram.h>
  12 using namespace BamTools;
  13 using namespace std;
  14
  15 /*! \struct BamTools::SamProgram
  16     \brief Represents a SAM program record.
  17
  18     Provides direct read/write access to the SAM header program records.
  19
  20     \sa \samSpecURL
  21 */
  22 /*! \var SamProgram::CommandLine
  23     \brief corresponds to \@PG CL:\<CommandLine\>
  24 */
  25 /*! \var SamProgram::ID
  26     \brief corresponds to \@PG ID:\<ID\>
  27
  28     Required for valid SAM header.
  29 */
  30 /*! \var SamProgram::Name
  31     \brief corresponds to \@PG PN:\<Name\>
  32 */
  33 /*! \var SamProgram::PreviousProgramID
  34     \brief corresponds to \@PG PP:\<PreviousProgramID\>
  35 */
  36 /*! \var SamProgram::Version
  37     \brief corresponds to \@PG VN:\<Version\>
  38 */
  39 /*! \var SamProgram::NextProgramID
  40     \internal
  41     Holds ID of the "next" program record in a SamProgramChain
  42 */
  43
  44 /*! \fn SamProgram::SamProgram(void)
  45     \brief default constructor
  46 */
  47 SamProgram::SamProgram(void)
  48     : CommandLine("")
  49     , ID("")
  50     , Name("")
  51     , PreviousProgramID("")
  52     , Version("")
  53     , NextProgramID("")
  54 { }
  55
  56 /*! \fn SamProgram::SamProgram(const std::string& id)
  57     \brief constructs program record with \a id
  58
  59     \param id desired program record ID
  60 */
  61 SamProgram::SamProgram(const std::string& id)
  62     : CommandLine("")
  63     , ID(id)
  64     , Name("")
  65     , PreviousProgramID("")
  66     , Version("")
  67     , NextProgramID("")
  68 { }
  69
  70 /*! \fn SamProgram::SamProgram(const SamProgram& other)
  71     \brief copy constructor
  72 */
  73 SamProgram::SamProgram(const SamProgram& other)
  74     : CommandLine(other.CommandLine)
  75     , ID(other.ID)
  76     , Name(other.Name)
  77     , PreviousProgramID(other.PreviousProgramID)
  78     , Version(other.Version)
  79     , NextProgramID(other.NextProgramID)
  80 { }
  81
  82 /*! \fn SamProgram::~SamProgram(void)
  83     \brief destructor
  84 */
  85 SamProgram::~SamProgram(void) { }
  86
  87 /*! \fn void SamProgram::Clear(void)
  88     \brief Clears all data fields.
  89 */
  90 void SamProgram::Clear(void) {
  91     CommandLine.clear();
  92     ID.clear();
  93     Name.clear();
  94     PreviousProgramID.clear();
  95     Version.clear();
  96     NextProgramID.clear();
  97 }
  98
  99 /*! \fn bool SamProgram::HasCommandLine(void) const
 100     \brief Returns \c true if program record contains \@PG: CL:\<CommandLine\>
 101 */
 102 bool SamProgram::HasCommandLine(void) const {
 103     return (!CommandLine.empty());
 104 }
 105
 106 /*! \fn bool SamProgram::HasID(void) const
 107     \brief Returns \c true if program record contains \@PG: ID:\<ID\>
 108 */
 109 bool SamProgram::HasID(void) const {
 110     return (!ID.empty());
 111 }
 112
 113 /*! \fn bool SamProgram::HasName(void) const
 114     \brief Returns \c true if program record contains \@PG: PN:\<Name\>
 115 */
 116 bool SamProgram::HasName(void) const {
 117     return (!Name.empty());
 118 }
 119
 120 /*! \fn bool SamProgram::HasNextProgramID(void) const
 121     \internal
 122     \return true if program has a "next" record in a SamProgramChain
 123 */
 124 bool SamProgram::HasNextProgramID(void) const {
 125     return (!NextProgramID.empty());
 126 }
 127
 128 /*! \fn bool SamProgram::HasPreviousProgramID(void) const
 129     \brief Returns \c true if program record contains \@PG: PP:\<PreviousProgramID\>
 130 */
 131 bool SamProgram::HasPreviousProgramID(void) const {
 132     return (!PreviousProgramID.empty());
 133 }
 134
 135 /*! \fn bool SamProgram::HasVersion(void) const
 136     \brief Returns \c true if program record contains \@PG: VN:\<Version\>
 137 */
 138 bool SamProgram::HasVersion(void) const {
 139     return (!Version.empty());
 140 }