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: 20 March 2011 (DB)
   7 // ---------------------------------------------------------------------------
   8 // Provides direct read/write access to the SAM sequence data fields.
   9 // ***************************************************************************
  10
  11 #include <api/SamSequence.h>
  12 #include <sstream>
  13 using namespace BamTools;
  14 using namespace std;
  15
  16 /*! \struct BamTools::SamSequence
  17     \brief Represents a SAM sequence entry.
  18
  19     Provides direct read/write access to the SAM sequence data fields.
  20
  21     \sa http://samtools.sourceforge.net/SAM-1.3.pdf
  22 */
  23 /*! \var SamSequence::Name
  24     \brief corresponds to \@SQ SN:\<Name\>
  25 */
  26 /*! \var SamSequence::Length
  27     \brief corresponds to \@SQ LN:\<Length\>
  28 */
  29 /*! \var SamSequence::AssemblyID
  30     \brief corresponds to \@SQ AS:\<AssemblyID\>
  31 */
  32 /*! \var SamSequence::Checksum
  33     \brief corresponds to \@SQ M5:\<Checksum\>
  34 */
  35 /*! \var SamSequence::URI
  36     \brief corresponds to \@SQ UR:\<URI\>
  37 */
  38 /*! \var SamSequence::Species
  39     \brief corresponds to \@SQ SP:\<Species\>
  40 */
  41
  42 /*! \fn SamSequence::SamSequence(void)
  43     \brief default constructor
  44 */
  45 SamSequence::SamSequence(void)
  46     : Name("")
  47     , Length("")
  48     , AssemblyID("")
  49     , Checksum("")
  50     , URI("")
  51     , Species("")
  52 { }
  53
  54 /*! \fn SamSequence::SamSequence(const std::string& name, const int& length)
  55     \brief constructs sequence with \a name and \a length
  56
  57     \param name desired sequence name
  58     \param length desired sequence length (numeric value)
  59 */
  60 SamSequence::SamSequence(const std::string& name, const int& length)
  61     : Name(name)
  62     , AssemblyID("")
  63     , Checksum("")
  64     , URI("")
  65     , Species("")
  66 {
  67     stringstream s("");
  68     s << length;
  69     Length = s.str();
  70 }
  71
  72 /*! \fn SamSequence::SamSequence(const SamSequence& other)
  73     \brief copy constructor
  74 */
  75 SamSequence::SamSequence(const SamSequence& other)
  76     : Name(other.Name)
  77     , Length(other.Length)
  78     , AssemblyID(other.AssemblyID)
  79     , Checksum(other.Checksum)
  80     , URI(other.URI)
  81     , Species(other.Species)
  82 { }
  83
  84 /*! \fn SamSequence::~SamSequence(void)
  85     \brief destructor
  86 */
  87 SamSequence::~SamSequence(void) { }
  88
  89 /*! \fn void SamSequence::Clear(void)
  90     \brief Clears all data fields.
  91 */
  92 void SamSequence::Clear(void) {
  93     Name.clear();
  94     Length.clear();
  95     AssemblyID.clear();
  96     Checksum.clear();
  97     URI.clear();
  98     Species.clear();
  99 }
 100
 101 /*! \fn bool SamSequence::HasName(void) const
 102     \brief Returns \c true if sequence contains \@SQ SN:\<Name\>
 103 */
 104 bool SamSequence::HasName(void) const {
 105     return (!Name.empty());
 106 }
 107
 108 /*! \fn bool SamSequence::HasLength(void) const
 109     \brief Returns \c true if sequence contains \@SQ LN:\<Length\>
 110 */
 111 bool SamSequence::HasLength(void) const {
 112     return (!Length.empty());
 113 }
 114
 115 /*! \fn bool SamSequence::HasAssemblyID(void) const
 116     \brief Returns \c true if sequence contains \@SQ AS:\<AssemblyID\>
 117 */
 118 bool SamSequence::HasAssemblyID(void) const {
 119     return (!AssemblyID.empty());
 120 }
 121
 122 /*! \fn bool SamSequence::HasChecksum(void) const
 123     \brief Returns \c true if sequence contains \@SQ M5:\<Checksum\>
 124 */
 125 bool SamSequence::HasChecksum(void) const {
 126     return (!Checksum.empty());
 127 }
 128
 129 /*! \fn bool SamSequence::HasURI(void) const
 130     \brief Returns \c true if sequence contains \@SQ UR:\<URI\>
 131 */
 132 bool SamSequence::HasURI(void) const {
 133     return (!URI.empty());
 134 }
 135
 136 /*! \fn bool SamSequence::HasSpecies(void) const
 137     \brief Returns \c true if sequence contains \@SQ SP:\<Species\>
 138 */
 139 bool SamSequence::HasSpecies(void) const {
 140     return (!Species.empty());
 141 }