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: 18 April 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 \samSpecURL
  22 */
  23 /*! \var SamSequence::AssemblyID
  24     \brief corresponds to \@SQ AS:\<AssemblyID\>
  25 */
  26 /*! \var SamSequence::Checksum
  27     \brief corresponds to \@SQ M5:\<Checksum\>
  28 */
  29 /*! \var SamSequence::Length
  30     \brief corresponds to \@SQ LN:\<Length\>
  31
  32     Required for valid SAM header.
  33 */
  34 /*! \var SamSequence::Name
  35     \brief corresponds to \@SQ SN:\<Name\>
  36
  37     Required for valid SAM header.
  38 */
  39 /*! \var SamSequence::Species
  40     \brief corresponds to \@SQ SP:\<Species\>
  41 */
  42 /*! \var SamSequence::URI
  43     \brief corresponds to \@SQ UR:\<URI\>
  44 */
  45
  46 /*! \fn SamSequence::SamSequence(void)
  47     \brief default constructor
  48 */
  49 SamSequence::SamSequence(void)
  50     : AssemblyID("")
  51     , Checksum("")
  52     , Length("")
  53     , Name("")
  54     , Species("")
  55     , URI("")
  56 { }
  57
  58 /*! \fn SamSequence::SamSequence(const std::string& name, const int& length)
  59     \brief constructs sequence with \a name and \a length
  60
  61     \param name   desired sequence name
  62     \param length desired sequence length (numeric value)
  63 */
  64 SamSequence::SamSequence(const std::string& name,
  65                          const int& length)
  66     : AssemblyID("")
  67     , Checksum("")
  68     , Name(name)
  69     , Species("")
  70     , URI("")
  71 {
  72     stringstream s("");
  73     s << length;
  74     Length = s.str();
  75 }
  76
  77 /*! \fn SamSequence::SamSequence(const std::string& name, const std::string& length)
  78     \brief constructs sequence with \a name and \a length
  79
  80     \param name   desired sequence name
  81     \param length desired sequence length (string value)
  82 */
  83 SamSequence::SamSequence(const std::string& name,
  84                          const std::string& length)
  85     : AssemblyID("")
  86     , Checksum("")
  87     , Length(length)
  88     , Name(name)
  89     , Species("")
  90     , URI("")
  91 { }
  92
  93 /*! \fn SamSequence::SamSequence(const SamSequence& other)
  94     \brief copy constructor
  95 */
  96 SamSequence::SamSequence(const SamSequence& other)
  97     : AssemblyID(other.AssemblyID)
  98     , Checksum(other.Checksum)
  99     , Length(other.Length)
 100     , Name(other.Name)
 101     , Species(other.Species)
 102     , URI(other.URI)
 103 { }
 104
 105 /*! \fn SamSequence::~SamSequence(void)
 106     \brief destructor
 107 */
 108 SamSequence::~SamSequence(void) { }
 109
 110 /*! \fn void SamSequence::Clear(void)
 111     \brief Clears all data fields.
 112 */
 113 void SamSequence::Clear(void) {
 114     AssemblyID.clear();
 115     Checksum.clear();
 116     Length.clear();
 117     Name.clear();
 118     Species.clear();
 119     URI.clear();
 120 }
 121
 122 /*! \fn bool SamSequence::HasAssemblyID(void) const
 123     \brief Returns \c true if sequence contains \@SQ AS:\<AssemblyID\>
 124 */
 125 bool SamSequence::HasAssemblyID(void) const {
 126     return (!AssemblyID.empty());
 127 }
 128
 129 /*! \fn bool SamSequence::HasChecksum(void) const
 130     \brief Returns \c true if sequence contains \@SQ M5:\<Checksum\>
 131 */
 132 bool SamSequence::HasChecksum(void) const {
 133     return (!Checksum.empty());
 134 }
 135
 136 /*! \fn bool SamSequence::HasLength(void) const
 137     \brief Returns \c true if sequence contains \@SQ LN:\<Length\>
 138 */
 139 bool SamSequence::HasLength(void) const {
 140     return (!Length.empty());
 141 }
 142
 143 /*! \fn bool SamSequence::HasName(void) const
 144     \brief Returns \c true if sequence contains \@SQ SN:\<Name\>
 145 */
 146 bool SamSequence::HasName(void) const {
 147     return (!Name.empty());
 148 }
 149
 150 /*! \fn bool SamSequence::HasSpecies(void) const
 151     \brief Returns \c true if sequence contains \@SQ SP:\<Species\>
 152 */
 153 bool SamSequence::HasSpecies(void) const {
 154     return (!Species.empty());
 155 }
 156
 157 /*! \fn bool SamSequence::HasURI(void) const
 158     \brief Returns \c true if sequence contains \@SQ UR:\<URI\>
 159 */
 160 bool SamSequence::HasURI(void) const {
 161     return (!URI.empty());
 162 }