src/api/SamSequence.cpp

   1 // ***************************************************************************
   2 // SamSequence.cpp (c) 2010 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // ---------------------------------------------------------------------------
   5 // Last modified: 18 April 2011 (DB)
   6 // ---------------------------------------------------------------------------
   7 // Provides direct read/write access to the SAM sequence data fields.
   8 // ***************************************************************************
   9
  10 #include <api/SamSequence.h>
  11 #include <sstream>
  12 using namespace BamTools;
  13 using namespace std;
  14
  15 /*! \struct BamTools::SamSequence
  16     \brief Represents a SAM sequence entry.
  17
  18     Provides direct read/write access to the SAM sequence data fields.
  19
  20     \sa \samSpecURL
  21 */
  22 /*! \var SamSequence::AssemblyID
  23     \brief corresponds to \@SQ AS:\<AssemblyID\>
  24 */
  25 /*! \var SamSequence::Checksum
  26     \brief corresponds to \@SQ M5:\<Checksum\>
  27 */
  28 /*! \var SamSequence::Length
  29     \brief corresponds to \@SQ LN:\<Length\>
  30
  31     Required for valid SAM header.
  32 */
  33 /*! \var SamSequence::Name
  34     \brief corresponds to \@SQ SN:\<Name\>
  35
  36     Required for valid SAM header.
  37 */
  38 /*! \var SamSequence::Species
  39     \brief corresponds to \@SQ SP:\<Species\>
  40 */
  41 /*! \var SamSequence::URI
  42     \brief corresponds to \@SQ UR:\<URI\>
  43 */
  44
  45 /*! \fn SamSequence::SamSequence(void)
  46     \brief default constructor
  47 */
  48 SamSequence::SamSequence(void)
  49     : AssemblyID("")
  50     , Checksum("")
  51     , Length("")
  52     , Name("")
  53     , Species("")
  54     , URI("")
  55 { }
  56
  57 /*! \fn SamSequence::SamSequence(const std::string& name, const int& length)
  58     \brief constructs sequence with \a name and \a length
  59
  60     \param name   desired sequence name
  61     \param length desired sequence length (numeric value)
  62 */
  63 SamSequence::SamSequence(const std::string& name,
  64                          const int& length)
  65     : AssemblyID("")
  66     , Checksum("")
  67     , Name(name)
  68     , Species("")
  69     , URI("")
  70 {
  71     stringstream s("");
  72     s << length;
  73     Length = s.str();
  74 }
  75
  76 /*! \fn SamSequence::SamSequence(const std::string& name, const std::string& length)
  77     \brief constructs sequence with \a name and \a length
  78
  79     \param name   desired sequence name
  80     \param length desired sequence length (string value)
  81 */
  82 SamSequence::SamSequence(const std::string& name,
  83                          const std::string& length)
  84     : AssemblyID("")
  85     , Checksum("")
  86     , Length(length)
  87     , Name(name)
  88     , Species("")
  89     , URI("")
  90 { }
  91
  92 /*! \fn SamSequence::SamSequence(const SamSequence& other)
  93     \brief copy constructor
  94 */
  95 SamSequence::SamSequence(const SamSequence& other)
  96     : AssemblyID(other.AssemblyID)
  97     , Checksum(other.Checksum)
  98     , Length(other.Length)
  99     , Name(other.Name)
 100     , Species(other.Species)
 101     , URI(other.URI)
 102 { }
 103
 104 /*! \fn SamSequence::~SamSequence(void)
 105     \brief destructor
 106 */
 107 SamSequence::~SamSequence(void) { }
 108
 109 /*! \fn void SamSequence::Clear(void)
 110     \brief Clears all data fields.
 111 */
 112 void SamSequence::Clear(void) {
 113     AssemblyID.clear();
 114     Checksum.clear();
 115     Length.clear();
 116     Name.clear();
 117     Species.clear();
 118     URI.clear();
 119 }
 120
 121 /*! \fn bool SamSequence::HasAssemblyID(void) const
 122     \brief Returns \c true if sequence contains \@SQ AS:\<AssemblyID\>
 123 */
 124 bool SamSequence::HasAssemblyID(void) const {
 125     return (!AssemblyID.empty());
 126 }
 127
 128 /*! \fn bool SamSequence::HasChecksum(void) const
 129     \brief Returns \c true if sequence contains \@SQ M5:\<Checksum\>
 130 */
 131 bool SamSequence::HasChecksum(void) const {
 132     return (!Checksum.empty());
 133 }
 134
 135 /*! \fn bool SamSequence::HasLength(void) const
 136     \brief Returns \c true if sequence contains \@SQ LN:\<Length\>
 137 */
 138 bool SamSequence::HasLength(void) const {
 139     return (!Length.empty());
 140 }
 141
 142 /*! \fn bool SamSequence::HasName(void) const
 143     \brief Returns \c true if sequence contains \@SQ SN:\<Name\>
 144 */
 145 bool SamSequence::HasName(void) const {
 146     return (!Name.empty());
 147 }
 148
 149 /*! \fn bool SamSequence::HasSpecies(void) const
 150     \brief Returns \c true if sequence contains \@SQ SP:\<Species\>
 151 */
 152 bool SamSequence::HasSpecies(void) const {
 153     return (!Species.empty());
 154 }
 155
 156 /*! \fn bool SamSequence::HasURI(void) const
 157     \brief Returns \c true if sequence contains \@SQ UR:\<URI\>
 158 */
 159 bool SamSequence::HasURI(void) const {
 160     return (!URI.empty());
 161 }