Cleaned up intra-API includes & moved version numbers to 2.0.0

[bamtools.git] / src / api / SamSequence.cpp

diff --git a/src/api/SamSequence.cpp b/src/api/SamSequence.cpp
index 055460436e068b34ad2a51a37a44148600038286..dea176bd1f5438ebcbf1c680d474546ab2042f67 100644 (file)
--- a/src/api/SamSequence.cpp
+++ b/src/api/SamSequence.cpp
@@ -1,46 +1,161 @@
 // ***************************************************************************
 // SamSequence.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 23 December 2010 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
-// Provides functionality for querying/manipulating sequence data
-// *************************************************************************
+// Provides direct read/write access to the SAM sequence data fields.
+// ***************************************************************************
 
-#include <api/SamSequence.h>
+#include "api/SamSequence.h"
+#include <sstream>
 using namespace BamTools;
 using namespace std;
 
-// ctor
-SamSequence::SamSequence(const string& name)
-    : Name(name)
+/*! \struct BamTools::SamSequence
+    \brief Represents a SAM sequence entry.
+
+    Provides direct read/write access to the SAM sequence data fields.
+
+    \sa \samSpecURL
+*/
+/*! \var SamSequence::AssemblyID
+    \brief corresponds to \@SQ AS:\<AssemblyID\>
+*/
+/*! \var SamSequence::Checksum
+    \brief corresponds to \@SQ M5:\<Checksum\>
+*/
+/*! \var SamSequence::Length
+    \brief corresponds to \@SQ LN:\<Length\>
+
+    Required for valid SAM header.
+*/
+/*! \var SamSequence::Name
+    \brief corresponds to \@SQ SN:\<Name\>
+
+    Required for valid SAM header.
+*/
+/*! \var SamSequence::Species
+    \brief corresponds to \@SQ SP:\<Species\>
+*/
+/*! \var SamSequence::URI
+    \brief corresponds to \@SQ UR:\<URI\>
+*/
+
+/*! \fn SamSequence::SamSequence(void)
+    \brief default constructor
+*/
+SamSequence::SamSequence(void)
+    : AssemblyID("")
+    , Checksum("")
     , Length("")
-    , AssemblyID("")
+    , Name("")
+    , Species("")
+    , URI("")
+{ }
+
+/*! \fn SamSequence::SamSequence(const std::string& name, const int& length)
+    \brief constructs sequence with \a name and \a length
+
+    \param name   desired sequence name
+    \param length desired sequence length (numeric value)
+*/
+SamSequence::SamSequence(const std::string& name,
+                         const int& length)
+    : AssemblyID("")
     , Checksum("")
+    , Name(name)
+    , Species("")
     , URI("")
+{
+    stringstream s("");
+    s << length;
+    Length = s.str();
+}
+
+/*! \fn SamSequence::SamSequence(const std::string& name, const std::string& length)
+    \brief constructs sequence with \a name and \a length
+
+    \param name   desired sequence name
+    \param length desired sequence length (string value)
+*/
+SamSequence::SamSequence(const std::string& name,
+                         const std::string& length)
+    : AssemblyID("")
+    , Checksum("")
+    , Length(length)
+    , Name(name)
     , Species("")
+    , URI("")
 { }
 
-// dtor
-SamSequence::~SamSequence(void) {
-    Clear();
-}
+/*! \fn SamSequence::SamSequence(const SamSequence& other)
+    \brief copy constructor
+*/
+SamSequence::SamSequence(const SamSequence& other)
+    : AssemblyID(other.AssemblyID)
+    , Checksum(other.Checksum)
+    , Length(other.Length)
+    , Name(other.Name)
+    , Species(other.Species)
+    , URI(other.URI)
+{ }
+
+/*! \fn SamSequence::~SamSequence(void)
+    \brief destructor
+*/
+SamSequence::~SamSequence(void) { }
 
-// clear all contents
+/*! \fn void SamSequence::Clear(void)
+    \brief Clears all data fields.
+*/
 void SamSequence::Clear(void) {
-    Name.clear();
-    Length.clear();
     AssemblyID.clear();
     Checksum.clear();
-    URI.clear();
+    Length.clear();
+    Name.clear();
     Species.clear();
+    URI.clear();
+}
+
+/*! \fn bool SamSequence::HasAssemblyID(void) const
+    \brief Returns \c true if sequence contains \@SQ AS:\<AssemblyID\>
+*/
+bool SamSequence::HasAssemblyID(void) const {
+    return (!AssemblyID.empty());
 }
 
-// convenience methods to check if SamSequence contains these values:
-bool SamSequence::HasName(void) const       { return (!Name.empty());       }
-bool SamSequence::HasLength(void) const     { return (!Length.empty());     }
-bool SamSequence::HasAssemblyID(void) const { return (!AssemblyID.empty()); }
-bool SamSequence::HasChecksum(void) const   { return (!Checksum.empty());   }
-bool SamSequence::HasURI(void) const        { return (!URI.empty());        }
-bool SamSequence::HasSpecies(void) const    { return (!Species.empty());    }
+/*! \fn bool SamSequence::HasChecksum(void) const
+    \brief Returns \c true if sequence contains \@SQ M5:\<Checksum\>
+*/
+bool SamSequence::HasChecksum(void) const {
+    return (!Checksum.empty());
+}
+
+/*! \fn bool SamSequence::HasLength(void) const
+    \brief Returns \c true if sequence contains \@SQ LN:\<Length\>
+*/
+bool SamSequence::HasLength(void) const {
+    return (!Length.empty());
+}
+
+/*! \fn bool SamSequence::HasName(void) const
+    \brief Returns \c true if sequence contains \@SQ SN:\<Name\>
+*/
+bool SamSequence::HasName(void) const {
+    return (!Name.empty());
+}
+
+/*! \fn bool SamSequence::HasSpecies(void) const
+    \brief Returns \c true if sequence contains \@SQ SP:\<Species\>
+*/
+bool SamSequence::HasSpecies(void) const {
+    return (!Species.empty());
+}
+
+/*! \fn bool SamSequence::HasURI(void) const
+    \brief Returns \c true if sequence contains \@SQ UR:\<URI\>
+*/
+bool SamSequence::HasURI(void) const {
+    return (!URI.empty());
+}