Brought API up to compliance with recent SAM Format Spec (v1.4-r962)

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

diff --git a/src/api/SamProgram.cpp b/src/api/SamProgram.cpp
new file mode 100644 (file)
index 0000000..b89a10b
--- /dev/null
+++ b/src/api/SamProgram.cpp
@@ -0,0 +1,140 @@
+// ***************************************************************************
+// SamProgram.cpp (c) 2011 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 19 April 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides direct read/write access to the SAM header program records.
+// ***************************************************************************
+
+#include <api/SamProgram.h>
+using namespace BamTools;
+using namespace std;
+
+/*! \struct BamTools::SamProgram
+    \brief Represents a SAM program record.
+
+    Provides direct read/write access to the SAM header program records.
+
+    \sa \samSpecURL
+*/
+/*! \var SamProgram::CommandLine
+    \brief corresponds to \@PG CL:\<CommandLine\>
+*/
+/*! \var SamProgram::ID
+    \brief corresponds to \@PG ID:\<ID\>
+
+    Required for valid SAM header.
+*/
+/*! \var SamProgram::Name
+    \brief corresponds to \@PG PN:\<Name\>
+*/
+/*! \var SamProgram::PreviousProgramID
+    \brief corresponds to \@PG PP:\<PreviousProgramID\>
+*/
+/*! \var SamProgram::Version
+    \brief corresponds to \@PG VN:\<Version\>
+*/
+/*! \var SamProgram::NextProgramID
+    \internal
+    Holds ID of the "next" program record in a SamProgramChain
+*/
+
+/*! \fn SamProgram::SamProgram(void)
+    \brief default constructor
+*/
+SamProgram::SamProgram(void)
+    : CommandLine("")
+    , ID("")
+    , Name("")
+    , PreviousProgramID("")
+    , Version("")
+    , NextProgramID("")
+{ }
+
+/*! \fn SamProgram::SamProgram(const std::string& id)
+    \brief constructs program record with \a id
+
+    \param id desired program record ID
+*/
+SamProgram::SamProgram(const std::string& id)
+    : CommandLine("")
+    , ID(id)
+    , Name("")
+    , PreviousProgramID("")
+    , Version("")
+    , NextProgramID("")
+{ }
+
+/*! \fn SamProgram::SamProgram(const SamProgram& other)
+    \brief copy constructor
+*/
+SamProgram::SamProgram(const SamProgram& other)
+    : CommandLine(other.CommandLine)
+    , ID(other.ID)
+    , Name(other.Name)
+    , PreviousProgramID(other.PreviousProgramID)
+    , Version(other.Version)
+    , NextProgramID(other.NextProgramID)
+{ }
+
+/*! \fn SamProgram::~SamProgram(void)
+    \brief destructor
+*/
+SamProgram::~SamProgram(void) { }
+
+/*! \fn void SamProgram::Clear(void)
+    \brief Clears all data fields.
+*/
+void SamProgram::Clear(void) {
+    CommandLine.clear();
+    ID.clear();
+    Name.clear();
+    PreviousProgramID.clear();
+    Version.clear();
+    NextProgramID.clear();
+}
+
+/*! \fn bool SamProgram::HasCommandLine(void) const
+    \brief Returns \c true if program record contains \@PG: CL:\<CommandLine\>
+*/
+bool SamProgram::HasCommandLine(void) const {
+    return (!CommandLine.empty());
+}
+
+/*! \fn bool SamProgram::HasID(void) const
+    \brief Returns \c true if program record contains \@PG: ID:\<ID\>
+*/
+bool SamProgram::HasID(void) const {
+    return (!ID.empty());
+}
+
+/*! \fn bool SamProgram::HasName(void) const
+    \brief Returns \c true if program record contains \@PG: PN:\<Name\>
+*/
+bool SamProgram::HasName(void) const {
+    return (!Name.empty());
+}
+
+/*! \fn bool SamProgram::HasNextProgramID(void) const
+    \internal
+    \return true if program has a "next" record in a SamProgramChain
+*/
+bool SamProgram::HasNextProgramID(void) const {
+    return (!NextProgramID.empty());
+}
+
+/*! \fn bool SamProgram::HasPreviousProgramID(void) const
+    \brief Returns \c true if program record contains \@PG: PP:\<PreviousProgramID\>
+*/
+bool SamProgram::HasPreviousProgramID(void) const {
+    return (!PreviousProgramID.empty());
+}
+
+/*! \fn bool SamProgram::HasVersion(void) const
+    \brief Returns \c true if program record contains \@PG: VN:\<Version\>
+*/
+bool SamProgram::HasVersion(void) const {
+    return (!Version.empty());
+}