X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FSamReadGroup.cpp;h=ce022ab5d3d84759f096fb5235abb31b0dc90b1d;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=8debc58c7a3f70024aec903ec2ab8295681535d5;hpb=dc965ab6cd68e6e4b29544ae7340c571b0c7cf9f;p=bamtools.git

diff --git a/src/api/SamReadGroup.cpp b/src/api/SamReadGroup.cpp
index 8debc58..ce022ab 100644
--- a/src/api/SamReadGroup.cpp
+++ b/src/api/SamReadGroup.cpp
@@ -1,81 +1,221 @@
 // ***************************************************************************
 // SamReadGroup.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 read group data
-// **************************************************************************
+// Provides direct read/write access to the SAM read group data fields.
+// ***************************************************************************
 
-#include <api/SamReadGroup.h>
+#include "api/SamReadGroup.h"
 using namespace BamTools;
 using namespace std;
 
-// default ctor
+/*! \struct BamTools::SamReadGroup
+    \brief Represents a SAM read group entry.
+
+    Provides direct read/write access to the SAM read group data fields.
+
+    \sa \samSpecURL
+*/
+/*! \var SamReadGroup::Description
+    \brief corresponds to \@RG DS:\<Description\>
+*/
+/*! \var SamReadGroup::FlowOrder
+    \brief corresponds to \@RG FO:\<FlowOrder\>
+*/
+/*! \var SamReadGroup::ID
+    \brief corresponds to \@RG ID:\<ID\>
+
+    Required for valid SAM header.
+*/
+/*! \var SamReadGroup::KeySequence
+    \brief corresponds to \@RG KS:\<KeySequence\>
+*/
+/*! \var SamReadGroup::Library
+    \brief corresponds to \@RG LB:\<Library\>
+*/
+/*! \var SamReadGroup::PlatformUnit
+    \brief corresponds to \@RG PU:\<PlatformUnit\>
+*/
+/*! \var SamReadGroup::PredictedInsertSize
+    \brief corresponds to \@RG PI:\<PredictedInsertSize\>
+*/
+/*! \var SamReadGroup::ProductionDate
+    \brief corresponds to \@RG DT:\<ProductionDate\>
+*/
+/*! \var SamReadGroup::Program
+    \brief corresponds to \@RG PG:\<Program\>
+*/
+/*! \var SamReadGroup::Sample
+    \brief corresponds to \@RG SM:\<Sample\>
+*/
+/*! \var SamReadGroup::SequencingCenter
+    \brief corresponds to \@RG CN:\<SequencingCenter\>
+*/
+/*! \var SamReadGroup::SequencingTechnology
+    \brief corresponds to \@RG PL:\<SequencingTechnology\>
+*/
+
+/*! \fn SamReadGroup::SamReadGroup(void)
+    \brief default constructor
+*/
 SamReadGroup::SamReadGroup(void)
-    : ID("")
-    , Sample("")
+    : Description("")
+    , FlowOrder("")
+    , ID("")
+    , KeySequence("")
     , Library("")
-    , Description("")
     , PlatformUnit("")
     , PredictedInsertSize("")
-    , SequencingCenter("")
     , ProductionDate("")
+    , Program("")
+    , Sample("")
+    , SequencingCenter("")
     , SequencingTechnology("")
 { }
 
-// ctor with provided ID
-SamReadGroup::SamReadGroup(const string& id)
-    : ID(id)
-    , Sample("")
+/*! \fn SamReadGroup::SamReadGroup(const std::string& id)
+    \brief constructs read group with \a id
+
+    \param id desired read group ID
+*/
+SamReadGroup::SamReadGroup(const std::string& id)
+    : Description("")
+    , FlowOrder("")
+    , ID(id)
+    , KeySequence("")
     , Library("")
-    , Description("")
     , PlatformUnit("")
     , PredictedInsertSize("")
-    , SequencingCenter("")
     , ProductionDate("")
+    , Program("")
+    , Sample("")
+    , SequencingCenter("")
     , SequencingTechnology("")
 { }
 
-// copy ctor
+/*! \fn SamReadGroup::SamReadGroup(const SamReadGroup& other)
+    \brief copy constructor
+*/
 SamReadGroup::SamReadGroup(const SamReadGroup& other)
-    : ID(other.ID)
-    , Sample(other.Sample)
+    : Description(other.Description)
+    , FlowOrder(other.FlowOrder)
+    , ID(other.ID)
+    , KeySequence(other.KeySequence)
     , Library(other.Library)
-    , Description(other.Description)
     , PlatformUnit(other.PlatformUnit)
     , PredictedInsertSize(other.PredictedInsertSize)
-    , SequencingCenter(other.SequencingCenter)
     , ProductionDate(other.ProductionDate)
+    , Program(other.Program)
+    , Sample(other.Sample)
+    , SequencingCenter(other.SequencingCenter)
     , SequencingTechnology(other.SequencingTechnology)
 { }
 
-// dtor
-SamReadGroup::~SamReadGroup(void) {
-    Clear();
-}
+/*! \fn SamReadGroup::~SamReadGroup(void)
+    \brief destructor
+*/
+SamReadGroup::~SamReadGroup(void) { }
 
-// clear all contents
+/*! \fn void SamReadGroup::Clear(void)
+    \brief Clears all data fields.
+*/
 void SamReadGroup::Clear(void) {
+    Description.clear();
+    FlowOrder.clear();
     ID.clear();
-    Sample.clear();
+    KeySequence.clear();
     Library.clear();
-    Description.clear();
     PlatformUnit.clear();
     PredictedInsertSize.clear();
-    SequencingCenter.clear();
     ProductionDate.clear();
+    Program.clear();
+    Sample.clear();
+    SequencingCenter.clear();
     SequencingTechnology.clear();
 }
 
-// convenience methods to check if SamReadGroup contains these values:
-bool SamReadGroup::HasID(void) const                   { return (!ID.empty());                   }
-bool SamReadGroup::HasSample(void) const               { return (!Sample.empty());               }
-bool SamReadGroup::HasLibrary(void) const              { return (!Library.empty());              }
-bool SamReadGroup::HasDescription(void) const          { return (!Description.empty());          }
-bool SamReadGroup::HasPlatformUnit(void) const         { return (!PlatformUnit.empty());         }
-bool SamReadGroup::HasPredictedInsertSize(void) const  { return (!PredictedInsertSize.empty());  }
-bool SamReadGroup::HasSequencingCenter(void) const     { return (!SequencingCenter.empty());     }
-bool SamReadGroup::HasProductionDate(void) const       { return (!ProductionDate.empty());       }
-bool SamReadGroup::HasSequencingTechnology(void) const { return (!SequencingTechnology.empty()); }
+/*! \fn bool SamReadGroup::HasDescription(void) const
+    \brief Returns \c true if read group contains \@RG DS:\<Description\>
+*/
+bool SamReadGroup::HasDescription(void) const {
+    return (!Description.empty());
+}
+
+/*! \fn bool SamReadGroup::HasFlowOrder(void) const
+    \brief Returns \c true if read group contains \@RG FO:\<FlowOrder\>
+*/
+bool SamReadGroup::HasFlowOrder(void) const {
+    return (!FlowOrder.empty());
+}
+
+/*! \fn bool SamReadGroup::HasID(void) const
+    \brief Returns \c true if read group contains \@RG: ID:\<ID\>
+*/
+bool SamReadGroup::HasID(void) const {
+    return (!ID.empty());
+}
+
+/*! \fn bool SamReadGroup::HasKeySequence(void) const
+    \brief Returns \c true if read group contains \@RG KS:\<KeySequence\>
+*/
+bool SamReadGroup::HasKeySequence(void) const {
+    return (!KeySequence.empty());
+}
+
+/*! \fn bool SamReadGroup::HasLibrary(void) const
+    \brief Returns \c true if read group contains \@RG LB:\<Library\>
+*/
+bool SamReadGroup::HasLibrary(void) const {
+    return (!Library.empty());
+}
+
+/*! \fn bool SamReadGroup::HasPlatformUnit(void) const
+    \brief Returns \c true if read group contains \@RG PU:\<PlatformUnit\>
+*/
+bool SamReadGroup::HasPlatformUnit(void) const {
+    return (!PlatformUnit.empty());
+}
+
+/*! \fn bool SamReadGroup::HasPredictedInsertSize(void) const
+    \brief Returns \c true if read group contains \@RG PI:\<PredictedInsertSize\>
+*/
+bool SamReadGroup::HasPredictedInsertSize(void) const {
+    return (!PredictedInsertSize.empty());
+}
+
+/*! \fn bool SamReadGroup::HasProductionDate(void) const
+    \brief Returns \c true if read group contains \@RG DT:\<ProductionDate\>
+*/
+bool SamReadGroup::HasProductionDate(void) const {
+    return (!ProductionDate.empty());
+}
+
+/*! \fn bool SamReadGroup::HasProgram(void) const
+    \brief Returns \c true if read group contains \@RG PG:\<Program\>
+*/
+bool SamReadGroup::HasProgram(void) const {
+    return (!Program.empty());
+}
+
+/*! \fn bool SamReadGroup::HasSample(void) const
+    \brief Returns \c true if read group contains \@RG SM:\<Sample\>
+*/
+bool SamReadGroup::HasSample(void) const {
+    return (!Sample.empty());
+}
+
+/*! \fn bool SamReadGroup::HasSequencingCenter(void) const
+    \brief Returns \c true if read group contains \@RG CN:\<SequencingCenter\>
+*/
+bool SamReadGroup::HasSequencingCenter(void) const {
+    return (!SequencingCenter.empty());
+}
+
+/*! \fn bool SamReadGroup::HasSequencingTechnology(void) const
+    \brief Returns \c true if read group contains \@RG PL:\<SequencingTechnology\>
+*/
+bool SamReadGroup::HasSequencingTechnology(void) const {
+    return (!SequencingTechnology.empty());
+}