// SamReadGroupDictionary.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
+// Last modified: 12 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides methods for operating on a collection of SamReadGroup entries.
// ***************************************************************************
-#include <api/SamReadGroupDictionary.h>
+#include "api/SamReadGroupDictionary.h"
using namespace BamTools;
-#include <algorithm>
#include <iostream>
using namespace std;
Provides methods for operating on a collection of SamReadGroup entries.
*/
+/*! \typedef BamTools::SamReadGroupIterator
+ \brief mutable iterator for SamReadGroupDictionary data
+
+ \note This iterator, dereferenced, actually points to a
+ std::pair<std::string, SamReadGroup>, NOT a "plain old" SamReadGroup.
+ To retrieve the read group object:
+
+ \code
+ SamReadGroupIterator iter;
+ SamReadGroup& rg = (*iter).second // OR iter->second;
+ \endcode
+*/
+
+/*! \typedef BamTools::SamReadGroupConstIterator
+ \brief const iterator for SamReadGroupDictionary data
+
+ \note This iterator, dereferenced, actually points to a
+ std::pair<std::string, SamReadGroup>, NOT a "plain old" SamReadGroup.
+ To retrieve the read group object:
+
+ \code
+ SamReadGroupConstIterator iter;
+ const SamReadGroup& sq = (*iter).second // OR iter->second;
+ \endcode
+*/
+
/*! \fn SamReadGroupDictionary::SamReadGroupDictionary(void)
\brief constructor
*/
*/
void SamReadGroupDictionary::Add(const SamReadGroup& readGroup) {
if ( IsEmpty() || !Contains(readGroup) )
- m_data.push_back(readGroup);
+ m_data[readGroup.ID] = readGroup;
}
/*! \fn void SamReadGroupDictionary::Add(const std::string& readGroupId)
SamReadGroupConstIterator rgIter = readGroups.ConstBegin();
SamReadGroupConstIterator rgEnd = readGroups.ConstEnd();
for ( ; rgIter != rgEnd; ++rgIter )
- Add(*rgIter);
+ Add(rgIter->second);
}
/*! \fn void SamReadGroupDictionary::Add(const std::vector<SamReadGroup>& readGroups)
\return \c true if dictionary contains a read group with this ID
*/
bool SamReadGroupDictionary::Contains(const std::string& readGroupId) const {
- return ( IndexOf(readGroupId) != (int)m_data.size() );
+ return ( m_data.find(readGroupId) != m_data.end() );
}
/*! \fn bool SamReadGroupDictionary::Contains(const SamReadGroup& readGroup) const
\return \c true if dictionary contains read group (matching on ID).
*/
bool SamReadGroupDictionary::Contains(const SamReadGroup& readGroup) const {
- return Contains( readGroup.ID );
+ return Contains(readGroup.ID);
}
/*! \fn SamReadGroupIterator SamReadGroupDictionary::End(void)
return m_data.end();
}
-/*! \fn int SamReadGroupDictionary::IndexOf(const std::string& readGroupId) const
- \internal
- \return index of read group if found. Otherwise, returns vector::size() (invalid index).
-*/
-int SamReadGroupDictionary::IndexOf(const std::string& readGroupId) const {
- SamReadGroupConstIterator begin = ConstBegin();
- SamReadGroupConstIterator iter = begin;
- SamReadGroupConstIterator end = ConstEnd();
- for ( ; iter != end; ++iter ) {
- const SamReadGroup& current = (*iter);
- if ( current.ID == readGroupId )
- break;
- }
- return distance( begin, iter );
-}
-
/*! \fn bool SamReadGroupDictionary::IsEmpty(void) const
\brief Returns \c true if dictionary contains no read groups
\sa Size()
\param[in] readGroup read group to remove (matches on ID)
*/
void SamReadGroupDictionary::Remove(const SamReadGroup& readGroup) {
- Remove( readGroup.ID );
+ Remove(readGroup.ID);
}
/*! \fn void SamReadGroupDictionary::Remove(const std::string& readGroupId)
\sa Remove()
*/
void SamReadGroupDictionary::Remove(const std::string& readGroupId) {
- if ( Contains(readGroupId) )
- m_data.erase( m_data.begin() + IndexOf(readGroupId) );
+ m_data.erase(readGroupId);
}
/*! \fn void SamReadGroupDictionary::Remove(const std::vector<SamReadGroup>& readGroups)
\return a modifiable reference to the SamReadGroup associated with the ID
*/
SamReadGroup& SamReadGroupDictionary::operator[](const std::string& readGroupId) {
-
- // look up read group ID
- int index = IndexOf(readGroupId);
-
- // if found, return read group at index
- if ( index != (int)m_data.size() )
- return m_data[index];
-
- // otherwise, append new read group and return reference
- else {
- SamReadGroup rg(readGroupId);
- m_data.push_back(rg);
- return m_data.back();
- }
+ if ( !Contains(readGroupId) )
+ m_data[readGroupId] = SamReadGroup(readGroupId);
+ return m_data[readGroupId];
}