// ***************************************************************************
// SamReadGroupDictionary.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 4 March 2011 (DB)
+// Last modified: 16 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;
*/
SamReadGroupDictionary::SamReadGroupDictionary(const SamReadGroupDictionary& other)
: m_data(other.m_data)
+ , m_lookupData(other.m_lookupData)
{ }
/*! \fn SamReadGroupDictionary::~SamReadGroupDictionary(void)
SamReadGroupDictionary::~SamReadGroupDictionary(void) { }
/*! \fn void SamReadGroupDictionary::Add(const SamReadGroup& readGroup)
- \brief Adds a read group to the dictionary.
+ \brief Appends a read group to the dictionary.
- Duplicate entries are discarded.
+ Duplicate entries are silently discarded.
- \param readGroup entry to be added
+ \param[in] readGroup entry to be added
*/
void SamReadGroupDictionary::Add(const SamReadGroup& readGroup) {
- if ( IsEmpty() || !Contains(readGroup) )
+ if ( IsEmpty() || !Contains(readGroup) ) {
m_data.push_back(readGroup);
+ m_lookupData[readGroup.ID] = m_data.size() - 1;
+ }
}
/*! \fn void SamReadGroupDictionary::Add(const std::string& readGroupId)
- \brief Adds a read group to the dictionary.
+ \brief Appends a read group to the dictionary.
This is an overloaded function.
- \param readGroupId ID of read group to be added
+ \param[in] readGroupId ID of read group to be added
\sa Add()
*/
void SamReadGroupDictionary::Add(const std::string& readGroupId) {
Add( SamReadGroup(readGroupId) );
}
+/*! \fn void SamReadGroupDictionary::Add(const SamReadGroupDictionary& readGroups)
+ \brief Appends another read group dictionary to this one.
+
+ This is an overloaded function.
+
+ \param[in] readGroups entries to be added
+ \sa Add()
+*/
+void SamReadGroupDictionary::Add(const SamReadGroupDictionary& readGroups) {
+ SamReadGroupConstIterator rgIter = readGroups.ConstBegin();
+ SamReadGroupConstIterator rgEnd = readGroups.ConstEnd();
+ for ( ; rgIter != rgEnd; ++rgIter )
+ Add(*rgIter);
+}
+
/*! \fn void SamReadGroupDictionary::Add(const std::vector<SamReadGroup>& readGroups)
- \brief Adds multiple read groups to the dictionary.
+ \brief Appends multiple read groups to the dictionary.
This is an overloaded function.
- \param readGroups entries to be added
+ \param[in] readGroups entries to be added
\sa Add()
*/
void SamReadGroupDictionary::Add(const std::vector<SamReadGroup>& readGroups) {
}
/*! \fn void SamReadGroupDictionary::Add(const std::vector<std::string>& readGroupIds)
- \brief Adds multiple read groups to the dictionary.
+ \brief Appends multiple read groups to the dictionary.
This is an overloaded function.
- \param readGroupIds IDs of read groups to be added
+ \param[in] readGroupIds IDs of read groups to be added
\sa Add()
*/
void SamReadGroupDictionary::Add(const std::vector<std::string>& readGroupIds) {
}
/*! \fn SamReadGroupConstIterator SamReadGroupDictionary::Begin(void) const
+ \return an STL const_iterator pointing to the first read group
This is an overloaded function.
- \return a const STL iterator pointing to the first read group
\sa ConstBegin(), End()
*/
SamReadGroupConstIterator SamReadGroupDictionary::Begin(void) const {
*/
void SamReadGroupDictionary::Clear(void) {
m_data.clear();
+ m_lookupData.clear();
}
/*! \fn SamReadGroupConstIterator SamReadGroupDictionary::ConstBegin(void) const
- \return a const STL iterator pointing to the first read group
+ \return an STL const_iterator pointing to the first read group
\sa Begin(), ConstEnd()
*/
SamReadGroupConstIterator SamReadGroupDictionary::ConstBegin(void) const {
}
/*! \fn SamReadGroupConstIterator SamReadGroupDictionary::ConstEnd(void) const
- \return a const STL iterator pointing to the imaginary entry after the last read group
+ \return an STL const_iterator pointing to the imaginary entry after the last read group
\sa ConstBegin(), End()
*/
SamReadGroupConstIterator SamReadGroupDictionary::ConstEnd(void) const {
/*! \fn bool SamReadGroupDictionary::Contains(const std::string& readGroupId) const
\brief Returns true if dictionary contains read group.
- This is an overloaded function.
-
- \param readGroupId search for read group matching this ID
+ \param[in] readGroupId search for read group matching this ID
\return \c true if dictionary contains a read group with this ID
*/
bool SamReadGroupDictionary::Contains(const std::string& readGroupId) const {
- return Contains( SamReadGroup(readGroupId) );
+ return ( m_lookupData.find(readGroupId) != m_lookupData.end() );
}
/*! \fn bool SamReadGroupDictionary::Contains(const SamReadGroup& readGroup) const
- \brief Returns true if dictionary contains read group.
- \param readGroup search for this read group
- \return \c true if dictionary contains read group
+ \brief Returns true if dictionary contains read group (matching on ID).
+
+ This is an overloaded function.
+
+ \param[in] readGroup search for this read group
+ \return \c true if dictionary contains read group (matching on ID).
*/
bool SamReadGroupDictionary::Contains(const SamReadGroup& readGroup) const {
- return ( IndexOf(readGroup) != (int)m_data.size() );
+ return Contains(readGroup.ID);
}
/*! \fn SamReadGroupIterator SamReadGroupDictionary::End(void)
}
/*! \fn SamReadGroupConstIterator SamReadGroupDictionary::End(void) const
+ \return an STL const_iterator pointing to the imaginary entry after the last read group
This is an overloaded function.
- \return a const STL iterator pointing to the imaginary entry after the last read group
\sa Begin(), ConstEnd()
*/
SamReadGroupConstIterator SamReadGroupDictionary::End(void) const {
return m_data.end();
}
-/*! \fn int SamReadGroupDictionary::IndexOf(const SamReadGroup& readGroup) const
- \internal
- \return index of read group if found. Otherwise, returns vector::size() (invalid index).
-*/
-int SamReadGroupDictionary::IndexOf(const SamReadGroup& readGroup) const {
- SamReadGroupConstIterator begin = ConstBegin();
- SamReadGroupConstIterator iter = begin;
- SamReadGroupConstIterator end = ConstEnd();
- for ( ; iter != end; ++iter ) {
- if ( *iter == readGroup )
- break;
- }
- return distance( begin, iter );
-}
-
/*! \fn bool SamReadGroupDictionary::IsEmpty(void) const
\brief Returns \c true if dictionary contains no read groups
\sa Size()
}
/*! \fn void SamReadGroupDictionary::Remove(const SamReadGroup& readGroup)
- \brief Removes read group from dictionary, if found.
- \param readGroup read group to remove
+ \brief Removes read group from dictionary, if found (matching on ID).
+
+ This is an overloaded function.
+
+ \param[in] readGroup read group to remove (matches on ID)
*/
void SamReadGroupDictionary::Remove(const SamReadGroup& readGroup) {
- if ( Contains(readGroup) )
- m_data.erase( m_data.begin() + IndexOf(readGroup) );
+ Remove(readGroup.ID);
}
/*! \fn void SamReadGroupDictionary::Remove(const std::string& readGroupId)
\brief Removes read group from dictionary, if found.
- This is an overloaded function.
-
- \param readGroupId ID of read group to remove
+ \param[in] readGroupId ID of read group to remove
\sa Remove()
*/
void SamReadGroupDictionary::Remove(const std::string& readGroupId) {
- Remove( SamReadGroup(readGroupId) );
+
+ // skip if empty dictionary or if ID unknown
+ if ( IsEmpty() || !Contains(readGroupId) )
+ return;
+
+ // update 'lookup index' for every entry after @readGroupId
+ const size_t indexToRemove = m_lookupData[readGroupId];
+ const size_t numEntries = m_data.size();
+ for ( size_t i = indexToRemove+1; i < numEntries; ++i ) {
+ const SamReadGroup& rg = m_data.at(i);
+ --m_lookupData[rg.ID];
+ }
+
+ // erase entry from containers
+ m_data.erase( Begin() + indexToRemove );
+ m_lookupData.erase(readGroupId);
}
/*! \fn void SamReadGroupDictionary::Remove(const std::vector<SamReadGroup>& readGroups)
- \brief Removes multiple read groups from dictionary.
+ \brief Removes multiple read groups from dictionary (matching on ID).
This is an overloaded function.
- \param readGroups read groups to remove
+ \param[in] readGroups read groups to remove
\sa Remove()
*/
void SamReadGroupDictionary::Remove(const std::vector<SamReadGroup>& readGroups) {
This is an overloaded function.
- \param readGroupIds IDs of the read groups to remove
+ \param[in] readGroupIds IDs of the read groups to remove
\sa Remove()
*/
void SamReadGroupDictionary::Remove(const std::vector<std::string>& readGroupIds) {
/*! \fn SamReadGroup& SamReadGroupDictionary::operator[](const std::string& readGroupId)
\brief Retrieves the modifiable SamReadGroup that matches \a readGroupId.
- NOTE - If the dictionary contains no read group matching this ID, this function inserts
- a new one with this ID, and returns a reference to it.
+ \note If the dictionary contains no read group matching this ID, this function inserts
+ a new one with this ID, and returns a reference to it. If you want to avoid this insertion
+ behavior, check the result of Contains() before using this operator.
- If you want to avoid this insertion behavior, check the result of Contains() before
- using this operator.
-
- \param readGroupId ID of read group to retrieve
+ \param[in] readGroupId ID of read group to retrieve
\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( SamReadGroup(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 {
+ if ( !Contains(readGroupId) ) {
SamReadGroup rg(readGroupId);
m_data.push_back(rg);
- return m_data.back();
+ m_lookupData[readGroupId] = m_data.size() - 1;
}
+
+ const size_t index = m_lookupData[readGroupId];
+ return m_data.at(index);
}
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