// ***************************************************************************
// SamSequenceDictionary.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 18 April 2011 (DB)
+// Last modified: 14 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides methods for operating on a collection of SamSequence entries.
// *************************************************************************
-#include <api/SamSequenceDictionary.h>
+#include "api/SamSequenceDictionary.h"
using namespace BamTools;
#include <iostream>
*/
SamSequenceDictionary::SamSequenceDictionary(const SamSequenceDictionary& other)
: m_data(other.m_data)
+ , m_lookupData(other.m_lookupData)
{ }
/*! \fn SamSequenceDictionary::~SamSequenceDictionary(void)
SamSequenceDictionary::~SamSequenceDictionary(void) { }
/*! \fn void SamSequenceDictionary::Add(const SamSequence& sequence)
- \brief Adds a sequence to the dictionary.
+ \brief Appends a sequence to the dictionary.
Duplicate entries are silently discarded.
- \param sequence entry to be added
+ \param[in] sequence entry to be added
*/
void SamSequenceDictionary::Add(const SamSequence& sequence) {
-
- // TODO: report error on attempted duplicate?
-
- if ( IsEmpty() || !Contains(sequence) )
+ if ( IsEmpty() || !Contains(sequence) ) {
m_data.push_back(sequence);
+ m_lookupData[sequence.Name] = sequence;
+ }
}
/*! \fn void SamSequenceDictionary::Add(const std::string& name, const int& length)
- \brief Adds a sequence to the dictionary.
+ \brief Appends a sequence to the dictionary.
This is an overloaded function.
- \param name name of sequence entry to be added
- \param length length of sequence entry to be added
+ \param[in] name name of sequence entry to be added
+ \param[in] length length of sequence entry to be added
\sa Add()
*/
void SamSequenceDictionary::Add(const std::string& name, const int& length) {
Add( SamSequence(name, length) );
}
+/*! \fn void SamSequenceDictionary::Add(const SamSequenceDictionary& sequences)
+ \brief Appends another sequence dictionary to this one
+
+ This is an overloaded function.
+
+ \param[in] sequences sequence dictionary to be appended
+ \sa Add()
+*/
+void SamSequenceDictionary::Add(const SamSequenceDictionary& sequences) {
+ SamSequenceConstIterator seqIter = sequences.ConstBegin();
+ SamSequenceConstIterator seqEnd = sequences.ConstEnd();
+ for ( ; seqIter != seqEnd; ++seqIter )
+ Add(*seqIter);
+}
+
/*! \fn void SamSequenceDictionary::Add(const std::vector<SamSequence>& sequences)
- \brief Adds multiple sequences to the dictionary.
+ \brief Appends multiple sequences to the dictionary.
This is an overloaded function.
- \param sequences entries to be added
+ \param[in] sequences entries to be added
\sa Add()
*/
void SamSequenceDictionary::Add(const std::vector<SamSequence>& sequences) {
}
/*! \fn void SamSequenceDictionary::Add(const std::map<std::string, int>& sequenceMap)
- \brief Adds multiple sequences to the dictionary.
+ \brief Appends multiple sequences to the dictionary.
This is an overloaded function.
- \param sequenceMap map of sequence entries (name => length) to be added
+ \param[in] sequenceMap map of sequence entries (name => length) to be added
\sa Add()
*/
void SamSequenceDictionary::Add(const std::map<std::string, int>& sequenceMap) {
*/
void SamSequenceDictionary::Clear(void) {
m_data.clear();
+ m_lookupData.clear();
}
/*! \fn SamSequenceConstIterator SamSequenceDictionary::ConstBegin(void) const
/*! \fn bool SamSequenceDictionary::Contains(const std::string& sequenceName) const
\brief Returns true if dictionary contains sequence.
- \param sequenceName search for sequence matching this name
+
+ \param[in] sequenceName search for sequence matching this name
\return \c true if dictionary contains a sequence with this name
*/
bool SamSequenceDictionary::Contains(const std::string& sequenceName) const {
- return ( IndexOf(sequenceName) != (int)m_data.size() );
+ return ( m_lookupData.find(sequenceName) != m_lookupData.end() );
}
/*! \fn bool SamSequenceDictionary::Contains(const SamSequence& sequence) const
This is an overloaded function.
- \param sequence search for this sequence
+ \param[in] sequence search for this sequence
\return \c true if dictionary contains sequence (matching on name)
*/
bool SamSequenceDictionary::Contains(const SamSequence& sequence) const {
- return ( IndexOf(sequence.Name) != (int)m_data.size() );
+ return Contains(sequence.Name);
}
/*! \fn SamSequenceIterator SamSequenceDictionary::End(void)
return m_data.end();
}
-/*! \fn int SamSequenceDictionary::IndexOf(const std::string& name) const
- \internal
- \return index of sequence if found (matching on name). Otherwise, returns vector::size() (invalid index).
-*/
-int SamSequenceDictionary::IndexOf(const std::string& name) const {
- SamSequenceConstIterator begin = ConstBegin();
- SamSequenceConstIterator iter = begin;
- SamSequenceConstIterator end = ConstEnd();
- for ( ; iter != end; ++iter ) {
- const SamSequence& currentSeq = (*iter);
- if ( currentSeq.Name == name )
- break;
- }
- return distance( begin, iter );
-}
-
/*! \fn bool SamSequenceDictionary::IsEmpty(void) const
\brief Returns \c true if dictionary contains no sequences
\sa Size()
This is an overloaded function.
- \param sequence SamSequence to remove (matching on name)
+ \param[in] sequence SamSequence to remove (matching on name)
*/
void SamSequenceDictionary::Remove(const SamSequence& sequence) {
- Remove( sequence.Name );
+ Remove(sequence.Name);
}
/*! \fn void SamSequenceDictionary::Remove(const std::string& sequenceName)
\brief Removes sequence from dictionary, if found.
- \param sequenceName name of sequence to remove
+ \param[in] sequenceName name of sequence to remove
\sa Remove()
*/
void SamSequenceDictionary::Remove(const std::string& sequenceName) {
- if ( Contains(sequenceName) )
- m_data.erase( m_data.begin() + IndexOf(sequenceName) );
+
+ SamSequenceIterator seqIter = Begin();
+ SamSequenceIterator seqEnd = End();
+ for ( size_t i = 0 ; seqIter != seqEnd; ++seqIter, ++i ) {
+ SamSequence& seq = (*seqIter);
+ if( seq.Name == sequenceName ) {
+ m_data.erase( Begin() + i );
+ }
+ }
+
+ m_lookupData.erase(sequenceName);
}
/*! \fn void SamSequenceDictionary::Remove(const std::vector<SamSequence>& sequences)
This is an overloaded function.
- \param sequences sequences to remove
+ \param[in] sequences sequences to remove
\sa Remove()
*/
void SamSequenceDictionary::Remove(const std::vector<SamSequence>& sequences) {
This is an overloaded function.
- \param sequenceNames names of the sequences to remove
+ \param[in] sequenceNames names of the sequences to remove
\sa Remove()
*/
void SamSequenceDictionary::Remove(const std::vector<std::string>& sequenceNames) {
/*! \fn SamSequence& SamSequenceDictionary::operator[](const std::string& sequenceName)
\brief Retrieves the modifiable SamSequence that matches \a sequenceName.
- NOTE - If the dictionary contains no sequence matching this name, this function inserts
- a new one with this name (length:0), and returns a reference to it.
-
- If you want to avoid this insertion behavior, check the result of Contains() before
- using this operator.
+ \note If the dictionary contains no sequence matching this name, this function inserts
+ a new one with this name (length:0), and returns a reference to it. If you want to avoid
+ this insertion behavior, check the result of Contains() before using this operator.
- \param sequenceName name of sequence to retrieve
+ \param[in] sequenceName name of sequence to retrieve
\return a modifiable reference to the SamSequence associated with the name
*/
SamSequence& SamSequenceDictionary::operator[](const std::string& sequenceName) {
-
- // look up sequence ID
- int index = IndexOf(sequenceName);
-
- // if found, return sequence at index
- if ( index != (int)m_data.size() )
- return m_data[index];
-
- // otherwise, append new sequence and return reference
- else {
- m_data.push_back( SamSequence(sequenceName, 0) );
- return m_data.back();
+ if ( !Contains(sequenceName) ) {
+ SamSequence seq(sequenceName, 0);
+ m_data.push_back(seq);
+ m_lookupData[sequenceName] = seq;
}
+ return m_lookupData[sequenceName];
}
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