// ***************************************************************************
// SamSequenceDictionary.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 20 March 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides methods for operating on a collection of SamSequence entries.
// *************************************************************************
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 discarded.
+ Duplicate entries are silently discarded.
- \param sequence entry to be added
+ \param[in] sequence entry to be added
*/
void SamSequenceDictionary::Add(const SamSequence& sequence) {
if ( IsEmpty() || !Contains(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) {
}
/*! \fn SamSequenceConstIterator SamSequenceDictionary::Begin(void) const
+ \return an STL const_iterator pointing to the first sequence
This is an overloaded function.
- \return a const STL iterator pointing to the first sequence
\sa ConstBegin(), End()
*/
SamSequenceConstIterator SamSequenceDictionary::Begin(void) const {
}
/*! \fn SamSequenceConstIterator SamSequenceDictionary::ConstBegin(void) const
- \return a const STL iterator pointing to the first sequence
+ \return an STL const_iterator pointing to the first sequence
\sa Begin(), ConstEnd()
*/
SamSequenceConstIterator SamSequenceDictionary::ConstBegin(void) const {
}
/*! \fn SamSequenceConstIterator SamSequenceDictionary::ConstEnd(void) const
- \return a const STL iterator pointing to the imaginary entry after the last sequence
+ \return an STL const_iterator pointing to the imaginary entry after the last sequence
\sa End(), ConstBegin()
*/
SamSequenceConstIterator SamSequenceDictionary::ConstEnd(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 {
}
/*! \fn bool SamSequenceDictionary::Contains(const SamSequence& sequence) const
- \brief Returns true if dictionary contains sequence.
- \param sequence search for this sequence
- \return \c true if dictionary contains sequence
+ \brief Returns true if dictionary contains sequence (matches on name).
+
+ This is an overloaded function.
+
+ \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) != (int)m_data.size() );
+ return ( IndexOf(sequence.Name) != (int)m_data.size() );
}
/*! \fn SamSequenceIterator SamSequenceDictionary::End(void)
}
/*! \fn SamSequenceConstIterator SamSequenceDictionary::End(void) const
+ \return an STL const_iterator pointing to the imaginary entry after the last sequence
This is an overloaded function.
- \return a const STL iterator pointing to the imaginary entry after the last sequence
\sa Begin(), ConstEnd()
*/
SamSequenceConstIterator SamSequenceDictionary::End(void) const {
return m_data.end();
}
-/*! \fn int SamSequenceDictionary::IndexOf(const SamSequence& sequence) const
- \internal
-
- Uses operator==(SamSequence, SamSequence)
-
- \return index of sequence if found. Otherwise, returns vector::size() (invalid index).
-*/
-int SamSequenceDictionary::IndexOf(const SamSequence& sequence) const {
- SamSequenceConstIterator begin = ConstBegin();
- SamSequenceConstIterator iter = begin;
- SamSequenceConstIterator end = ConstEnd();
- for ( ; iter != end; ++iter ) {
- const SamSequence& currentSeq = (*iter);
- if ( currentSeq == sequence )
- break;
- }
- return distance( begin, iter );
-}
-
/*! \fn int SamSequenceDictionary::IndexOf(const std::string& name) const
\internal
-
- Use comparison of SamSequence::Name to \a name
-
- \return index of sequence if found. Otherwise, returns vector::size() (invalid index).
+ \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();
}
/*! \fn void SamSequenceDictionary::Remove(const SamSequence& sequence)
- \brief Removes sequence from dictionary, if found.
- \param sequence sequence to remove
+ \brief Removes sequence from dictionary, if found (matches on name).
+
+ This is an overloaded function.
+
+ \param[in] sequence SamSequence to remove (matching on name)
*/
void SamSequenceDictionary::Remove(const SamSequence& sequence) {
- if ( Contains(sequence) )
- m_data.erase( m_data.begin() + IndexOf(sequence) );
+ 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) {
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, 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) {