// SamReadGroupDictionary.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 18 April 2011 (DB)
+// Last modified: 10 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>
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 silently discarded.
- \param readGroup entry to be added
+ \param[in] readGroup entry to be added
*/
void SamReadGroupDictionary::Add(const SamReadGroup& readGroup) {
-
- // TODO: report error on attempted duplicate?
-
if ( IsEmpty() || !Contains(readGroup) )
m_data.push_back(readGroup);
}
/*! \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 bool SamReadGroupDictionary::Contains(const std::string& readGroupId) const
\brief Returns true if dictionary contains read group.
- \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 {
This is an overloaded function.
- \param readGroup search for this read group
+ \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 {
This is an overloaded function.
- \param readGroup read group to remove (matches on ID)
+ \param[in] readGroup read group to remove (matches on ID)
*/
void SamReadGroupDictionary::Remove(const SamReadGroup& readGroup) {
Remove( readGroup.ID );
/*! \fn void SamReadGroupDictionary::Remove(const std::string& readGroupId)
\brief Removes read group from dictionary, if found.
- \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) {
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.
-
- If you want to avoid this insertion behavior, check the result of Contains() before
- using this operator.
+ \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.
- \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) {