Version 2.2.2

[bamtools.git] / src / api / SamReadGroupDictionary.cpp

diff --git a/src/api/SamReadGroupDictionary.cpp b/src/api/SamReadGroupDictionary.cpp
index c501773e58baa69455b59d8e06496c7d7d70a7ab..007221a7cd030e0fd2a1d68e8086340d95a7e8e0 100644 (file)
--- a/src/api/SamReadGroupDictionary.cpp
+++ b/src/api/SamReadGroupDictionary.cpp
@@ -2,7 +2,7 @@
 // SamReadGroupDictionary.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
+// Last modified: 16 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides methods for operating on a collection of SamReadGroup entries.
 // ***************************************************************************
@@ -10,7 +10,6 @@
 #include "api/SamReadGroupDictionary.h"
 using namespace BamTools;
 
-#include <algorithm>
 #include <iostream>
 using namespace std;
 
@@ -30,6 +29,7 @@ SamReadGroupDictionary::SamReadGroupDictionary(void) { }
 */
 SamReadGroupDictionary::SamReadGroupDictionary(const SamReadGroupDictionary& other)
     : m_data(other.m_data)
+    , m_lookupData(other.m_lookupData)
 { }
 
 /*! \fn SamReadGroupDictionary::~SamReadGroupDictionary(void)
@@ -45,8 +45,10 @@ SamReadGroupDictionary::~SamReadGroupDictionary(void) { }
     \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)
@@ -130,6 +132,7 @@ SamReadGroupConstIterator SamReadGroupDictionary::Begin(void) const {
 */
 void SamReadGroupDictionary::Clear(void) {
     m_data.clear();
+    m_lookupData.clear();
 }
 
 /*! \fn SamReadGroupConstIterator SamReadGroupDictionary::ConstBegin(void) const
@@ -155,7 +158,7 @@ SamReadGroupConstIterator SamReadGroupDictionary::ConstEnd(void) const {
     \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_lookupData.find(readGroupId) != m_lookupData.end() );
 }
 
 /*! \fn bool SamReadGroupDictionary::Contains(const SamReadGroup& readGroup) const
@@ -167,7 +170,7 @@ bool SamReadGroupDictionary::Contains(const std::string& readGroupId) 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)
@@ -189,22 +192,6 @@ SamReadGroupConstIterator SamReadGroupDictionary::End(void) const {
     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()
@@ -221,7 +208,7 @@ bool SamReadGroupDictionary::IsEmpty(void) const {
     \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)
@@ -231,8 +218,22 @@ void SamReadGroupDictionary::Remove(const SamReadGroup& readGroup) {
     \sa Remove()
 */
 void SamReadGroupDictionary::Remove(const std::string& readGroupId) {
-    if ( Contains(readGroupId) )
-        m_data.erase( m_data.begin() + IndexOf(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)
@@ -285,17 +286,12 @@ int SamReadGroupDictionary::Size(void) const {
 */
 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 {
+    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);
 }