Major speedup in SamSequenceDictionary & SamReadGroupDictionary classes

[bamtools.git] / src / api / SamSequenceDictionary.h

diff --git a/src/api/SamSequenceDictionary.h b/src/api/SamSequenceDictionary.h
index 8e2401e7740e79223002f2c37ba1a70fffe548ba..a583f046e10ec78a73394bdcb0906c0fa79e4b6b 100644 (file)
--- a/src/api/SamSequenceDictionary.h
+++ b/src/api/SamSequenceDictionary.h
@@ -2,7 +2,7 @@
 // SamSequenceDictionary.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 1 October 2011
+// Last modified: 12 October 2011
 // ---------------------------------------------------------------------------
 // Provides methods for operating on a collection of SamSequence entries.
 // ***************************************************************************
@@ -10,15 +10,15 @@
 #ifndef SAM_SEQUENCE_DICTIONARY_H
 #define SAM_SEQUENCE_DICTIONARY_H
 
-#include <api/api_global.h>
-#include <api/SamSequence.h>
-#include <string>
+#include "api/api_global.h"
+#include "api/SamSequence.h"
 #include <map>
+#include <string>
 #include <vector>
 
 namespace BamTools {
 
-typedef std::vector<SamSequence>             SamSequenceContainer;
+typedef std::map<std::string, SamSequence>   SamSequenceContainer;
 typedef SamSequenceContainer::iterator       SamSequenceIterator;
 typedef SamSequenceContainer::const_iterator SamSequenceConstIterator;
 
@@ -74,10 +74,6 @@ class API_EXPORT SamSequenceDictionary {
         SamSequenceConstIterator End(void) const;           // returns const_iterator to end()
         SamSequenceConstIterator ConstEnd(void) const;      // returns const_iterator to end()
 
-    // internal methods
-    private:
-        int IndexOf(const std::string& name) const;
-
     // data members
     private:
         SamSequenceContainer m_data;