// SamSequenceDictionary.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 18 April 2011
+// Last modified: 12 October 2011
// ---------------------------------------------------------------------------
// Provides methods for operating on a collection of SamSequence entries.
// ***************************************************************************
#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;
void Add(const std::string& name, const int& length);
// adds multiple sequences
+ void Add(const SamSequenceDictionary& sequences);
void Add(const std::vector<SamSequence>& sequences);
void Add(const std::map<std::string, int>& sequenceMap);
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;