1 // ***************************************************************************
2 // SamSequenceDictionary.h (c) 2010 Derek Barnett
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 23 December 2010 (DB)
7 // ---------------------------------------------------------------------------
8 // Provides container operations for collection of sequence entries
9 // *************************************************************************
11 #ifndef SAM_SEQUENCE_DICTIONARY_H
12 #define SAM_SEQUENCE_DICTIONARY_H
14 #include <api/api_global.h>
15 #include <api/SamSequence.h>
21 typedef std::vector<SamSequence> SamSequenceContainer;
22 typedef SamSequenceContainer::iterator SamSequenceIterator;
23 typedef SamSequenceContainer::const_iterator SamSequenceConstIterator;
25 class API_EXPORT SamSequenceDictionary {
29 SamSequenceDictionary(void);
30 ~SamSequenceDictionary(void);
32 // query/modify sequence data
35 void Add(const SamSequence& sequence);
36 void Add(const std::string& sequenceNames);
38 // add multiple sequences
39 void Add(const std::vector<SamSequence>& sequences);
40 void Add(const std::vector<std::string>& sequenceNames);
42 // clear all sequence records
45 // returns true if dictionary contains this sequence
46 bool Contains(const SamSequence& sequence) const;
47 bool Contains(const std::string& sequenceName) const;
49 // returns true if dictionary is empty
50 bool IsEmpty(void) const;
52 // remove a single sequence (does nothing if sequence not found)
53 void Remove(const SamSequence& sequence);
54 void Remove(const std::string& sequenceName);
56 // remove multiple sequences
57 void Remove(const std::vector<SamSequence>& sequences);
58 void Remove(const std::vector<std::string>& sequenceNames);
60 // returns size of dictionary (number of current elements)
63 // retrieves the SamSequence object associated with this name
64 // if sequenceName is unknown, a new SamSequence is created with this name (and invalid length 0)
65 // and a reference to this new sequence entry is returned (like std::map)
67 // * To avoid these partial entries being created, it is recommended to check
68 // for existence first using Contains()
69 SamSequence& operator[](const std::string& sequenceName);
71 // retrieve sequence iterators
72 // these are typedefs for STL iterators and thus are compatible with STL containers/algorithms
74 SamSequenceIterator Begin(void);
75 SamSequenceConstIterator Begin(void) const;
76 SamSequenceConstIterator ConstBegin(void) const;
77 SamSequenceIterator End(void);
78 SamSequenceConstIterator End(void) const;
79 SamSequenceConstIterator ConstEnd(void) const;
83 int IndexOf(const SamSequence& sequence) const;
84 int IndexOf(const std::string& sequenceName) const;
88 SamSequenceContainer m_data;
91 } // namespace BamTools
93 #endif // SAM_SEQUENCE_DICTIONARY