BamTools  2.5.2
SamSequenceDictionary.h
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1 // ***************************************************************************
2 // SamSequenceDictionary.h (c) 2010 Derek Barnett
3 // Marth Lab, Department of Biology, Boston College
4 // ---------------------------------------------------------------------------
5 // Last modified: 16 October 2011
6 // ---------------------------------------------------------------------------
7 // Provides methods for operating on a collection of SamSequence entries.
8 // ***************************************************************************
9 
10 #ifndef SAM_SEQUENCE_DICTIONARY_H
11 #define SAM_SEQUENCE_DICTIONARY_H
12 
13 #include <cstddef>
14 #include <map>
15 #include <string>
16 #include <vector>
17 #include "api/SamSequence.h"
18 #include "api/api_global.h"
19 
20 namespace BamTools {
21 
22 typedef std::vector<SamSequence> SamSequenceContainer;
23 typedef SamSequenceContainer::iterator SamSequenceIterator;
24 typedef SamSequenceContainer::const_iterator SamSequenceConstIterator;
25 
26 class API_EXPORT SamSequenceDictionary
27 {
28 
29  // ctor & dtor
30 public:
32 
33  // query/modify sequence data
34 public:
35  // adds a sequence
36  void Add(const SamSequence& sequence);
37  void Add(const std::string& name, const int& length);
38 
39  // adds multiple sequences
40  void Add(const SamSequenceDictionary& sequences);
41  void Add(const std::vector<SamSequence>& sequences);
42  void Add(const std::map<std::string, int>& sequenceMap);
43 
44  // clears all sequence entries
45  void Clear();
46 
47  // returns true if dictionary contains this sequence
48  bool Contains(const SamSequence& sequence) const;
49  bool Contains(const std::string& sequenceName) const;
50 
51  // returns true if dictionary is empty
52  bool IsEmpty() const;
53 
54  // removes sequence, if found
55  void Remove(const SamSequence& sequence);
56  void Remove(const std::string& sequenceName);
57 
58  // removes multiple sequences
59  void Remove(const std::vector<SamSequence>& sequences);
60  void Remove(const std::vector<std::string>& sequenceNames);
61 
62  // returns number of sequences in dictionary
63  int Size() const;
64 
65  // retrieves a modifiable reference to the SamSequence object associated with this name
66  SamSequence& operator[](const std::string& sequenceName);
67 
68  // retrieve STL-compatible iterators
69 public:
70  SamSequenceIterator Begin(); // returns iterator to begin()
71  SamSequenceConstIterator Begin() const; // returns const_iterator to begin()
72  SamSequenceConstIterator ConstBegin() const; // returns const_iterator to begin()
73  SamSequenceIterator End(); // returns iterator to end()
74  SamSequenceConstIterator End() const; // returns const_iterator to end()
75  SamSequenceConstIterator ConstEnd() const; // returns const_iterator to end()
76 
77  // data members
78 private:
79  SamSequenceContainer m_data;
80  std::map<std::string, std::size_t> m_lookupData;
81 };
82 
83 } // namespace BamTools
84 
85 #endif // SAM_SEQUENCE_DICTIONARY_H
Container of SamSequence entries.
Definition: SamSequenceDictionary.h:27
Contains all BamTools classes & methods.
Definition: Sort.h:24
SamSequenceContainer::const_iterator SamSequenceConstIterator
Definition: SamSequenceDictionary.h:24
std::vector< SamSequence > SamSequenceContainer
Definition: SamSequenceDictionary.h:22
SamSequenceContainer::iterator SamSequenceIterator
Definition: SamSequenceDictionary.h:23
Represents a SAM sequence entry.
Definition: SamSequence.h:21