BamTools 2.5.2
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SamSequenceDictionary.h
Go to the documentation of this file.
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
20namespace BamTools {
21
22typedef std::vector<SamSequence> SamSequenceContainer;
23typedef SamSequenceContainer::iterator SamSequenceIterator;
24typedef SamSequenceContainer::const_iterator SamSequenceConstIterator;
25
26class API_EXPORT SamSequenceDictionary
27{
28
29 // ctor & dtor
30public:
32
33 // query/modify sequence data
34public:
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
69public:
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
78private:
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