src/api/SamSequenceDictionary.h

   1 // ***************************************************************************
   2 // SamSequenceDictionary.h (c) 2010 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 18 April 2011
   7 // ---------------------------------------------------------------------------
   8 // Provides methods for operating on a collection of SamSequence entries.
   9 // ***************************************************************************
  10
  11 #ifndef SAM_SEQUENCE_DICTIONARY_H
  12 #define SAM_SEQUENCE_DICTIONARY_H
  13
  14 #include <api/api_global.h>
  15 #include <api/SamSequence.h>
  16 #include <string>
  17 #include <map>
  18 #include <vector>
  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     // ctor & dtor
  29     public:
  30         SamSequenceDictionary(void);
  31         SamSequenceDictionary(const SamSequenceDictionary& other);
  32         ~SamSequenceDictionary(void);
  33
  34     // query/modify sequence data
  35     public:
  36         // adds a sequence
  37         void Add(const SamSequence& sequence);
  38         void Add(const std::string& name, const int& length);
  39
  40         // adds multiple 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(void);
  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(void) 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(void) 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(void);               // returns iterator to begin()
  71         SamSequenceConstIterator Begin(void) const;         // returns const_iterator to begin()
  72         SamSequenceConstIterator ConstBegin(void) const;    // returns const_iterator to begin()
  73         SamSequenceIterator      End(void);                 // returns iterator to end()
  74         SamSequenceConstIterator End(void) const;           // returns const_iterator to end()
  75         SamSequenceConstIterator ConstEnd(void) const;      // returns const_iterator to end()
  76
  77     // internal methods
  78     private:
  79         int IndexOf(const std::string& name) const;
  80
  81     // data members
  82     private:
  83         SamSequenceContainer m_data;
  84 };
  85
  86 } // namespace BamTools
  87
  88 #endif // SAM_SEQUENCE_DICTIONARY_H
  89