src/api/SamSequenceDictionary.h

   1 // ***************************************************************************
   2 // SamSequenceDictionary.h (c) 2010 Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // ---------------------------------------------------------------------------
   5 // Last modified: 18 April 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 <api/api_global.h>
  14 #include <api/SamSequence.h>
  15 #include <string>
  16 #include <map>
  17 #include <vector>
  18
  19 namespace BamTools {
  20
  21 typedef std::vector<SamSequence>             SamSequenceContainer;
  22 typedef SamSequenceContainer::iterator       SamSequenceIterator;
  23 typedef SamSequenceContainer::const_iterator SamSequenceConstIterator;
  24
  25 class API_EXPORT SamSequenceDictionary {
  26
  27     // ctor & dtor
  28     public:
  29         SamSequenceDictionary(void);
  30         SamSequenceDictionary(const SamSequenceDictionary& other);
  31         ~SamSequenceDictionary(void);
  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 std::vector<SamSequence>& sequences);
  41         void Add(const std::map<std::string, int>& sequenceMap);
  42
  43         // clears all sequence entries
  44         void Clear(void);
  45
  46         // returns true if dictionary contains this sequence
  47         bool Contains(const SamSequence& sequence) const;
  48         bool Contains(const std::string& sequenceName) const;
  49
  50         // returns true if dictionary is empty
  51         bool IsEmpty(void) const;
  52
  53         // removes sequence, if found
  54         void Remove(const SamSequence& sequence);
  55         void Remove(const std::string& sequenceName);
  56
  57         // removes multiple sequences
  58         void Remove(const std::vector<SamSequence>& sequences);
  59         void Remove(const std::vector<std::string>& sequenceNames);
  60
  61         // returns number of sequences in dictionary
  62         int Size(void) const;
  63
  64         // retrieves a modifiable reference to the SamSequence object associated with this name
  65         SamSequence& operator[](const std::string& sequenceName);
  66
  67     // retrieve STL-compatible iterators
  68     public:
  69         SamSequenceIterator      Begin(void);               // returns iterator to begin()
  70         SamSequenceConstIterator Begin(void) const;         // returns const_iterator to begin()
  71         SamSequenceConstIterator ConstBegin(void) const;    // returns const_iterator to begin()
  72         SamSequenceIterator      End(void);                 // returns iterator to end()
  73         SamSequenceConstIterator End(void) const;           // returns const_iterator to end()
  74         SamSequenceConstIterator ConstEnd(void) const;      // returns const_iterator to end()
  75
  76     // internal methods
  77     private:
  78         int IndexOf(const std::string& name) const;
  79
  80     // data members
  81     private:
  82         SamSequenceContainer m_data;
  83 };
  84
  85 } // namespace BamTools
  86
  87 #endif // SAM_SEQUENCE_DICTIONARY_H
  88