Added SAM header-handling classes for read/write/validate.

[bamtools.git] / src / api / SamSequenceDictionary.h

diff --git a/src/api/SamSequenceDictionary.h b/src/api/SamSequenceDictionary.h
new file mode 100644 (file)
index 0000000..bcd1652
--- /dev/null
+++ b/src/api/SamSequenceDictionary.h
@@ -0,0 +1,94 @@
+// ***************************************************************************
+// SamSequenceDictionary.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 23 December 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides container operations for collection of sequence entries
+// *************************************************************************
+
+#ifndef SAM_SEQUENCE_DICTIONARY_H
+#define SAM_SEQUENCE_DICTIONARY_H
+
+#include <api/api_global.h>
+#include <api/SamSequence.h>
+#include <string>
+#include <vector>
+
+namespace BamTools {
+
+typedef std::vector<SamSequence>             SamSequenceContainer;
+typedef SamSequenceContainer::iterator       SamSequenceIterator;
+typedef SamSequenceContainer::const_iterator SamSequenceConstIterator;
+
+class API_EXPORT SamSequenceDictionary {
+
+    // ctor & dtor
+    public:
+        SamSequenceDictionary(void);
+        ~SamSequenceDictionary(void);
+
+    // query/modify sequence data
+    public:
+        // add a sequence
+        void Add(const SamSequence& sequence);
+        void Add(const std::string& sequenceNames);
+
+        // add multiple sequences
+        void Add(const std::vector<SamSequence>& sequences);
+        void Add(const std::vector<std::string>& sequenceNames);
+
+        // clear all sequence records
+        void Clear(void);
+
+        // returns true if dictionary contains this sequence
+        bool Contains(const SamSequence& sequence) const;
+        bool Contains(const std::string& sequenceName) const;
+
+        // returns true if dictionary is empty
+        bool IsEmpty(void) const;
+
+        // remove a single sequence (does nothing if sequence not found)
+        void Remove(const SamSequence& sequence);
+        void Remove(const std::string& sequenceName);
+
+        // remove multiple sequences
+        void Remove(const std::vector<SamSequence>& sequences);
+        void Remove(const std::vector<std::string>& sequenceNames);
+
+        // returns size of dictionary (number of current elements)
+        int Size(void) const;
+
+        // retrieves the SamSequence object associated with this name
+        // if sequenceName is unknown, a new SamSequence is created with this name (and invalid length 0)
+        // and a reference to this new sequence entry is returned (like std::map)
+        //
+        // * To avoid these partial entries being created, it is recommended to check
+        //   for existence first using Contains()
+        SamSequence& operator[](const std::string& sequenceName);
+
+    // retrieve sequence iterators
+    // these are typedefs for STL iterators and thus are compatible with STL containers/algorithms
+    public:
+        SamSequenceIterator      Begin(void);
+        SamSequenceConstIterator Begin(void) const;
+        SamSequenceConstIterator ConstBegin(void) const;
+        SamSequenceIterator      End(void);
+        SamSequenceConstIterator End(void) const;
+        SamSequenceConstIterator ConstEnd(void) const;
+
+    // internal methods
+    private:
+        int IndexOf(const SamSequence& sequence) const;
+        int IndexOf(const std::string& sequenceName) const;
+
+    // data members
+    private:
+        SamSequenceContainer m_data;
+};
+
+} // namespace BamTools
+
+#endif // SAM_SEQUENCE_DICTIONARY 
+