Brought API up to compliance with recent SAM Format Spec (v1.4-r962)

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

diff --git a/src/api/SamProgramChain.h b/src/api/SamProgramChain.h
new file mode 100644 (file)
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+++ b/src/api/SamProgramChain.h
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+// ***************************************************************************
+// SamProgramChain.h (c) 2011 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 19 April 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides methods for operating on a SamProgram record "chain"
+// ***************************************************************************
+
+#ifndef SAM_PROGRAMCHAIN_H
+#define SAM_PROGRAMCHAIN_H
+
+#include <api/api_global.h>
+#include <api/SamProgram.h>
+#include <string>
+#include <vector>
+
+namespace BamTools {
+
+// chain is *NOT* sorted in any order
+// use First()/Last() to retrieve oldest/newest programs, respectively
+typedef std::vector<SamProgram>             SamProgramContainer;
+typedef SamProgramContainer::iterator       SamProgramIterator;
+typedef SamProgramContainer::const_iterator SamProgramConstIterator;
+
+class API_EXPORT SamProgramChain {
+
+    // ctor & dtor
+    public:
+        SamProgramChain(void);
+        SamProgramChain(const SamProgramChain& other);
+        ~SamProgramChain(void);
+
+    // query/modify program data
+    public:
+        // appends a program record to the chain
+        void Add(SamProgram& program);
+        void Add(std::vector<SamProgram>& programs);
+
+        // clears all read group entries
+        void Clear(void);
+
+        // returns true if chain contains this program record (matches on ID)
+        bool Contains(const SamProgram& program) const;
+        bool Contains(const std::string& programId) const;
+
+        // returns the first (oldest) program in the chain
+        SamProgram& First(void);
+        const SamProgram& First(void) const;
+
+        // returns true if chain is empty
+        bool IsEmpty(void) const;
+
+        // returns last (most recent) program in the chain
+        SamProgram& Last(void);
+        const SamProgram& Last(void) const;
+
+        // returns number of program records in the chain
+        int Size(void) const;
+
+        // retrieves a modifiable reference to the SamProgram object associated with this ID
+        SamProgram& operator[](const std::string& programId);
+
+    // retrieve STL-compatible iterators
+    public:
+        SamProgramIterator      Begin(void);              // returns iterator to begin()
+        SamProgramConstIterator Begin(void) const;        // returns const_iterator to begin()
+        SamProgramConstIterator ConstBegin(void) const;   // returns const_iterator to begin()
+        SamProgramIterator      End(void);                // returns iterator to end()
+        SamProgramConstIterator End(void) const;          // returns const_iterator to end()
+        SamProgramConstIterator ConstEnd(void) const;     // returns const_iterator to end()
+
+    // internal methods
+    private:
+        int IndexOf(const std::string& programId) const;
+        const std::string NextIdFor(const std::string& programId) const;
+
+    // data members
+    private:
+        SamProgramContainer m_data;
+};
+
+} // namespace BamTools
+
+#endif // SAM_PROGRAMCHAIN_H