SamProgramChain.h

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// ***************************************************************************
// SamProgramChain.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 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