GenericSamInterface.h

/*
 *  Copyright (C) 2010  Regents of the University of Michigan
 *
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
#ifndef __GENERIC_SAM_INTERFACE_H__
#define __GENERIC_SAM_INTERFACE_H__
 
#include "SamStatus.h"
#include "InputFile.h"
#include "SamFileHeader.h"
#include "SamRecord.h"
 
class GenericSamInterface
{
public:
    GenericSamInterface();
    virtual ~GenericSamInterface();
   
    // Pure virtual method that reads the header section from the specified file
    // and stores it in the passed in header, returns false and sets the status
    // on failure.
    // Will be implemented specifically for sam/bam files.
    virtual bool readHeader(IFILE filePtr, SamFileHeader& header,
                            SamStatus& status) = 0;
 
    // Pure virtual method that writes the specified header into the specified
    // file, returns false and sets the status on failure.
    // Will be implemented specifically for sam/bam files.
    virtual bool writeHeader(IFILE filePtr, SamFileHeader& header,
                             SamStatus& status) = 0;
 
    // Pure virtual method that reads the next record from the specified file 
    // and stores it in the passed in record.
    // Will be implemented specifically for sam/bam files.
    // TODO On error, a more detailed message is appended to statusMsg.
    virtual void readRecord(IFILE filePtr, SamFileHeader& header, 
                            SamRecord& record, 
                            SamStatus& samStatus) = 0;
   
    // Pure virtual method that writes the specified record into the specified
    // file.
    // Will be implemented specifically for sam/bam files.
    virtual SamStatus::Status writeRecord(IFILE filePtr, SamFileHeader& header,
                                          SamRecord& record,
                                          SamRecord::SequenceTranslation translation) = 0;
 
    virtual bool isEOF(IFILE filePtr);
};
 
#endif