00001 /* 00002 * Copyright (C) 2010 Regents of the University of Michigan 00003 * 00004 * This program is free software: you can redistribute it and/or modify 00005 * it under the terms of the GNU General Public License as published by 00006 * the Free Software Foundation, either version 3 of the License, or 00007 * (at your option) any later version. 00008 * 00009 * This program is distributed in the hope that it will be useful, 00010 * but WITHOUT ANY WARRANTY; without even the implied warranty of 00011 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00012 * GNU General Public License for more details. 00013 * 00014 * You should have received a copy of the GNU General Public License 00015 * along with this program. If not, see <http://www.gnu.org/licenses/>. 00016 */ 00017 00018 #ifndef __GENERIC_SAM_INTERFACE_H__ 00019 #define __GENERIC_SAM_INTERFACE_H__ 00020 00021 #include "SamStatus.h" 00022 #include "InputFile.h" 00023 #include "SamFileHeader.h" 00024 #include "SamRecord.h" 00025 00026 class GenericSamInterface 00027 { 00028 public: 00029 GenericSamInterface(); 00030 virtual ~GenericSamInterface(); 00031 00032 // Pure virtual method that reads the header section from the specified file 00033 // and stores it in the passed in header. 00034 // Will be implemented specifically for sam/bam files. 00035 virtual SamStatus::Status readHeader(IFILE filePtr, 00036 SamFileHeader& header) = 0; 00037 00038 // Pure virtual method that writes the specified header into the specified 00039 // file. 00040 // Will be implemented specifically for sam/bam files. 00041 virtual SamStatus::Status writeHeader(IFILE filePtr, 00042 SamFileHeader& header) = 0; 00043 00044 // Pure virtual method that reads the next record from the specified file 00045 // and stores it in the passed in record. 00046 // Will be implemented specifically for sam/bam files. 00047 // TODO On error, a more detailed message is appended to statusMsg. 00048 virtual void readRecord(IFILE filePtr, SamFileHeader& header, 00049 SamRecord& record, 00050 SamStatus& samStatus) = 0; 00051 00052 // Pure virtual method that writes the specified record into the specified 00053 // file. 00054 // Will be implemented specifically for sam/bam files. 00055 virtual SamStatus::Status writeRecord(IFILE filePtr, SamFileHeader& header, 00056 SamRecord& record, 00057 SamRecord::SequenceTranslation translation) = 0; 00058 00059 }; 00060 00061 #endif
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