/usr/include/kmer/seq/seqFile.H is in libkmer-dev 0~20150903+r2013-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 | #ifndef SEQFILE_H
#define SEQFILE_H
#include "util.h"
// General flow of the constructors is:
// Clear all data
// Open the file
// Set _filename, _typename
// Read/build the index structure
// Position the file to the first read
// Set _numberOfSequences (IMPORTANT, and subtle)
class seqFile {
protected:
seqFile(const char *filename) {};
seqFile() {};
public:
virtual ~seqFile() {};
protected:
virtual seqFile *openFile(const char *filename) = 0;
public:
virtual const char *getSourceName(void) { return(_filename); };
virtual const char *getFileTypeName(void) { return(_typename); };
virtual bool randomAccessSupported(void) { return(_randomAccessSupported); };
virtual uint32 getNumberOfSequences(void) { return(_numberOfSequences); };
public:
virtual uint32 find(const char *sequencename) = 0;
virtual uint32 getSequenceLength(uint32 id) = 0;
virtual bool getSequence(uint32 id,
char *&h, uint32 &hLen, uint32 &hMax,
char *&s, uint32 &sLen, uint32 &sMax) = 0;
virtual bool getSequence(uint32 iid,
uint32 bgn, uint32 end, char *s) = 0;
protected:
char _filename[FILENAME_MAX];
char _typename[FILENAME_MAX];
bool _randomAccessSupported;
uint32 _numberOfSequences;
friend class seqFactory;
};
#endif // SEQFILE_H
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