/usr/include/kmer/seq/fastaStdin.H is in libkmer-dev 0~20150903+r2013-3.
This file is owned by root:root, with mode 0o644.
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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 55 56 | #ifndef FASTASTDIN_H
#define FASTASTDIN_H
#include "util++.H"
#include "bio++.H"
#include "seqFile.H"
class fastaStdin : public seqFile {
protected:
fastaStdin(const char *filename);
fastaStdin();
public:
~fastaStdin();
protected:
seqFile *openFile(const char *filename);
public:
uint32 getNumberOfSequences(void);
public:
uint32 find(const char *sequencename);
uint32 getSequenceLength(uint32 iid);
bool getSequence(uint32 iid,
char *&h, uint32 &hLen, uint32 &hMax,
char *&s, uint32 &sLen, uint32 &sMax);
bool getSequence(uint32 iid,
uint32 bgn, uint32 end, char *s);
private:
void clear(void);
bool loadNextSequence(char *&h, uint32 &hLen, uint32 &hMax,
char *&s, uint32 &sLen, uint32 &sMax);
readBuffer *_rb;
uint32 _nextIID;
FILE *_pipe;
char *_header;
uint32 _headerLen;
uint32 _headerMax;
char *_sequence;
uint32 _sequenceLen;
uint32 _sequenceMax;
friend class seqFactory;
};
#endif // FASTASTDIN_H
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