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root/gclib/gclib/AceParser.h
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# Line 1 | Line 1
1 < #ifndef ACEPARSER_H
2 < #define ACEPARSER_H
3 < #include "LayoutParser.h"
4 <
5 < class AceParser : public LayoutParser {
6 < protected:
7 <  virtual LytSeqInfo* addSeq(char* s, LytCtgData* ctg);
8 <  char* readSeq(LytSeqInfo* seqinfo=NULL); //assumes the next line is just sequence data
9 <                   //reads everything until after the next empty line
10 <
11 < public:
12 <  AceParser(const char* filename):LayoutParser(filename) {}
13 <  virtual bool open();
14 <  virtual bool parse(fnLytSeq* seqfn=NULL); //load all the file offsets
15 <  virtual bool parseContigs(); //load contigs' file offsets
16 <  virtual bool loadContig(int ctgidx, fnLytSeq* seqfn=NULL,
17 <                     bool re_pos=true); //for loading by browsing
18 <  //sequence loading - only by request
19 <  virtual char getFileType() { return 'A'; }
20 <  virtual char* getSeq(LytSeqInfo* seqinfo);
21 <  virtual char* getContigSeq(LytCtgData* ctgdata);
22 < };
23 <
24 < #endif
1 > #ifndef ACEPARSER_H
2 > #define ACEPARSER_H
3 > #include "LayoutParser.h"
4 >
5 > class AceParser : public LayoutParser {
6 > protected:
7 >  virtual LytSeqInfo* addSeq(char* s, LytCtgData* ctg);
8 >  char* readSeq(LytSeqInfo* seqinfo=NULL); //assumes the next line is just sequence data
9 >                   //reads everything until after the next empty line
10 >
11 > public:
12 >  AceParser(const char* filename):LayoutParser(filename) {}
13 >  virtual bool open();
14 >  virtual bool parse(fnLytSeq* seqfn=NULL); //load all the file offsets
15 >  virtual bool parseContigs(); //load contigs' file offsets
16 >  virtual bool loadContig(int ctgidx, fnLytSeq* seqfn=NULL,
17 >                     bool re_pos=true); //for loading by browsing
18 >  //sequence loading - only by request
19 >  virtual char getFileType() { return 'A'; }
20 >  virtual char* getSeq(LytSeqInfo* seqinfo);
21 >  virtual char* getContigSeq(LytCtgData* ctgdata);
22 > };
23 >
24 > #endif

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