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root/gclib/gclib/AceParser.h
Revision: 16
Committed: Mon Jul 18 20:56:02 2011 UTC (8 years, 3 months ago) by gpertea
File size: 876 byte(s)
Log Message:
sync with local source

Line File contents
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