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 |