ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
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 User Rev File contents
1 gpertea 16 #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