gclib/gclib/AceParser.h

#ifndef ACEPARSER_H
#define ACEPARSER_H
#include "LayoutParser.h"

class AceParser : public LayoutParser {
 protected:
  virtual LytSeqInfo* addSeq(char* s, LytCtgData* ctg);
  char* readSeq(LytSeqInfo* seqinfo=NULL); //assumes the next line is just sequence data
                   //reads everything until after the next empty line

 public:
  AceParser(const char* filename):LayoutParser(filename) {}
  virtual bool open();
  virtual bool parse(fnLytSeq* seqfn=NULL); //load all the file offsets
  virtual bool parseContigs(); //load contigs' file offsets
  virtual bool loadContig(int ctgidx, fnLytSeq* seqfn=NULL,
                     bool re_pos=true); //for loading by browsing
  //sequence loading - only by request
  virtual char getFileType() { return 'A'; }
  virtual char* getSeq(LytSeqInfo* seqinfo);
  virtual char* getContigSeq(LytCtgData* ctgdata);
};

#endif
Revision:	16
Committed:	Mon Jul 18 20:56:02 2011 UTC (13 years, 1 month 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