ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/gclib/gclib/GAlnExtend.h
(Generate patch)
# Line 5 | Line 5
5  
6   #include "GBase.h"
7   #include "GList.hh"
8 < #include <string.h>
8 > #include "gdna.h"
9  
10   //#define GDEBUG 1
11  
# Line 98 | Line 98
98  
99          if (GX_EDITOP_GET(oplast) == op) {
100              uint32 l=ops[opnum-1];
101 <            ops[opnum-1]=GX_EDITOP_CONS((GX_EDITOP_GET(l)),
101 >            ops[opnum-1]=GX_EDITOP_CONS((GX_EDITOP_GET(l)),
102                 (GX_EDITOP_VAL(l) + k));
103              }
104          else {
# Line 346 | Line 346
346         a_len=0;
347             b_len=0;
348             if (ed_script==NULL) return;
349 <           for (uint32 i=0; i<ed_script->opnum; i++) {
349 >           for (uint32 i=0; i<ed_script->opnum; i++) {
350                    int num=((ed_script->ops[i]) >> 2);
351                    char op_type = 3 - ( ed_script->ops[i] & gxEDIT_OP_MASK );
352                    if (op_type == 3 || op_type < 0 )
# Line 371 | Line 371
371             }
372  
373   #ifdef GDEBUG
374 <        void printAlignment(FILE* f, const char* sa, int sa_len,
374 >        void printAlignment(FILE* f, const char* sa, int sa_len,
375                       const char* sb, int sb_len) {
376                  //print seq A
377             char al[1024]; //display buffer for seq A
# Line 436 | Line 436
436         }
437   #endif
438    };
439 <  
439 >
440   struct GXAlnInfo {
441   const char *qseq;
442   int ql,qr;
# Line 613 | Line 613
613   };
614  
615  
616 < GXBandSet* collectSeeds_R(GList<GXSeed>& seeds, const char* seqa, int a_len, const char* seqb, int b_len); //for overlap at 3' end of seqb
616 > uint16 get6mer(char* p);
617 > void table6mers(const char* s, int slen, GVec<uint16>* amers[]);
618 >
619 > GXBandSet* collectSeeds_R(GList<GXSeed>& seeds, const char* seqa, int a_len, GVec<uint16>* amers[],
620 >         const char* seqb, int b_len); //for overlap at 3' end of seqb
621  
622 < GXBandSet* collectSeeds_L(GList<GXSeed>& seeds, const char* seqa, int a_len, const char* seqb, int b_len); //for overlap at 5' end of seqb
622 > GXBandSet* collectSeeds_L(GList<GXSeed>& seeds, const char* seqa, int a_len, GVec<uint16>* amers[],
623 >        const char* seqb, int b_len); //for overlap at 5' end of seqb
624  
625   void printEditScript(GXEditScript* ed_script);
626  
# Line 713 | Line 718
718   GXAlnInfo* GreedyAlign(const char* q_seq,  int q_alnstart, const char* s_seq, int s_alnstart,
719          bool editscript=false, int reward=2, int penalty=3, int xdrop=8);
720  
721 < GXAlnInfo* match_LeftEnd(const char* seqa, int seqa_len, const char* seqb, int seqb_len,
722 <          CGreedyAlignData* gxmem=NULL, int min_pid=83);
723 < GXAlnInfo* match_RightEnd(const char* seqa, int seqa_len, const char* seqb, int seqb_len,
724 <          CGreedyAlignData* gxmem=NULL, int min_pid=73);
721 > GXAlnInfo* match_LeftEnd(const char* seqa, int seqa_len, GVec<uint16>* amers[],
722 >           const char* seqb, int seqb_len, CGreedyAlignData* gxmem=NULL, int min_pid=83);
723 > GXAlnInfo* match_RightEnd(const char* seqa, int seqa_len, GVec<uint16>* amers[],
724 >           const char* seqb, int seqb_len, CGreedyAlignData* gxmem=NULL, int min_pid=73);
725   #endif

Diff Legend

Removed lines
+ Added lines
< Changed lines
> Changed lines