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root/gclib/gclib/GAlnExtend.cpp
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# Line 5 | Line 5
5  
6   int GXMemPool::kMinSpace = 1000000;
7  
8 < #ifdef GDEBUG
8 > #ifdef TRIMDEBUG
9   char buf[6]={0x1B,'[', 'n','m','m','\0'};
10  
11   void color_fg(int c,FILE* f) {
# Line 899 | Line 899
899      alninfo->score=retscore;
900      if (gxmem->scaled) alninfo->score >>= 1;
901      alninfo->pid = 100 * (1 - ((double) numdiffs) / hsp_length);
902 < #ifdef GDEBUG
902 > #ifdef TRIMDEBUG
903      //if (ed_script_rev) {
904      //   GMessage("Final Edit script ::: ");
905      //   printEditScript(ed_script_rev);
# Line 937 | Line 937
937   GXAlnInfo* match_adaptor(GXSeqData& sd, GAlnTrimType trim_type, int minMatch,
938                                       CGreedyAlignData* gxmem, int min_pid) {
939    bool editscript=false;
940 <  #ifdef GDEBUG
940 >  #ifdef TRIMDEBUG
941     editscript=true;
942     if (trim_type==galn_TrimLeft) {
943           GMessage("=======> searching left (5') end : %s\n", sd.aseq);
# Line 955 | Line 955
955    GList<GXSeed> anchor_seeds(cmpSeedDiag, NULL, true); //stores unique seeds per diagonal
956    //did we find a shortcut?
957    if (alnbands->qmatch) {
958 <    #ifdef GDEBUG
958 >    #ifdef TRIMDEBUG
959       GMessage("::: Found a quick long match at %d, len %d\n",
960            alnbands->qmatch->b_ofs, alnbands->qmatch->len);
961      #endif
# Line 966 | Line 966
966      int top_band_count=0;
967      for (int b=0;b<alnbands->Count();b++) {
968         if (alnbands->Get(b)->score<6) break;
969 <       //#ifdef GDEBUG
969 >       //#ifdef TRIMDEBUG
970         //GMessage("\tBand %d score: %d\n", b, alnbands->Get(b)->score);
971         //#endif
972         top_band_count++;
# Line 976 | Line 976
976         //band.tested=true;
977         if (anchor_seeds.Count()>2 || top_band_count>max_top_bands) break;
978         }
979 <    //#ifdef GDEBUG
979 >    //#ifdef TRIMDEBUG
980      //GMessage("::: Collected %d anchor seeds.\n",anchor_seeds.Count());
981      //#endif
982      }
# Line 986 | Line 986
986      int a1=aseed.a_ofs+(aseed.len>>1)+1;
987      int a2=aseed.b_ofs+(aseed.len>>1)+1;
988      trimInfo.seedlen=aseed.len;
989 < #ifdef GDEBUG
989 > #ifdef TRIMDEBUG
990      GMessage("\t::: align from seed (%d, %d)of len %d.\n",aseed.a_ofs, aseed.b_ofs,
991             aseed.len);
992   #endif
# Line 1014 | Line 1014
1014                  int a1=aseed.a_ofs+halfseed+1;
1015                  int a2=aseed.b_ofs+halfseed+1;
1016                  trimInfo.seedlen=aseed.len;
1017 < #ifdef GDEBUG
1017 > #ifdef TRIMDEBUG
1018      GMessage("\t::: align from terminal seed (%d, %d)of len %d.\n",aseed.a_ofs, aseed.b_ofs,
1019             aseed.len);
1020   #endif
# Line 1028 | Line 1028
1028    //---- found all alignments
1029    delete alnbands;
1030    /*
1031 <  #ifdef GDEBUG
1031 >  #ifdef TRIMDEBUG
1032    //print all valid alignments found
1033    for (int i=0;i<galns.Count();i++) {
1034      GXAlnInfo* alninfo=galns[i];
# Line 1043 | Line 1043
1043    */
1044    if (galns.Count()) {
1045      GXAlnInfo* bestaln=galns.Shift();
1046 <    #ifdef GDEBUG
1046 >    #ifdef TRIMDEBUG
1047        GMessage("Best alignment: a(%d..%d) align to b(%d..%d), score=%d, pid=%4.2f\n", bestaln->ql, bestaln->qr,
1048            bestaln->sl, bestaln->sr, bestaln->score, bestaln->pid);
1049        if (bestaln->gapinfo!=NULL) {

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