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root/gclib/gclib/GAlnExtend.h
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# Line 466 | Line 466
466    bool operator<(GXAlnInfo& d) {
467      return ((score==d.score)? pid>d.pid : score>d.score);
468      }
469  bool operator>(GXAlnInfo& d) {
470    return ((score==d.score)? pid<d.pid : score<d.score);
471    }
469    bool operator==(GXAlnInfo& d) {
470      return (score==d.score && pid==d.pid);
471      }
# Line 484 | Line 481
481     bool operator<(GXSeed& d){
482        return ((b_ofs==d.b_ofs) ? a_ofs<d.a_ofs : b_ofs<d.b_ofs);
483        }
487   bool operator>(GXSeed& d){
488      return ((b_ofs==d.b_ofs) ? a_ofs>d.a_ofs : b_ofs>d.b_ofs);
489      }
484     bool operator==(GXSeed& d){
485        return (b_ofs==d.b_ofs && a_ofs==d.a_ofs); //should never be the case, seeds are uniquely constructed
486        }
# Line 554 | Line 548
548          int a_gap=scur.a_ofs-sprev.a_ofs-sprev.len;
549          int max_gap=b_gap;
550          int min_gap=a_gap;
551 <        if (min_gap>max_gap) swap(max_gap, min_gap);
551 >        if (min_gap>max_gap) Gswap(max_gap, min_gap);
552          int _penalty=0;
553          if (min_gap<0) { //overlap
554                 if (max_gap>0) { _penalty=GMAX((-min_gap), max_gap); }
# Line 574 | Line 568
568       //return ((score==d.score) ? seeds.Count()>d.seeds.Count() : score>d.score);
569       return ((score==d.score) ? w_min_b<d.w_min_b : score>d.score);
570       }
577  bool operator>(GXBand& d){
578     //return ((score==d.score) ? seeds.Count()<d.seeds.Count() : score<d.score);
579    return ((score==d.score) ? w_min_b>d.w_min_b : score<d.score);
580     }
571    bool operator==(GXBand& d){
572      //return (score==d.score && seeds.Count()==d.seeds.Count());
573       return (score==d.score && w_min_b==d.w_min_b);

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