public static void compute(double minScore,double topPercent,double maxExpected,float minPercentIdentity,IReadBlock readBlock,String classificationName,BitSet activeMatchesForClassification){
  activeMatchesForClassification.clear();
  for (int i=0; i < readBlock.getNumberOfAvailableMatchBlocks(); i++) {
    final IMatchBlock matchBlock=readBlock.getMatchBlock(i);
    if (!matchBlock.isIgnore() && matchBlock.getBitScore() >= minScore && matchBlock.getExpected() <= maxExpected && matchBlock.getPercentIdentity() >= minPercentIdentity) {
      if (matchBlock.getId(classificationName) > 0)       activeMatchesForClassification.set(i);
    }
  }
  float bestScore=0;
  for (int i=activeMatchesForClassification.nextSetBit(0); i != -1; i=activeMatchesForClassification.nextSetBit(i + 1)) {
    final IMatchBlock matchBlock=readBlock.getMatchBlock(i);
    float score=matchBlock.getBitScore();
    if (score > bestScore)     bestScore=score;
  }
  applyTopPercentFilter(topPercent,bestScore,minPercentIdentity,readBlock,activeMatchesForClassification);
}

public static void compute ( double minScore , double topPercent , double maxExpected , float minPercentIdentity , IReadBlock readBlock , String classificationName , BitSet activeMatchesForClassification ) { activeMatchesForClassification . clear ( ) ; for ( int i = 0 ; i < readBlock . getNumberOfAvailableMatchBlocks ( ) ; i ++ ) { final IMatchBlock matchBlock = readBlock . getMatchBlock ( i ) ; if ( ! matchBlock . isIgnore ( ) && matchBlock . getBitScore ( ) >= minScore && matchBlock . getExpected ( ) <= maxExpected && matchBlock . getPercentIdentity ( ) >= minPercentIdentity ) { if ( matchBlock . getId ( classificationName ) > 0 ) activeMatchesForClassification . set ( i ) ; } } float bestScore = 0 ; for ( int i = activeMatchesForClassification . nextSetBit ( 0 ) ; i != - 1 ; i = activeMatchesForClassification . nextSetBit ( i + 1 ) ) { final IMatchBlock matchBlock = readBlock . getMatchBlock ( i ) ; float score = matchBlock . getBitScore ( ) ; if ( score > bestScore ) bestScore = score ; } applyTopPercentFilter ( topPercent , bestScore , minPercentIdentity , readBlock , activeMatchesForClassification ) ; }
get the set of matches active for the given read
