Пример #1
0
  /**
   * Conditions checked are: score above the threshold, order higher than 1 and refinement
   * succeeded.
   *
   * @return true if significant, false otherwise
   */
  public boolean isSignificant() {

    // In any case if the order is 1 it is asymmetric
    if (symmOrder < 2) return false;

    // If the TM-Score is below the threshold
    if (selfAlignment.getTMScore() < params.getScoreThreshold()) return false;

    // If the refinement was attempted
    if (params.getRefineMethod() != RefineMethod.NOT_REFINED) {
      // Check for minimum length
      if (multipleAlignment.getCoreLength() < params.getMinCoreLength()) return false;
      // Allow 90% of original TM-Score theshold
      if (multipleAlignment.getScore(MultipleAlignmentScorer.AVGTM_SCORE)
          < params.getScoreThreshold() * 0.9) return false;
      return true;
    }

    return true;
  }
Пример #2
0
 public void setParams(CESymmParameters params) {
   this.params = params.clone();
 }
Пример #3
0
  @Override
  public CESymmParameters clone() {

    CESymmParameters p = new CESymmParameters();

    p.maxSymmOrder = maxSymmOrder;
    p.symmType = symmType;
    p.orderDetectorMethod = orderDetectorMethod;
    p.userOrder = userOrder;
    p.refineMethod = refineMethod;
    p.optimization = optimization;
    p.rndSeed = rndSeed;
    p.symmLevels = symmLevels;
    p.unrefinedScoreThreshold = unrefinedScoreThreshold;
    p.refinedScoreThreshold = refinedScoreThreshold;
    p.sseThreshold = sseThreshold;
    p.minCoreLength = minCoreLength;
    p.distanceCutoff = distanceCutoff;
    p.gaps = gaps;
    p.optimizationSteps = optimizationSteps;

    p.winSize = winSize;
    p.rmsdThr = rmsdThr;
    p.rmsdThrJoin = rmsdThrJoin;
    p.scoringStrategy = scoringStrategy;
    p.maxGapSize = maxGapSize;
    p.showAFPRanges = showAFPRanges;
    p.maxOptRMSD = maxOptRMSD;
    p.gapOpen = gapOpen;
    p.gapExtension = gapExtension;
    p.distanceIncrement = distanceIncrement;
    p.oRmsdThr = oRmsdThr;
    p.maxNrIterationsForOptimization = maxNrIterationsForOptimization;
    p.seqWeight = seqWeight;

    return p;
  }