/**
* 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;
}
public void setParams(CESymmParameters params) {
this.params = params.clone();
}
@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;
}