public boolean isSignificant() {

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

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

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

		return true;
	}
public boolean isSignificant ( ) { if ( numRepeats < 2 ) return false ; if ( selfAlignment . getTMScore ( ) < params . getUnrefinedScoreThreshold ( ) ) return false ; if ( params . getRefineMethod ( ) != RefineMethod . NOT_REFINED ) { if ( multipleAlignment == null || multipleAlignment . getCoreLength ( ) < params . getMinCoreLength ( ) ) return false ; if ( multipleAlignment . getScore ( MultipleAlignmentScorer . AVGTM_SCORE ) < params . getRefinedScoreThreshold ( ) ) return false ; return true ; } return true ; }
Conditions checked are: score above the threshold, number of repeats
higher than 1 and refinement succeeded.

@return true if significant, false otherwise