* matchOnShortestSequence = false
* matchGaps = true except false for PCA by PID (to match SeqSpace)
*/
+ boolean includeGapGap = true;
+ boolean includeGapResidue = true;
+ boolean matchOnShortestLength = false;
boolean matchGap = true;
if (doPCA && (sm instanceof PIDModel))
{
matchGap = false;
}
- return new SimilarityParams(true, matchGap, true, false);
+ return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength);
}
/**