package jalview.analysis;
import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.DistanceScoreModelI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityScoreModelI;
{
this.sequence = sqs;
this.node = new Vector<SequenceNode>();
+ if (!(treeType.equals(NEIGHBOUR_JOINING)))
+ {
+ treeType = AVERAGE_DISTANCE;
+ }
this.type = treeType;
this.pwtype = modelType;
if (seqView != null)
sdata.addOperation(CigarArray.M, end - start + 1);
this.seqData = new AlignmentView(sdata, start);
}
- // System.err.println("Made seqData");// dbg
- if (!(treeType.equals(NEIGHBOUR_JOINING)))
- {
- treeType = AVERAGE_DISTANCE;
- }
if (sm == null && !(modelType.equals("PID")))
{
noseqs = i++;
+ // TODO pass choice of params from GUI in constructo
if (sm instanceof DistanceScoreModelI)
{
- distance = ((DistanceScoreModelI) sm).findDistances(seqData);
+ distance = ((DistanceScoreModelI) sm).findDistances(seqData,
+ SimilarityParams.Jalview);
}
else if (sm instanceof SimilarityScoreModelI)
{
/*
* compute similarity and invert it to give a distance measure
*/
- MatrixI result = ((SimilarityScoreModelI) sm)
- .findSimilarities(seqData);
+ MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
+ seqData, SimilarityParams.Jalview);
result.reverseRange(true);
distance = result;
}