protected SimilarityParamsI scoreParams;
+ private AlignmentViewport avport;
+
private AlignmentView seqStrings; // redundant? (see seqData)
/**
SimilarityParamsI scoreParameters)
{
int start, end;
+ avport = av;
boolean selview = av.getSelectionGroup() != null
&& av.getSelectionGroup().getSize() > 1;
seqStrings = av.getAlignmentView(selview);
return distances;
}
- public AlignmentView getSeqData()
+ public ScoreModelI getScoreModel()
+ {
+ return scoreModel;
+ }
+
+ public SimilarityParamsI getScoreParams()
+ {
+ return scoreParams;
+ }
+
+ public AlignmentViewport getAvport()
{
- return seqData;
+ return avport;
}
}