double maxDistValue;
- double maxheight;
+ double maxHeight;
int ycount;
Vector<SequenceNode> node;
+ protected ScoreModelI scoreModel;
+
+ protected SimilarityParamsI scoreParams;
+
private AlignmentView seqStrings; // redundant? (see seqData)
/**
{
if (nd == null)
{
- return maxheight;
+ return maxHeight;
}
if ((nd.left() == null) && (nd.right() == null))
{
nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
- if (nd.height > maxheight)
+ if (nd.height > maxHeight)
{
return nd.height;
}
else
{
- return maxheight;
+ return maxHeight;
}
}
else
}
else
{
- maxheight = 0;
+ maxHeight = 0;
nd.height = (float) 0.0;
}
- maxheight = findHeight((SequenceNode) (nd.left()));
- maxheight = findHeight((SequenceNode) (nd.right()));
+ maxHeight = findHeight((SequenceNode) (nd.left()));
+ maxHeight = findHeight((SequenceNode) (nd.right()));
}
- return maxheight;
+ return maxHeight;
}
/**
*/
protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)
{
- distances = sm.findDistances(seqData, scoreOptions);
+
+ this.scoreModel = sm;
+ this.scoreParams = scoreOptions;
+
+ distances = scoreModel.findDistances(seqData, scoreParams);
makeLeaves();
return distances;
}
+ public AlignmentView getSeqData()
+ {
+ return seqData;
+ }
+
}