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JAL-2844 line drawing at mouse click added on top of Aptx
[jalview.git]
/
src
/
jalview
/
analysis
/
TreeBuilder.java
diff --git
a/src/jalview/analysis/TreeBuilder.java
b/src/jalview/analysis/TreeBuilder.java
index
b794368
..
c4a94eb
100644
(file)
--- a/
src/jalview/analysis/TreeBuilder.java
+++ b/
src/jalview/analysis/TreeBuilder.java
@@
-67,13
+67,19
@@
public abstract class TreeBuilder
double maxDistValue;
double maxDistValue;
- double maxheight;
+ double maxHeight;
int ycount;
Vector<SequenceNode> node;
int ycount;
Vector<SequenceNode> node;
- private AlignmentView seqStrings;
+ protected ScoreModelI scoreModel;
+
+ protected SimilarityParamsI scoreParams;
+
+ private AlignmentViewport avport;
+
+ private AlignmentView seqStrings; // redundant? (see seqData)
/**
* Constructor
/**
* Constructor
@@
-86,6
+92,7
@@
public abstract class TreeBuilder
SimilarityParamsI scoreParameters)
{
int start, end;
SimilarityParamsI scoreParameters)
{
int start, end;
+ avport = av;
boolean selview = av.getSelectionGroup() != null
&& av.getSelectionGroup().getSize() > 1;
seqStrings = av.getAlignmentView(selview);
boolean selview = av.getSelectionGroup() != null
&& av.getSelectionGroup().getSize() > 1;
seqStrings = av.getAlignmentView(selview);
@@
-125,20
+132,20
@@
public abstract class TreeBuilder
{
if (nd == null)
{
{
if (nd == null)
{
- return maxheight;
+ return maxHeight;
}
if ((nd.left() == null) && (nd.right() == null))
{
nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
}
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 nd.height;
}
else
{
- return maxheight;
+ return maxHeight;
}
}
else
}
}
else
@@
-149,15
+156,15
@@
public abstract class TreeBuilder
}
else
{
}
else
{
- maxheight = 0;
+ maxHeight = 0;
nd.height = (float) 0.0;
}
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;
}
/**
}
/**
@@
-295,7
+302,11
@@
public abstract class TreeBuilder
*/
protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)
{
*/
protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)
{
- distances = sm.findDistances(seqData, scoreOptions);
+
+ this.scoreModel = sm;
+ this.scoreParams = scoreOptions;
+
+ distances = scoreModel.findDistances(seqData, scoreParams);
makeLeaves();
makeLeaves();
@@
-479,4
+490,24
@@
public abstract class TreeBuilder
return seqStrings;
}
return seqStrings;
}
+ public MatrixI getDistances()
+ {
+ return distances;
+ }
+
+ public ScoreModelI getScoreModel()
+ {
+ return scoreModel;
+ }
+
+ public SimilarityParamsI getScoreParams()
+ {
+ return scoreParams;
+ }
+
+ public AlignmentViewport getAvport()
+ {
+ return avport;
+ }
+
}
}