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JAL-2428 pass AlignmentView to TreeModel so Show Input Data works
[jalview.git]
/
src
/
jalview
/
analysis
/
TreeBuilder.java
diff --git
a/src/jalview/analysis/TreeBuilder.java
b/src/jalview/analysis/TreeBuilder.java
index
f28c6bc
..
5347ba2
100644
(file)
--- a/
src/jalview/analysis/TreeBuilder.java
+++ b/
src/jalview/analysis/TreeBuilder.java
@@
-55,6
+55,8
@@
public abstract class TreeBuilder
Vector<SequenceNode> node;
Vector<SequenceNode> node;
+ private AlignmentView seqStrings;
+
/**
* Constructor
*
/**
* Constructor
*
@@
-68,7
+70,7
@@
public abstract class TreeBuilder
int start, end;
boolean selview = av.getSelectionGroup() != null
&& av.getSelectionGroup().getSize() > 1;
int start, end;
boolean selview = av.getSelectionGroup() != null
&& av.getSelectionGroup().getSize() > 1;
- AlignmentView seqStrings = av.getAlignmentView(selview);
+ seqStrings = av.getAlignmentView(selview);
if (!selview)
{
start = 0;
if (!selview)
{
start = 0;
@@
-277,6
+279,7
@@
public abstract class TreeBuilder
{
/*
* compute similarity and invert it to give a distance measure
{
/*
* compute similarity and invert it to give a distance measure
+ * reverseRange(true) converts maximum similarity to zero distance
*/
MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
seqData, scoreOptions);
*/
MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
seqData, scoreOptions);
@@
-458,4
+461,9
@@
public abstract class TreeBuilder
}
}
}
}
+ public AlignmentView getOriginalData()
+ {
+ return seqStrings;
+ }
+
}
}