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forester as submodule with InternalFrame + start of distance conversion
[jalview.git]
/
src
/
jalview
/
analysis
/
TreeCalculator.java
diff --git
a/src/jalview/analysis/TreeCalculator.java
b/src/jalview/analysis/TreeCalculator.java
index
49c66bf
..
84deba2
100644
(file)
--- a/
src/jalview/analysis/TreeCalculator.java
+++ b/
src/jalview/analysis/TreeCalculator.java
@@
-36,11
+36,12
@@
public class TreeCalculator extends Thread// add threading
String treeType;
String scoreModelName; // if tree computed
String treeType;
String scoreModelName; // if tree computed
+
/**
*
* @param treeAlgo
* @param substitutionMatrix
/**
*
* @param treeAlgo
* @param substitutionMatrix
- * @param params
+ * @param calculateParams
*/
public TreeCalculator(String treeAlgo, String substitutionMatrix,
SimilarityParamsI calculateParams)
*/
public TreeCalculator(String treeAlgo, String substitutionMatrix,
SimilarityParamsI calculateParams)
@@
-50,6
+51,11
@@
public class TreeCalculator extends Thread// add threading
this.similarityParams = calculateParams;
}
this.similarityParams = calculateParams;
}
+ /**
+ *
+ * @param alignViewport
+ * @return
+ */
public TreeBuilder makeTree(AlignViewport alignViewport)
{
ScoreModelI sm = ScoreModels.getInstance().getScoreModel(scoreModelName,
public TreeBuilder makeTree(AlignViewport alignViewport)
{
ScoreModelI sm = ScoreModels.getInstance().getScoreModel(scoreModelName,