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
+
   /**
    * 
    * @param treeAlgo
    * @param substitutionMatrix
-   * @param params
+   * @param calculateParams
    */
   public TreeCalculator(String treeAlgo, String substitutionMatrix,
           SimilarityParamsI calculateParams)
@@ -50,6 +51,11 @@ public class TreeCalculator extends Thread// add threading
     this.similarityParams = calculateParams;
   }
 
+  /**
+   * 
+   * @param alignViewport
+   * @return
+   */
   public TreeBuilder makeTree(AlignViewport alignViewport)
   {
     ScoreModelI sm = ScoreModels.getInstance().getScoreModel(scoreModelName,