Tests for Aptx tree created from a Phylogeny object added

[jalview.git] / src / jalview / analysis / TreeCalculator.java

diff --git a/src/jalview/analysis/TreeCalculator.java b/src/jalview/analysis/TreeCalculator.java
index 7ccee92..84deba2 100644 (file)
--- a/src/jalview/analysis/TreeCalculator.java
+++ b/src/jalview/analysis/TreeCalculator.java
@@ -20,27 +20,86 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
+import jalview.gui.AlignViewport;
 
 /**
  * @author kjvanderheide
  *
  */
-public class TreeCalculator
+public class TreeCalculator extends Thread// add threading
 {
+  SimilarityParamsI similarityParams;
+
+  String treeType;
+
+  String scoreModelName; // if tree computed
 
   /**
    * 
    * @param treeAlgo
    * @param substitutionMatrix
-   * @param params
+   * @param calculateParams
    */
   public TreeCalculator(String treeAlgo, String substitutionMatrix,
           SimilarityParamsI calculateParams)
   {
-    // TODO Auto-generated constructor stub
+    this.treeType = treeAlgo;
+    this.scoreModelName = substitutionMatrix;
+    this.similarityParams = calculateParams;
+  }
+
+  /**
+   * 
+   * @param alignViewport
+   * @return
+   */
+  public TreeBuilder makeTree(AlignViewport alignViewport)
+  {
+    ScoreModelI sm = ScoreModels.getInstance().getScoreModel(scoreModelName,
+            alignViewport.getAlignPanel());
+
+    TreeBuilder builtTree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
+            ? new NJTree(alignViewport, sm, similarityParams)
+            : new AverageDistanceTree(alignViewport, sm, similarityParams);
+
+    return builtTree;
+
+  }
+
+  public SimilarityParamsI getSimilarityParams()
+  {
+    return similarityParams;
+  }
+
+  public void setSimilarityParams(SimilarityParamsI similarityParams)
+  {
+    this.similarityParams = similarityParams;
+  }
+
+  public String getTreeType()
+  {
+    return treeType;
+  }
+
+  public void setTreeType(String treeType)
+  {
+    this.treeType = treeType;
   }
 
+  public String getScoreModelName()
+  {
+    return scoreModelName;
+  }
+
+  public void setScoreModelName(String scoreModelName)
+  {
+    this.scoreModelName = scoreModelName;
+  }
+
+
 
 
 }