From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Tue, 10 Oct 2017 12:41:44 +0000 (+0100)
Subject: Start of programmatically creating Aptx trees
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=833fafa77f2f63bea98ce1d6e1e4ee3e46e7bd53;p=jalview.git

Start of programmatically creating Aptx trees
---

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 414ca39..b794368 100644
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -467,6 +467,7 @@ public abstract class TreeBuilder
       sn.setElement(sequences[i]);
       sn.setName(sequences[i].getName());
       node.addElement(sn);
+
       BitSet bs = new BitSet();
       bs.set(i);
       clusters.addElement(bs);
diff --git a/src/jalview/analysis/TreeCalculator.java b/src/jalview/analysis/TreeCalculator.java
index 49c66bf..84deba2 100644
--- 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,
diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
index 07b5bb4..1b1c981 100644
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
@@ -1,15 +1,30 @@
 package jalview.ext.archaeopteryx;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
+import jalview.datamodel.SequenceI;
+import jalview.math.MatrixI;
 
 import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
 
-public class ArchaeopteryxTreeBuilder extends Phylogeny
+public class ArchaeopteryxTreeBuilder extends Phylogeny // cannot inherit
+                                                        // TreeBuilder as that
+                                                        // demands the use of
+                                                        // SequenceNode (instead
+                                                        // of PhylogenyNode)
 {
-  List<PhylogenyNode> nodes = Collections
-          .synchronizedList(new ArrayList<PhylogenyNode>());
+  protected SequenceI[] sequences;
+
+  protected MatrixI distances;
+
+  public ArchaeopteryxTreeBuilder(TreeModel treeModel)
+  {
+
+  }
+
+  public ArchaeopteryxTreeBuilder(TreeBuilder tree)
+  {
+
+  }
   
 }
diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index d0315a6..bae1808 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -481,7 +481,8 @@ public class CalculationChooser extends JPanel
       TreeModel tree = new TreeModel(calculatedTree);
       openTreePanel(tree, treeAlgo, substitutionMatrix);
 
-      ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder();
+      ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder(
+              tree);
 
 
     }
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 67ac836..5fab37f 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -86,6 +86,8 @@ public class TreePanel extends GTreePanel
    * 
    * @param ap
    * @param tree
+   * @param treeType
+   * @param substitutionMatrix
    */
   public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
           String substitutionMatrix)
@@ -108,7 +110,6 @@ public class TreePanel extends GTreePanel
    * @param newtree
    * @param theTitle
    * @param inputData
-   * @param viewport
    */
   public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
           String theTitle, AlignmentView inputData)