Merge branch 'kjvdh/features/PhylogenyViewer' of

[jalview.git] / src / jalview / gui / TreePanel.java

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 366b97f..e8f78d8 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -21,13 +21,7 @@
 package jalview.gui;
 
 import jalview.analysis.AlignmentSorter;
-import jalview.analysis.AverageDistanceTree;
-import jalview.analysis.NJTree;
-import jalview.analysis.TreeBuilder;
 import jalview.analysis.TreeModel;
-import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.OrderCommand;
@@ -41,7 +35,6 @@ import jalview.datamodel.NodeTransformI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
-import jalview.ext.archaeopteryx.ArchaeopteryxInit;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.NewickFile;
@@ -75,14 +68,12 @@ import org.jibble.epsgraphics.EpsGraphics2D;
  */
 public class TreePanel extends GTreePanel
 {
-  String treeType;
+  String substitutionMatrix;
 
-  String scoreModelName; // if tree computed
+  String treeType;
 
   String treeTitle; // if tree loaded
 
-  SimilarityParamsI similarityParams;
-
   TreeCanvas treeCanvas;
 
   TreeModel tree;
@@ -93,28 +84,38 @@ public class TreePanel extends GTreePanel
    * Creates a new TreePanel object.
    * 
    * @param ap
-   * @param type
-   * @param modelName
-   * @param options
+   * @param tree
+   * @param treeType
+   * @param substitutionMatrix
    */
-  public TreePanel(AlignmentPanel ap, String type, String modelName,
-          SimilarityParamsI options)
+  public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
+          String substitutionMatrix)
   {
     super();
-    this.similarityParams = options;
-    initTreePanel(ap, type, modelName, null, null);
+    this.treeType = treeType;
+    this.substitutionMatrix = substitutionMatrix;
+    this.tree = tree;
+    initTreePanel(ap, tree);
 
     // We know this tree has distances. JBPNote TODO: prolly should add this as
     // a userdefined default
     // showDistances(true);
   }
 
+  /**
+   * Creates a new TreePanel object.
+   * 
+   * @param alignPanel
+   * @param newtree
+   * @param theTitle
+   * @param inputData
+   */
   public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
           String theTitle, AlignmentView inputData)
   {
     super();
     this.treeTitle = theTitle;
-    initTreePanel(alignPanel, null, null, newtree, inputData);
+    initTreePanel(alignPanel, newtree, inputData);
   }
 
   public AlignmentI getAlignment()
@@ -127,17 +128,44 @@ public class TreePanel extends GTreePanel
     return treeCanvas.av;
   }
 
-  void initTreePanel(AlignmentPanel ap, String type, String modelName,
-          NewickFile newTree, AlignmentView inputData)
+  /**
+   * Initialize a tree panel based on a calculated tree
+   * 
+   * @param ap
+   * @param tree
+   */
+  void initTreePanel(AlignmentPanel ap, TreeModel tree)
+  {
+    buildTreeCanvas(ap);
+
+    TreeLoader tl = new TreeLoader(null, null);
+    tl.start();
+
+  }
+
+  /**
+   * Initialize a tree panel based on a loaded in tree file.
+   * 
+   * @param ap
+   * @param loadedTree
+   * @param inputData
+   */
+  void initTreePanel(AlignmentPanel ap, 
+          NewickFile loadedTree, AlignmentView inputData)
   {
+    buildTreeCanvas(ap);
+
+    TreeLoader tl = new TreeLoader(loadedTree, inputData);
+    tl.start();
+  }
 
-    av = ap.av;
-    this.treeType = type;
-    this.scoreModelName = modelName;
+public void buildTreeCanvas(AlignmentPanel ap) { 
+     av = ap.av;
 
     treeCanvas = new TreeCanvas(this, ap, scrollPane);
     scrollPane.setViewportView(treeCanvas);
 
+
     PaintRefresher.Register(this, ap.av.getSequenceSetId());
 
     buildAssociatedViewMenu();
@@ -172,8 +200,7 @@ public class TreePanel extends GTreePanel
     });
 
 
-    TreeLoader tl = new TreeLoader(newTree, inputData);
-    tl.start();
+  
 
   }
 
@@ -281,22 +308,12 @@ public class TreePanel extends GTreePanel
 
 
       }
-      else
-      {
-        ScoreModelI sm = ScoreModels.getInstance()
-                .getScoreModel(scoreModelName, treeCanvas.ap);
-        TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
-                ? new NJTree(av, sm, similarityParams)
-                : new AverageDistanceTree(av, sm, similarityParams);
-        tree = new TreeModel(njtree);
-        showDistances(true);
-
-
-
-      }
-      ArchaeopteryxInit archae = new ArchaeopteryxInit(tree);
-      archae.startArchaeopteryx();
+      showTree(tree);
 
+    }
+      
+    public void showTree(TreeModel tree)
+    {
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
       treeCanvas.setTree(tree);
@@ -307,6 +324,7 @@ public class TreePanel extends GTreePanel
       {
         sortByTree_actionPerformed();
       }
+
     }
   }
 
@@ -501,7 +519,7 @@ public class TreePanel extends GTreePanel
    * @param e
    */
   @Override
-  public void sortByTree_actionPerformed()
+  public void sortByTree_actionPerformed()// modify for Aptx
   {
 
     if (treeCanvas.applyToAllViews)
@@ -563,13 +581,14 @@ public class TreePanel extends GTreePanel
 
   public CommandI sortAlignmentIn(AlignmentPanel ap)
   {
+    // TODO: move to alignment view controller
     AlignmentViewport viewport = ap.av;
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
     CommandI undo;
     undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, false);
     return undo;
   }
 
@@ -841,29 +860,31 @@ public class TreePanel extends GTreePanel
    * 
    * @return
    */
-  public String getPanelTitle()
+  public String getPanelTitle() // to be moved/fixed
   {
     if (treeTitle != null)
     {
       return treeTitle;
     }
-
-    /*
-     * i18n description of Neighbour Joining or Average Distance method
-     */
-    String treecalcnm = MessageManager
-            .getString("label.tree_calc_" + treeType.toLowerCase());
-
-    /*
-     * short score model name (long description can be too long)
-     */
-    String smn = scoreModelName;
-
-    /*
-     * put them together as <method> Using <model>
-     */
-    final String ttl = MessageManager.formatMessage("label.treecalc_title",
-            treecalcnm, smn);
-    return ttl;
+    else
+    {
+      /*
+       * i18n description of Neighbour Joining or Average Distance method
+       */
+      String treecalcnm = MessageManager
+              .getString("label.tree_calc_" + treeType.toLowerCase());
+
+      /*
+       * short score model name (long description can be too long)
+       */
+      String smn = substitutionMatrix;
+
+      /*
+       * put them together as <method> Using <model>
+       */
+      final String ttl = MessageManager
+              .formatMessage("label.treecalc_title", treecalcnm, smn);
+      return ttl;
+    }
   }
 }