X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=f1ba97b368e6316a508e749f4d8e488146d59ed9;hb=bd894ca9f2aae448653d7431ab8a170e1105e85c;hp=80f0c73c4ea80fd1b78880a858086ef7ae50f10e;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 80f0c73..f1ba97b 100755
--- 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;
@@ -74,14 +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;
@@ -92,28 +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;
+    initNewTreePanel(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);
+    initLoadedTreePanel(alignPanel, newtree, inputData);
   }
 
   public AlignmentI getAlignment()
@@ -126,17 +128,30 @@ public class TreePanel extends GTreePanel
     return treeCanvas.av;
   }
 
-  void initTreePanel(AlignmentPanel ap, String type, String modelName,
+  void initNewTreePanel(AlignmentPanel ap, TreeModel tree)
+  {
+    buildTreeCanvas(ap);
+
+    TreeLoader tl = new TreeLoader(null, null);
+    tl.start();
+
+  }
+  void initLoadedTreePanel(AlignmentPanel ap, 
           NewickFile newTree, AlignmentView inputData)
   {
+    buildTreeCanvas(ap);
+
+    TreeLoader tl = new TreeLoader(newTree, 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();
@@ -170,8 +185,8 @@ public class TreePanel extends GTreePanel
       }
     });
 
-    TreeLoader tl = new TreeLoader(newTree, inputData);
-    tl.start();
+
+  
 
   }
 
@@ -243,57 +258,59 @@ public class TreePanel extends GTreePanel
 
   class TreeLoader extends Thread
   {
-    private NewickFile newtree;
+    private NewickFile newTree;
 
     private AlignmentView odata = null;
 
     public TreeLoader(NewickFile newickFile, AlignmentView inputData)
     {
-      this.newtree = newickFile;
+      this.newTree = newickFile;
       this.odata = inputData;
 
-      if (newickFile != null)
+      if (newTree != null)
       {
         // Must be outside run(), as Jalview2XML tries to
         // update distance/bootstrap visibility at the same time
-        showBootstrap(newickFile.HasBootstrap());
-        showDistances(newickFile.HasDistances());
+        showBootstrap(newTree.hasBootstrap());
+        showDistances(newTree.hasDistances());
+
       }
+
     }
 
     @Override
     public void run()
     {
 
-      if (newtree != null)
+      if (newTree != null)
       {
         tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
-                newtree);
+                newTree);
         if (tree.getOriginalData() == null)
         {
           originalSeqData.setVisible(false);
         }
+
+
+
       }
-      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);
-      }
+      showTree(tree);
 
+    }
+      
+    public void showTree(TreeModel tree)
+    {
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
       treeCanvas.setTree(tree);
       treeCanvas.repaint();
+
       av.setCurrentTree(tree);
       if (av.getSortByTree())
       {
         sortByTree_actionPerformed();
       }
+
     }
   }
 
@@ -493,7 +510,7 @@ public class TreePanel extends GTreePanel
 
     if (treeCanvas.applyToAllViews)
     {
-      final ArrayList<CommandI> commands = new ArrayList<CommandI>();
+      final ArrayList<CommandI> commands = new ArrayList<>();
       for (AlignmentPanel ap : PaintRefresher
               .getAssociatedPanels(av.getSequenceSetId()))
       {
@@ -793,19 +810,17 @@ public class TreePanel extends GTreePanel
             }
             if (newname == null)
             {
-              SequenceFeature sf[] = sq.getSequenceFeatures();
-              for (int i = 0; sf != null && i < sf.length; i++)
+              List<SequenceFeature> features = sq.getFeatures()
+                      .getPositionalFeatures(labelClass);
+              for (SequenceFeature feature : features)
               {
-                if (sf[i].getType().equals(labelClass))
+                if (newname == null)
+                {
+                  newname = feature.getDescription();
+                }
+                else
                 {
-                  if (newname == null)
-                  {
-                    newname = new String(sf[i].getDescription());
-                  }
-                  else
-                  {
-                    newname = newname + "; " + sf[i].getDescription();
-                  }
+                  newname = newname + "; " + feature.getDescription();
                 }
               }
             }
@@ -830,29 +845,31 @@ 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;
+    }
   }
 }