JAL-2826 added action performed for hiding collapsed sequences

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 67ac836..e8f78d8 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -35,7 +35,6 @@ import jalview.datamodel.NodeTransformI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
-import jalview.ext.archaeopteryx.ArchaeopteryxNewickInit;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.NewickFile;
@@ -86,6 +85,8 @@ public class TreePanel extends GTreePanel
    * 
    * @param ap
    * @param tree
+   * @param treeType
+   * @param substitutionMatrix
    */
   public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
           String substitutionMatrix)
@@ -94,7 +95,7 @@ public class TreePanel extends GTreePanel
     this.treeType = treeType;
     this.substitutionMatrix = substitutionMatrix;
     this.tree = tree;
-    initNewTreePanel(ap, tree);
+    initTreePanel(ap, tree);
 
     // We know this tree has distances. JBPNote TODO: prolly should add this as
     // a userdefined default
@@ -108,14 +109,13 @@ public class TreePanel extends GTreePanel
    * @param newtree
    * @param theTitle
    * @param inputData
-   * @param viewport
    */
   public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
           String theTitle, AlignmentView inputData)
   {
     super();
     this.treeTitle = theTitle;
-    initLoadedTreePanel(alignPanel, newtree, inputData);
+    initTreePanel(alignPanel, newtree, inputData);
   }
 
   public AlignmentI getAlignment()
@@ -128,7 +128,13 @@ public class TreePanel extends GTreePanel
     return treeCanvas.av;
   }
 
-  void initNewTreePanel(AlignmentPanel ap, TreeModel tree)
+  /**
+   * Initialize a tree panel based on a calculated tree
+   * 
+   * @param ap
+   * @param tree
+   */
+  void initTreePanel(AlignmentPanel ap, TreeModel tree)
   {
     buildTreeCanvas(ap);
 
@@ -136,12 +142,20 @@ public class TreePanel extends GTreePanel
     tl.start();
 
   }
-  void initLoadedTreePanel(AlignmentPanel ap, 
-          NewickFile newTree, AlignmentView inputData)
+
+  /**
+   * 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(newTree, inputData);
+    TreeLoader tl = new TreeLoader(loadedTree, inputData);
     tl.start();
   }
 
@@ -311,8 +325,6 @@ public void buildTreeCanvas(AlignmentPanel ap) {
         sortByTree_actionPerformed();
       }
 
-      ArchaeopteryxNewickInit archae = new ArchaeopteryxNewickInit(tree);
-      archae.startArchaeopteryx();
     }
   }
 
@@ -507,7 +519,7 @@ public void buildTreeCanvas(AlignmentPanel ap) {
    * @param e
    */
   @Override
-  public void sortByTree_actionPerformed()
+  public void sortByTree_actionPerformed()// modify for Aptx
   {
 
     if (treeCanvas.applyToAllViews)
@@ -569,13 +581,14 @@ public void buildTreeCanvas(AlignmentPanel ap) {
 
   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;
   }