Features now an array

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index f086162..9c1e42e 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -38,7 +38,6 @@ import java.util.*;
 \r
 import javax.imageio.*;\r
 \r
-import javax.swing.*;\r
 import java.beans.PropertyChangeEvent;\r
 \r
 \r
@@ -75,7 +74,7 @@ public class TreePanel extends GTreePanel
       initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
 \r
       // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
-      treeCanvas.setShowDistances(true);\r
+      showDistances(true);\r
     }\r
 \r
     /**\r
@@ -94,6 +93,11 @@ public class TreePanel extends GTreePanel
       initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
     }\r
 \r
+    public AlignmentI getAlignment()\r
+    {\r
+      return treeCanvas.av.getAlignment();\r
+    }\r
+\r
 \r
     void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
                        String pwtype, int s, int e, NewickFile newTree)\r
@@ -143,6 +147,13 @@ public class TreePanel extends GTreePanel
       public TreeLoader(NewickFile newtree)\r
       {\r
         this.newtree = newtree;\r
+        if (newtree != null)\r
+        {\r
+          // Must be outside run(), as Jalview2XML tries to\r
+          // update distance/bootstrap visibility at the same time\r
+          showBootstrap(newtree.HasBootstrap());\r
+          showDistances(newtree.HasDistances());\r
+        }\r
       }\r
 \r
       public void run()\r
@@ -155,56 +166,44 @@ public class TreePanel extends GTreePanel
         tree.reCount(tree.getTopNode());\r
         tree.findHeight(tree.getTopNode());\r
         treeCanvas.setTree(tree);\r
-        if(newtree!=null)\r
-        {\r
-          treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
-          treeCanvas.setShowDistances(newtree.HasDistances());\r
-        }\r
-\r
-        setViewStateFromTreeCanvas(treeCanvas);\r
 \r
         treeCanvas.repaint();\r
 \r
       }\r
     }\r
 \r
+    public void showDistances(boolean b)\r
+    {\r
+      treeCanvas.setShowDistances(b);\r
+      distanceMenu.setSelected(b);\r
+    }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public NJTree getTree()\r
+    public void showBootstrap(boolean b)\r
     {\r
-        return tree;\r
+      treeCanvas.setShowBootstrap(b);\r
+      bootstrapMenu.setSelected(b);\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param tree DOCUMENT ME!\r
-     */\r
-    private void setViewStateFromTreeCanvas(TreeCanvas tree)\r
+    public void showPlaceholders(boolean b)\r
     {\r
-        // update view menu state from treeCanvas render state\r
-        distanceMenu.setSelected(tree.showDistances);\r
-        bootstrapMenu.setSelected(tree.showBootstrap);\r
-        placeholdersMenu.setSelected(tree.markPlaceholders);\r
+      placeholdersMenu.setState(b);\r
+      treeCanvas.setMarkPlaceholders(b);\r
     }\r
 \r
+\r
+\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
-     * @param tree DOCUMENT ME!\r
+     * @return DOCUMENT ME!\r
      */\r
-    private void setTreeCanvasFromViewState(TreeCanvas tree)\r
+    public NJTree getTree()\r
     {\r
-        // update view menu state from treeCanvas render state\r
-        tree.showDistances = distanceMenu.isSelected();\r
-        tree.showBootstrap = bootstrapMenu.isSelected();\r
-        tree.markPlaceholders = placeholdersMenu.isSelected();\r
+        return tree;\r
     }\r
 \r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -237,7 +236,7 @@ public class TreePanel extends GTreePanel
         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
 \r
         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
-        cap.setText(fout.print(false, true));\r
+        cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));\r
     }\r
 \r
     /**\r
@@ -264,7 +263,7 @@ public class TreePanel extends GTreePanel
             try\r
             {\r
                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
-                String output = fout.print(false, true); // distances only\r
+                String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());\r
                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
                             choice));\r
                 out.println(output);\r