ShowDistances, placeHolders and bootstraps have their own methods

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 603a80f..fea4704 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -75,7 +75,7 @@ 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
@@ -143,6 +143,13 @@ 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 +162,44 @@ 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
@@ -311,15 +306,15 @@ public class TreePanel extends GTreePanel
             return;\r
         }\r
 \r
-        FontChooser fontchooser = new FontChooser(this);\r
+        new FontChooser(this);\r
     }\r
 \r
-    public Font getFont()\r
+    public Font getTreeFont()\r
     {\r
-      return treeCanvas.font;\r
+        return treeCanvas.font;\r
     }\r
 \r
-    public void setFont(Font font)\r
+    public void setTreeFont(Font font)\r
     {\r
       if(treeCanvas!=null)\r
       treeCanvas.setFont(font);\r