Feature Groups added

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index e38e03a..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
 \r
 import javax.imageio.*;\r
 \r

-import javax.swing.*;\r

 import java.beans.PropertyChangeEvent;\r
 \r
 \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
       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
     }\r
 \r
     /**\r

@@ -94,6 +93,11 @@ public class TreePanel extends GTreePanel
       initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
     }\r
 \r
       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
 \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
       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
       }\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
         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
 \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

-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public NJTree getTree()\r
+    public void showBootstrap(boolean b)\r

     {\r
     {\r

-        return tree;\r
+      treeCanvas.setShowBootstrap(b);\r
+      bootstrapMenu.setSelected(b);\r

     }\r
 \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
     {\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
+\r

     /**\r
      * DOCUMENT ME!\r
      *\r
     /**\r
      * DOCUMENT ME!\r
      *\r

-     * @param tree DOCUMENT ME!\r
+     * @return DOCUMENT ME!\r

      */\r
      */\r

-    private void setTreeCanvasFromViewState(TreeCanvas tree)\r
+    public NJTree getTree()\r

     {\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

+\r

     /**\r
      * DOCUMENT ME!\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
         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
     }\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
             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
                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
                             choice));\r
                 out.println(output);\r

@@ -304,33 +303,25 @@ public class TreePanel extends GTreePanel
      *\r
      * @param e DOCUMENT ME!\r
      */\r
      *\r
      * @param e DOCUMENT ME!\r
      */\r

-    public void fontSize_actionPerformed(ActionEvent e)\r
+    public void font_actionPerformed(ActionEvent e)\r

     {\r
         if (treeCanvas == null)\r
         {\r
             return;\r
         }\r
 \r
     {\r
         if (treeCanvas == null)\r
         {\r
             return;\r
         }\r
 \r

-        String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +\r
-                1);\r
-\r
-        Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
-                "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,\r
-                null,\r
-                new String[]\r
-                {\r
-                    "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"\r
-                }, "Font Size - " + size);\r
-\r
-        if (selection != null)\r
-        {\r
-            fontSize.setText("Font Size - " + selection);\r
+        new FontChooser(this);\r
+    }\r

 \r
 \r

-            int i = Integer.parseInt(selection.toString());\r
-            treeCanvas.setFontSize(i);\r
-        }\r
+    public Font getTreeFont()\r
+    {\r
+        return treeCanvas.font;\r
+    }\r

 \r
 \r

-        scrollPane.setViewportView(treeCanvas);\r
+    public void setTreeFont(Font font)\r
+    {\r
+      if(treeCanvas!=null)\r
+      treeCanvas.setFont(font);\r

     }\r
 \r
     /**\r
     }\r
 \r
     /**\r