Right mouse works with cursor mode

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

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 61b0546..b3fc3b3 100755 (executable)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -37,6 +37,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   int end;\r
   TreeCanvas treeCanvas;\r
   NJTree tree;\r
+  AlignViewport av;\r
 \r
   public NJTree getTree()\r
   {\r
@@ -53,8 +54,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
    * @param s DOCUMENT ME!\r
    * @param e DOCUMENT ME!\r
    */\r
-  public TreePanel(AlignViewport av, Vector seqVector, String type,\r
-                   String pwtype, int s, int e)\r
+  public TreePanel(AlignViewport av, String type, String pwtype)\r
   {\r
     try\r
     {\r
@@ -66,7 +66,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       ex.printStackTrace();\r
     }\r
 \r
-    initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+    initTreePanel(av, type, pwtype, null);\r
   }\r
 \r
   /**\r
@@ -78,8 +78,10 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
    * @param type DOCUMENT ME!\r
    * @param pwtype DOCUMENT ME!\r
    */\r
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
-                   String type, String pwtype)\r
+  public TreePanel(AlignViewport av,\r
+                   String type,\r
+                   String pwtype,\r
+                   NewickFile newtree)\r
   {\r
     try\r
     {\r
@@ -91,25 +93,20 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       e.printStackTrace();\r
     }\r
 \r
-    initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
+    initTreePanel(av, type, pwtype, newtree);\r
   }\r
 \r
 \r
-  void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
-                     String pwtype, int s, int e, NewickFile newTree)\r
+  void initTreePanel(AlignViewport av,\r
+                     String type,\r
+                     String pwtype,\r
+                     NewickFile newTree)\r
   {\r
 \r
+    this.av = av;\r
     this.type = type;\r
     this.pwtype = pwtype;\r
 \r
-    start = s;\r
-    end = e;\r
-\r
-    seq = new Sequence[seqVector.size()];\r
-    for(int i=0; i<seqVector.size(); i++)\r
-      seq[i] = (SequenceI)seqVector.elementAt(i);\r
-\r
-\r
     treeCanvas = new TreeCanvas(av, scrollPane);\r
     scrollPane.add(treeCanvas);\r
 \r
@@ -119,9 +116,31 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 \r
   }\r
 \r
+  void showOriginalData()\r
+  {\r
+    // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
+    // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
+    // or create a selection box around columns in alignment view\r
+    // test Alignment(SeqCigar[])\r
+    Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.\r
+        getGapCharacter());\r
+\r
+    if (alAndColsel != null && alAndColsel[0]!=null)\r
+     {\r
+       Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);\r
+       AlignFrame af = new AlignFrame(al,\r
+             av.applet,\r
+             "Original Data for Tree",\r
+             false);\r
+\r
+      af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1] );\r
+     }\r
+  }\r
+\r
   class TreeLoader extends Thread\r
   {\r
     NewickFile newtree;\r
+    jalview.datamodel.AlignmentView odata=null;\r
 \r
     public TreeLoader(NewickFile newtree)\r
     {\r
@@ -131,9 +150,34 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
     public void run()\r
     {\r
       if(newtree!=null)\r
-        tree = new NJTree(seq, newtree);\r
-      else\r
-        tree = new NJTree(seq, type, pwtype, start, end);\r
+      {\r
+        if (odata == null)\r
+          tree = new NJTree(av.alignment.getSequencesArray(),\r
+                            newtree);\r
+        else\r
+          tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);\r
+\r
+        }\r
+        else\r
+        {\r
+          int start, end;\r
+          SequenceI [] seqs;\r
+          AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
+          if(av.getSelectionGroup()==null)\r
+          {\r
+            start = 0;\r
+            end = av.alignment.getWidth();\r
+            seqs = av.alignment.getSequencesArray();\r
+          }\r
+          else\r
+          {\r
+            start = av.getSelectionGroup().getStartRes();\r
+            end = av.getSelectionGroup().getEndRes()+1;\r
+            seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+          }\r
+\r
+          tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
+        }\r
 \r
       tree.reCount(tree.getTopNode());\r
       tree.findHeight(tree.getTopNode());\r
@@ -149,6 +193,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 \r
       treeCanvas.repaint();\r
 \r
+      av.setCurrentTree(tree);\r
+\r
     }\r
   }\r
 \r
@@ -158,6 +204,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       newickOutput_actionPerformed();\r
     else if(evt.getSource()==fontSize)\r
       fontSize_actionPerformed();\r
+    else if(evt.getSource()==inputData)\r
+      showOriginalData();\r
   }\r
 \r
   public void itemStateChanged(ItemEvent evt)\r
@@ -209,6 +257,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   }\r
 \r
 \r
+\r
+\r
   BorderLayout borderLayout1 = new BorderLayout();\r
   protected ScrollPane scrollPane = new ScrollPane();\r
   MenuBar jMenuBar1 = new MenuBar();\r
@@ -220,6 +270,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
   Menu fileMenu = new Menu();\r
   MenuItem newickOutput = new MenuItem();\r
+  MenuItem inputData = new MenuItem();\r
 \r
   private void jbInit() throws Exception {\r
       setLayout(borderLayout1);\r
@@ -240,6 +291,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       fileMenu.setLabel("File");\r
       newickOutput.setLabel("Newick Format");\r
       newickOutput.addActionListener(this);\r
+    inputData.setLabel("Input Data...");\r
 \r
     add(scrollPane, BorderLayout.CENTER);\r
       jMenuBar1.add(fileMenu);\r
@@ -250,6 +302,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       jMenu2.add(bootstrapMenu);\r
       jMenu2.add(placeholdersMenu);\r
     fileMenu.add(newickOutput);\r
+    fileMenu.add(inputData);\r
+    inputData.addActionListener(this);\r
   }\r
 \r
 }\r