Applet has hidden regions

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

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 9c71a15..b3fc3b3 100755 (executable)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -116,9 +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
@@ -127,19 +149,20 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 \r
     public void run()\r
     {\r
-      if (newtree != null)\r
-        tree = new NJTree(av.alignment.getSequencesArray(),\r
-                          newtree);\r
-      else\r
+      if(newtree!=null)\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
-          String[] seqStrings = null;\r
-//          if (av.hasHiddenColumns)\r
-  //        {\r
-    //        seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null); // av.getSelectionAsString();\r
-      //    }\r
-\r
+          AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
           if(av.getSelectionGroup()==null)\r
           {\r
             start = 0;\r
@@ -153,7 +176,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
             seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
           }\r
 \r
-          tree = new NJTree(seqs, null, type, pwtype, start, end);\r
+          tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
         }\r
 \r
       tree.reCount(tree.getTopNode());\r
@@ -181,6 +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
@@ -245,6 +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
@@ -265,6 +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
@@ -275,6 +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