Multiple Views

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index a25b01d..06f8269 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -65,13 +65,13 @@ public class TreePanel extends GTreePanel
      * @param s DOCUMENT ME!\r
      * @param e DOCUMENT ME!\r
      */\r
-    public TreePanel(AlignViewport av, String type, String pwtype)\r
+    public TreePanel(AlignmentPanel ap, String type, String pwtype)\r
     {\r
       super();\r
-      initTreePanel(av, type, pwtype, null);\r
+      initTreePanel(ap, type, pwtype, null);\r
 \r
       // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
-      showDistances(true);\r
+      // showDistances(true);\r
     }\r
 \r
     /**\r
@@ -83,13 +83,13 @@ public class TreePanel extends GTreePanel
      * @param type DOCUMENT ME!\r
      * @param pwtype DOCUMENT ME!\r
      */\r
-    public TreePanel(AlignViewport av,\r
-                     NewickFile newtree,\r
+    public TreePanel(AlignmentPanel ap,\r
                      String type,\r
-                     String pwtype)\r
+                     String pwtype,\r
+                     NewickFile newtree)\r
     {\r
       super();\r
-      initTreePanel(av, type, pwtype, newtree);\r
+      initTreePanel(ap, type, pwtype, newtree);\r
     }\r
 \r
     public AlignmentI getAlignment()\r
@@ -98,14 +98,15 @@ public class TreePanel extends GTreePanel
     }\r
 \r
 \r
-    void initTreePanel(AlignViewport av, String type,  String pwtype,\r
+    void initTreePanel(AlignmentPanel ap, String type,  String pwtype,\r
                        NewickFile newTree)\r
     {\r
 \r
+      av = ap.av;\r
       this.type = type;\r
       this.pwtype = pwtype;\r
 \r
-      treeCanvas = new TreeCanvas(av, scrollPane);\r
+      treeCanvas = new TreeCanvas(ap, scrollPane);\r
       scrollPane.setViewportView(treeCanvas);\r
 \r
       av.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
@@ -137,7 +138,7 @@ public class TreePanel extends GTreePanel
     class TreeLoader extends Thread\r
     {\r
       NewickFile newtree;\r
-\r
+      jalview.datamodel.AlignmentView odata=null;\r
       public TreeLoader(NewickFile newtree)\r
       {\r
         this.newtree = newtree;\r
@@ -154,18 +155,21 @@ public class TreePanel extends GTreePanel
       {\r
 \r
         if(newtree!=null)\r
-          tree = new NJTree(av.alignment.getSequencesArray(),\r
-                            newtree);\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
+          if (!tree.hasOriginalSequenceData())\r
+            allowOriginalSeqData(false);\r
+        }\r
         else\r
         {\r
           int start, end;\r
           SequenceI [] seqs;\r
-          String [] seqStrings = null;\r
-          if (av.hasHiddenColumns)\r
-          {\r
-            seqStrings = av.getSelectionAsString();\r
-          }\r
-\r
+          AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
           if(av.getSelectionGroup()==null)\r
           {\r
             start = 0;\r
@@ -180,15 +184,14 @@ public class TreePanel extends GTreePanel
           }\r
 \r
           tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
+          showDistances(true);\r
         }\r
 \r
 \r
         tree.reCount(tree.getTopNode());\r
         tree.findHeight(tree.getTopNode());\r
         treeCanvas.setTree(tree);\r
-\r
         treeCanvas.repaint();\r
-\r
         av.setCurrentTree(tree);\r
 \r
       }\r
@@ -212,6 +215,9 @@ public class TreePanel extends GTreePanel
       treeCanvas.setMarkPlaceholders(b);\r
     }\r
 \r
+    private void allowOriginalSeqData(boolean b) {\r
+      originalSeqData.setVisible(b);\r
+    }\r
 \r
 \r
 \r
@@ -312,10 +318,49 @@ public class TreePanel extends GTreePanel
 \r
     public void originalSeqData_actionPerformed(ActionEvent e)\r
     {\r
-      CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
-      cap.setText(tree.printOriginalSequenceData());\r
-      Desktop.addInternalFrame(cap, "Original Data",\r
-          400, 400);\r
+      if (!tree.hasOriginalSequenceData())\r
+      {\r
+        jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");\r
+        return;\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
+\r
+      if (alAndColsel != null && alAndColsel[0]!=null)\r
+       {\r
+         // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);\r
+\r
+         Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);\r
+         Alignment dataset = av.getAlignment().getDataset();\r
+         if (dataset != null)\r
+         {\r
+           al.setDataset(dataset);\r
+         }\r
+\r
+         if (true)\r
+         {\r
+           // make a new frame!\r
+           AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],\r
+                                           AlignFrame.DEFAULT_WIDTH,\r
+                                           AlignFrame.DEFAULT_HEIGHT\r
+);\r
+\r
+           //>>>This is a fix for the moment, until a better solution is found!!<<<\r
+           // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());\r
+\r
+       //           af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
+       //                                     msaorder);\r
+\r
+           Desktop.addInternalFrame(af, "Original Data for " + this.title,\r
+                                    AlignFrame.DEFAULT_WIDTH,\r
+                                    AlignFrame.DEFAULT_HEIGHT);\r
+         }\r
+       }\r
     }\r
 \r
 \r