X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=3fa7643b497f141e0c9e3afb11d61c99db93d3c0;hb=c42fcf7bf5cfcf51e67dd0f683edb9ab6683d157;hp=bde218ca639c8b6e01fa1024a4734c4f1b9024f9;hpb=d187567c926fed31f9cd9bda0dc112bc4d1b1261;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index bde218c..3fa7643 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -137,7 +137,7 @@ public class TreePanel extends GTreePanel
     class TreeLoader extends Thread
     {
       NewickFile newtree;
-      jalview.datamodel.CigarArray odata=null;
+      jalview.datamodel.AlignmentView odata=null;
       public TreeLoader(NewickFile newtree)
       {
         this.newtree = newtree;
@@ -153,8 +153,8 @@ public class TreePanel extends GTreePanel
       public void run()
       {
 
-        if(newtree!=null) {
-
+        if(newtree!=null)
+        {
           if (odata==null) {
             tree = new NJTree(av.alignment.getSequencesArray(),
                               newtree);
@@ -168,7 +168,7 @@ public class TreePanel extends GTreePanel
         {
           int start, end;
           SequenceI [] seqs;
-          CigarArray seqStrings = av.getViewAsCigars(av.getSelectionGroup()!=null);
+          AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
           if(av.getSelectionGroup()==null)
           {
             start = 0;
@@ -213,6 +213,7 @@ public class TreePanel extends GTreePanel
       placeholdersMenu.setState(b);
       treeCanvas.setMarkPlaceholders(b);
     }
+
     private void allowOriginalSeqData(boolean b) {
       originalSeqData.setVisible(b);
     }
@@ -316,16 +317,46 @@ public class TreePanel extends GTreePanel
 
     public void originalSeqData_actionPerformed(ActionEvent e)
     {
-      String originalData = tree.printOriginalSequenceData(av.getGapCharacter());
-      if (originalData!=null) {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        cap.setText(originalData);
-        Desktop.addInternalFrame(cap, "Original Data",
-                                 400, 400);
-      } else {
-        System.err.println("IMPLEMENTATION BUG! originalSeqData is not available.");
+      if (!tree.hasOriginalSequenceData())
+      {
+        jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+        return;
       }
-
+      // decide if av alignment is sufficiently different to original data to warrant a new window to be created
+      // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+      // or create a selection box around columns in alignment view
+      // test Alignment(SeqCigar[])
+      Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
+          getGapCharacter());
+
+
+      if (alAndColsel != null && alAndColsel[0]!=null)
+       {
+         // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+         Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+         Alignment dataset = av.getAlignment().getDataset();
+         if (dataset != null)
+         {
+           al.setDataset(dataset);
+         }
+
+         if (true)
+         {
+           // make a new frame!
+           AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1]);
+
+           //>>>This is a fix for the moment, until a better solution is found!!<<<
+           // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
+
+       //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
+       //                                     msaorder);
+
+           Desktop.addInternalFrame(af, "Original Data for " + this.title,
+                                    AlignFrame.NEW_WINDOW_WIDTH,
+                                    AlignFrame.NEW_WINDOW_HEIGHT);
+         }
+       }
     }