X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=d30602843d9735a79451089c36d86e6de6a460f6;hb=3596077c79b7aa2051b9aaa978481004b513101c;hp=190f15cf811164411174a79b2044c7c7d54acf0e;hpb=623d576bab61337289656eab9e4e26cf63e0afc0;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 190f15c..d306028 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -71,7 +71,7 @@ public class TreePanel extends GTreePanel
       initTreePanel(av, type, pwtype, null);
 
       // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
-      showDistances(true);
+      // showDistances(true);
     }
 
     /**
@@ -137,7 +137,7 @@ public class TreePanel extends GTreePanel
     class TreeLoader extends Thread
     {
       NewickFile newtree;
-
+      jalview.datamodel.AlignmentView odata=null;
       public TreeLoader(NewickFile newtree)
       {
         this.newtree = newtree;
@@ -153,19 +153,22 @@ public class TreePanel extends GTreePanel
       public void run()
       {
 
-        if(newtree!=null)
-          tree = new NJTree(av.alignment.getSequencesArray(),
-                            newtree);
+        if(newtree!=null) {
+
+          if (odata==null) {
+            tree = new NJTree(av.alignment.getSequencesArray(),
+                              newtree);
+          } else {
+            tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+          }
+          if (!tree.hasOriginalSequenceData())
+            allowOriginalSeqData(false);
+        }
         else
         {
           int start, end;
           SequenceI [] seqs;
-          String [] seqStrings = null;
-          if (av.hasHiddenColumns)
-          {
-            seqStrings = av.getSelectionAsString();
-          }
-
+          AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
           if(av.getSelectionGroup()==null)
           {
             start = 0;
@@ -180,15 +183,14 @@ public class TreePanel extends GTreePanel
           }
 
           tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+          showDistances(true);
         }
 
 
         tree.reCount(tree.getTopNode());
         tree.findHeight(tree.getTopNode());
         treeCanvas.setTree(tree);
-
         treeCanvas.repaint();
-
         av.setCurrentTree(tree);
 
       }
@@ -211,7 +213,9 @@ public class TreePanel extends GTreePanel
       placeholdersMenu.setState(b);
       treeCanvas.setMarkPlaceholders(b);
     }
-
+    private void allowOriginalSeqData(boolean b) {
+      originalSeqData.setVisible(b);
+    }
 
 
 
@@ -312,10 +316,46 @@ public class TreePanel extends GTreePanel
 
     public void originalSeqData_actionPerformed(ActionEvent e)
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer();
-      cap.setText(tree.printOriginalSequenceData());
-      Desktop.addInternalFrame(cap, "Original Data",
-          400, 400);
+      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);
+         }
+       }
     }