X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=a0de6824a291386da4b9807b98afe325a2d166be;hb=e33cdacd2ac2836504375c538574a0f1cafec7e3;hp=f636257634463dad9d239241173bcdc313a9b0a9;hpb=9470a791baa6d2d9daba2a225d4189617632b869;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index f636257..a0de682 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.CigarArray 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.getViewAsString(true);
-          }
-
+          CigarArray seqStrings = av.getViewAsCigars(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 +316,16 @@ 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);
+      String originalData = tree.printOriginalSequenceData();
+      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.");
+      }
+
     }