Reinstated 'create tree from selected region only' with better indication that only...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index afb1f0c..4d97f49 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1068,34 +1068,51 @@ public class AlignFrame extends GAlignFrame
 
   void NewTreePanel(String type, String pwType, String title)
   {
-    //are the sequences aligned?
-    if(!viewport.alignment.isAligned())
-    {
-      JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
-                                   +"Try using the Pad function in the edit menu,\n"
-                                  +"or one of the multiple sequence alignment web services.",
-                                    "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
-      return;
-    }
-
+    String ltitle;
     final TreePanel tp;
     if (viewport.getSelectionGroup() != null &&
         viewport.getSelectionGroup().getSize() > 3)
     {
+      int s=0;
+      SequenceGroup sg = viewport.getSelectionGroup();
+
+      /* Decide if the selection is a column region */
+      while (s<sg.sequences.size()) {
+        if (((SequenceI) sg.sequences.elementAt(s++)).getLength()<sg.getEndRes()) {
+          JOptionPane.showMessageDialog(Desktop.desktop,
+                                        "The selected region to create a tree may\nonly contain residues or gaps.\n"
+                                       +"Try using the Pad function in the edit menu,\n"
+                                      +"or one of the multiple sequence alignment web services.",
+                                        "Sequences in selection are not aligned", JOptionPane.WARNING_MESSAGE);
+          return;
+        }
+
+      }
+      title=title+" on region";
       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
                          pwType,
-                         0, viewport.alignment.getWidth());
+                         sg.getStartRes(), sg.getEndRes());
     }
     else
     {
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, 0, viewport.alignment.getWidth());
-    }
+
+     //are the sequences aligned?
+     if(!viewport.alignment.isAligned())
+     {
+       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
+                                     +"Try using the Pad function in the edit menu,\n"
+                                     +"or one of the multiple sequence alignment web services.",
+                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
+       return;
+     }
+     tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                        type, pwType, 0, viewport.alignment.getWidth());
+   }
 
    addTreeMenuItem(tp, title);
    viewport.setCurrentTree(tp.getTree());
 
-   Desktop.addInternalFrame(tp, title, 600, 500);
+   Desktop.addInternalFrame(tp, title+" from "+this.title, 600, 500);
   }
 
   public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {