From f4fd7b0e74572c8fddbfe9e3e55bc624f8ba0c6a Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 27 Sep 2006 14:35:43 +0000
Subject: [PATCH] fixed tree building exception when one residue or a single
 column of residues is selected.

---
 src/jalview/appletgui/AlignViewport.java |    4 ++--
 src/jalview/gui/AlignFrame.java          |   12 +++++++++---
 src/jalview/gui/AlignViewport.java       |    4 ++--
 3 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 0fd974b..87753f4 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -940,9 +940,9 @@ public class AlignViewport
       }
       // Final match if necessary.
       if (last<end)
-        selection.addOperation(CigarArray.M, end-last);
+        selection.addOperation(CigarArray.M, end-last+1);
     } else {
-      selection.addOperation(CigarArray.M, end-start);
+      selection.addOperation(CigarArray.M, end-start+1);
     }
     return selection;
   }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 807b6e3..ef228df 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2166,9 +2166,15 @@ public class AlignFrame
   {
     TreePanel tp;
 
-    if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize(false) > 3))
-    {
+    if (viewport.getSelectionGroup() != null) {
+      if (viewport.getSelectionGroup().getSize(false) < 3) {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "You need to have more than two sequences selected to build a tree!",
+                                      "Not enough sequences",
+                                      JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+
       int s = 0;
       SequenceGroup sg = viewport.getSelectionGroup();
 
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 30113c3..05a52dd 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1334,9 +1334,9 @@ public class AlignViewport
         }
         // Final match if necessary.
         if (last<end)
-          selection.addOperation(CigarArray.M, end-last);
+          selection.addOperation(CigarArray.M, end-last+1);
       } else {
-        selection.addOperation(CigarArray.M, end-start);
+        selection.addOperation(CigarArray.M, end-start+1);
       }
       return selection;
     }
-- 
1.7.10.2