From 966e2e639242c252f4ed9e5f0e3e91b0389bd2de Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 7 Dec 2005 16:37:26 +0000
Subject: [PATCH] Submissions for secondary structure prediction are now
 filtered to remove empty sequences and user is informed if
 no non-empty sequences exist.

---
 src/jalview/gui/AlignFrame.java |   24 ++++++++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8c31ed0..81e5564 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2208,7 +2208,16 @@ public class AlignFrame
   {
     SequenceI seq = null;
     SequenceI[] msa = null;
+/*
+         if (predictindex==-1) {
 
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "The alignment contains no columns or residues usable for prediction!",
+                                                "Invalid Alignment Selection", JOptionPane.WARNING_MESSAGE);
+          this.
+          return;
+        }
+*/
     if ( (viewport.getSelectionGroup() != null) &&
         (viewport.getSelectionGroup().getSize() > 0))
     {
@@ -2439,7 +2448,18 @@ public class AlignFrame
           {
             public void actionPerformed(ActionEvent e)
             {
-              SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
+              SequenceI[] msa = SeqsetUtils.getNonEmptySequenceSet(gatherSeqOrMsaForSecStrPrediction());
+              if (msa==null) {
+                JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    "There are no columns or residues usable for prediction!\n"
+                    +"There must be valid residues in at least one\n"
+                    +"of the sequences in the alignment,\n"
+                    +"or in the currently selected region.",
+                    "Invalid Input for Secondary Structure Prediction",
+                    JOptionPane.WARNING_MESSAGE);
+                return;
+              }
+
               if (msa.length == 1)
               {
                 // Single Sequence prediction
@@ -2449,7 +2469,7 @@ public class AlignFrame
               {
                 if (msa.length > 1)
                 {
-                  // Single Sequence prediction
+                  // Aligned Sequences prediction
                   jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
                       title, msa);
                 }
-- 
1.7.10.2