From b58a17a47d215b541be4d8057eb88072c599087e Mon Sep 17 00:00:00 2001
From: Charles Ofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 27 Nov 2014 10:13:39 +0000
Subject: [PATCH] JAL-1604 Entire sequence submision for MSA job bugfix

---
 src/jalview/gui/AlignFrame.java      |   15 +++++++++++++++
 src/jalview/ws/jws2/MsaWSClient.java |    8 ++++----
 2 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 07c4a54..2a804ad 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4184,6 +4184,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
        */
       msa = viewport.getAlignmentView(true);
     }
+    else if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() == 1)
+    {
+      int option = JOptionPane
+              .showConfirmDialog(
+this,
+                      "More than one sequece group selection is required for this Job, click \n'Cancel' to edit your selection or 'Ok' to submit the entire sequence.",
+                      "Invalid selection",
+                      JOptionPane.OK_CANCEL_OPTION);
+      if (option == JOptionPane.OK_OPTION)
+      {
+        msa = viewport.getAlignmentView(false);
+      }
+
+    }
     else
     {
       /*
diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index c3661c3..39be454 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -212,7 +212,7 @@ public class MsaWSClient extends Jws2Client
     JOptionPane
             .showMessageDialog(
                     alignFrame,
-                    "A minimum of two sequences with at least three non-gap character \nis required to perform this operation",
+                    "All selected sequence for this job must have a  minimum of \nthree non-gap character to perform this operation",
                     "Invalid selection", JOptionPane.INFORMATION_MESSAGE);
 
     return false;
@@ -300,7 +300,7 @@ public class MsaWSClient extends Jws2Client
         {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
 
-          if (isValidAlignment(msa))
+          if (msa != null && isValidAlignment(msa))
           {
           new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
                   true, alignFrame.getViewport().getAlignment()
@@ -325,7 +325,7 @@ public class MsaWSClient extends Jws2Client
           {
             AlignmentView msa = alignFrame.gatherSequencesForAlignment();
 
-            if (isValidAlignment(msa))
+            if (msa != null && isValidAlignment(msa))
             {
             new MsaWSClient(service, null, null, true, alignFrame
                     .getTitle(), msa, withGaps, true, alignFrame
@@ -382,7 +382,7 @@ public class MsaWSClient extends Jws2Client
                 AlignmentView msa = alignFrame
                         .gatherSequencesForAlignment();
 
-                if (isValidAlignment(msa))
+                if (msa != null && isValidAlignment(msa))
                 {
                 new MsaWSClient(service, preset, alignFrame.getTitle(),
                         msa, false, true, alignFrame.getViewport()
-- 
1.7.10.2