X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCrossRefAction.java;h=2d1dfd4701c034b0be5ff9110dd337eb40034bc7;hb=405e8b16ccb9b1297e1158ace036f0b1634dac67;hp=cb315d603bdcd4f9aac3875a719717009bb1d764;hpb=c4baa6ec459f004be9c3b3d50cfbb29212b13312;p=jalview.git

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index cb315d6..2d1dfd4 100644
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -37,6 +37,8 @@ import jalview.ws.SequenceFetcher;
 import java.util.ArrayList;
 import java.util.List;
 
+import javax.swing.JOptionPane;
+
 /**
  * Factory constructor and runnable for discovering and displaying
  * cross-references for a set of aligned sequences
@@ -65,10 +67,9 @@ public class CrossRefAction implements Runnable
   public void run()
   {
     final long sttime = System.currentTimeMillis();
-    alignFrame.setProgressBar(
-            MessageManager.formatMessage(
-                    "status.searching_for_sequences_from",
-                    new Object[] { source }), sttime);
+    alignFrame.setProgressBar(MessageManager.formatMessage(
+            "status.searching_for_sequences_from", new Object[]
+            { source }), sttime);
     try
     {
       AlignmentI alignment = alignFrame.getViewport().getAlignment();
@@ -83,8 +84,8 @@ public class CrossRefAction implements Runnable
                         + " now searching for " + (dna ? "DNA" : "Protein")
                         + " Context.");
       }
-      AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
-              source, dna);
+      AlignmentI xrefs = new CrossRef(sel, dataset)
+              .findXrefSequences(source, dna);
       if (xrefs == null)
       {
         return;
@@ -119,6 +120,10 @@ public class CrossRefAction implements Runnable
                   xrefsAlignment.getSequencesArray());
           if (copyAlignment.getHeight() == 0)
           {
+            JvOptionPane.showMessageDialog(alignFrame,
+                    MessageManager.getString("label.cant_map_cds"),
+                    MessageManager.getString("label.operation_failed"),
+                    JvOptionPane.OK_OPTION);
             System.err.println("Failed to make CDS alignment");
           }
 
@@ -153,8 +158,8 @@ public class CrossRefAction implements Runnable
 
         if (copyAlignment.getHeight() <= 0)
         {
-          System.err.println("No Sequences generated for xRef type "
-                  + source);
+          System.err.println(
+                  "No Sequences generated for xRef type " + source);
           return;
         }
         /*
@@ -186,8 +191,9 @@ public class CrossRefAction implements Runnable
       {
         newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
       }
-      String newtitle = String.format("%s %s %s", MessageManager
-              .getString(dna ? "label.proteins" : "label.nucleotides"),
+      String newtitle = String.format("%s %s %s",
+              dna ? MessageManager.getString("label.proteins")
+                      : MessageManager.getString("label.nucleotides"),
               MessageManager.getString("label.for"), alignFrame.getTitle());
       newFrame.setTitle(newtitle);
 
@@ -236,7 +242,7 @@ public class CrossRefAction implements Runnable
       String linkedTitle = MessageManager
               .getString("label.linked_view_title");
       Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
-      sf.adjustDivider();
+      sf.adjustInitialLayout();
 
       // finally add the top, then bottom frame to the view list
       xrefViews.add(dna ? copyThis.alignPanel : newFrame.alignPanel);
@@ -251,8 +257,8 @@ public class CrossRefAction implements Runnable
     } finally
     {
       alignFrame.setProgressBar(MessageManager.formatMessage(
-              "status.finished_searching_for_sequences_from",
-              new Object[] { source }), sttime);
+              "status.finished_searching_for_sequences_from", new Object[]
+              { source }), sttime);
     }
   }
 
@@ -273,9 +279,8 @@ public class CrossRefAction implements Runnable
     for (int s = 0; s < sprods.length; s++)
     {
       sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
-      if (dataset.getSequences() == null
-              || !dataset.getSequences().contains(
-                      sprods[s].getDatasetSequence()))
+      if (dataset.getSequences() == null || !dataset.getSequences()
+              .contains(sprods[s].getDatasetSequence()))
       {
         dataset.addSequence(sprods[s].getDatasetSequence());
       }