X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=81e55644b6b34e941aa0fc24f6970fd085d1dc30;hb=966e2e639242c252f4ed9e5f0e3e91b0389bd2de;hp=86d7cb67f9c194a084504ad588e7ee785b78941b;hpb=58f946af1280918a6f2893534e66104bc20a52c7;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 86d7cb6..81e5564 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -828,7 +828,10 @@ public class AlignFrame
         //!newAlignment
         for (int i = 0; i < sequences.length; i++)
         {
-          viewport.alignment.addSequence(sequences[i]);
+          Sequence newseq = new Sequence(sequences[i].getName(),
+              sequences[i].getSequence(), sequences[i].getStart(),
+              sequences[i].getEnd());
+          viewport.alignment.addSequence(newseq);
           if(sequences[i].getDatasetSequence()==null)
           {
              ////////////////////////////
@@ -838,10 +841,8 @@ public class AlignFrame
                                        AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
                                        sequences[i].getStart(),
                                        sequences[i].getEnd());
-            sequences[i].setDatasetSequence(ds);
+            newseq.setDatasetSequence(ds);
             viewport.alignment.getDataset().addSequence(ds);
-
-
           }
 
         }
@@ -977,6 +978,7 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
+    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.annotationPanel.activeRes = null;
     PaintRefresher.Refresh(null, viewport.alignment);
   }
@@ -2206,7 +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))
     {
@@ -2437,7 +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
@@ -2447,7 +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);
                 }