X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=498489d1902f15837bdebb04123fa04720363233;hb=df1c58f9669c477db082016aa919d6c6cc9da071;hp=6d49d12e9d583ae4e61304b70a81cc6be6793f52;hpb=a87f4c6fd568ccf29aaf3af0ad528da442ea921d;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 6d49d12..498489d 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -194,7 +194,7 @@ public class SequenceFetcher
         for (int i = 0; i < reply.length; i++)
           result.append(reply[i] + "\n");
 
-        parseResult(result.toString());
+        parseResult(result.toString(), null);
       }
     }
     else if (database.getSelectedItem().equals("PDB"))
@@ -210,7 +210,7 @@ public class SequenceFetcher
 
 
       if (result.length()>0)
-        parseResult(result.toString());
+        parseResult(result.toString(), null);
     }
     else if( database.getSelectedItem().equals("PFAM"))
     {
@@ -221,7 +221,7 @@ public class SequenceFetcher
            );
 
          if(result.length()>0)
-           parseResult( result.toString() );
+           parseResult( result.toString(), textfield.getText().toUpperCase() );
 
       }catch(java.io.IOException ex)
       {   result = null;    }
@@ -272,7 +272,7 @@ public class SequenceFetcher
       }
 
       //Then read in the features and apply them to the dataset
-      SequenceI[] sequence = parseResult(result.toString());
+      SequenceI[] sequence = parseResult(result.toString(), null);
       for (int i = 0; i < entries.size(); i++)
       {
         UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
@@ -336,23 +336,28 @@ public class SequenceFetcher
     return result;
   }
 
-  SequenceI[] parseResult(String result)
+  SequenceI[] parseResult(String result, String title)
   {
     String format = IdentifyFile.Identify(result, "Paste");
     SequenceI[] sequences = null;
 
     if (FormatAdapter.formats.contains(format))
     {
-      sequences = new FormatAdapter().readFile(result.toString(), "Paste",
-                                               format);
+      sequences = null;
+      try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
+                                               format);}
+      catch(Exception ex){}
+
       if (sequences != null && sequences.length > 0)
       {
         if (alignFrame == null)
         {
           AlignFrame af = new AlignFrame(new Alignment(sequences));
           af.currentFileFormat = format;
+          if(title==null)
+            title = "Retrieved from " + database.getSelectedItem();
           Desktop.addInternalFrame(af,
-                                   "Retrieved from " + database.getSelectedItem(),
+                                   title,
                                    AlignFrame.NEW_WINDOW_WIDTH,
                                    AlignFrame.NEW_WINDOW_HEIGHT);
           af.statusBar.setText("Successfully pasted alignment file");
@@ -370,7 +375,7 @@ public class SequenceFetcher
             alignFrame.viewport.alignment.addSequence(sequences[i]);
 
             ////////////////////////////
-            //Datset needs extension;
+            //Dataset needs extension;
             /////////////////////////////
             Sequence ds = new Sequence(sequences[i].getName(),
                                        AlignSeq.extractGaps("-. ",