javadoc

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 2ecdc89..34e8143 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -372,9 +372,11 @@ public class SequenceFetcher extends JPanel implements Runnable
     {
       error += "Please select the source database\n";
     }
-    com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
+    // TODO: make this transformation optional and configurable
+    com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("(\\s|[,; ])+",";"); //\\s+", "");
     textArea.setText(empty.replaceAll(textArea.getText()));
-    if (textArea.getText().length() == 0)
+    // see if there's anthing to search with
+    if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea.getText()))
     {
       error += "Please enter a (semi-colon separated list of) database id(s)";
     }
@@ -664,7 +666,19 @@ public class SequenceFetcher extends JPanel implements Runnable
         {
           title = "Retrieved from " + database.getSelectedItem();
         }
-
+        SequenceFeature[] sfs=null;
+        for (Enumeration sq=al.getSequences().elements(); sq.hasMoreElements();)
+        {
+          if ((sfs=((SequenceI)sq.nextElement()).getDatasetSequence().getSequenceFeatures())!=null)
+          {
+            if (sfs.length>0)
+            {
+              af.setShowSeqFeatures(true);
+              break;
+            }
+          }
+          
+        }
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);