Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / examples / groovy / stripUniprotPrefixes.groovy

diff --git a/examples/groovy/stripUniprotPrefixes.groovy b/examples/groovy/stripUniprotPrefixes.groovy
index e2bb129..5a01da4 100644 (file)
--- a/examples/groovy/stripUniprotPrefixes.groovy
+++ b/examples/groovy/stripUniprotPrefixes.groovy
@@ -1,15 +1,35 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 
-def af = Jalview.getAlignframes();
+def af = Jalview.getAlignFrames();
 
 // walk through  all alignments, stripping off all text prior to and including last '|' symbol in sequence IDs
 
 for (ala in af)
 {
-       def al = ala.viewport.alignment;
+       def al = ala.getViewport().getAlignment();
        if (al!=null)
        {
                SequenceI[] seqs = al.getSequencesArray();
@@ -27,5 +47,6 @@ for (ala in af)
                        }
                }
        }
+       ala.repaint();
 }
-       
\ No newline at end of file
+