X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Fgroovy%2FselectColumnsByFeatureAndGroup.groovy;h=b8edaa7f25be83acf7e8a333e2f151b8b800d1d9;hb=9276cd700c1157d058538fc4e4676c3dce16deaa;hp=0a16391fa54f4c28d55ded4bb25d658f48a9dadd;hpb=cd340d96daf7a9f885cc1ec9061156f44ecc9fd4;p=jalview.git

diff --git a/examples/groovy/selectColumnsByFeatureAndGroup.groovy b/examples/groovy/selectColumnsByFeatureAndGroup.groovy
index 0a16391..b8edaa7 100644
--- a/examples/groovy/selectColumnsByFeatureAndGroup.groovy
+++ b/examples/groovy/selectColumnsByFeatureAndGroup.groovy
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -11,7 +31,7 @@ def nal=0;
 def nfeat=0;
 def nseq=0;
 
-for (ala in Jalview.getAlignframes()) {
+for (ala in Jalview.getAlignFrames()) {
   def al = ala.viewport.alignment;
     if (al!=null)
     {
@@ -21,7 +41,7 @@ for (ala in Jalview.getAlignframes()) {
       {
           def tfeat=0;
         if (sq!=null) {
-          SequenceFeature[] sf = sq.getDatasetSequence().getSequenceFeatures();
+          SequenceFeature[] sf = sq.getSequenceFeatures();
           for (sfpos in sf)
           {
             if (sfpos!=null && sfpos.getType().equals(toselect))
@@ -72,8 +92,8 @@ return "Found a total of ${nfeat} features across ${nseq} sequences in ${nal} al
     
 String getFeatureInput(){
         def swingBuilder = new SwingBuilder();
-        def response = JOptionPane.showInputDialog(
-                   null, 'Select columns by feature by type','Enter type of feature', JOptionPane.OK_OPTION)
+        def response = JvOptionPane.showInputDialog(
+                   null, 'Select columns by feature by type','Enter type of feature', JvOptionPane.OK_OPTION)
 
         return response
     }
\ No newline at end of file