JAL-4305 Isolate and unify the Jalview object from all the gubbins in jalview.bin...

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

diff --git a/examples/groovy/selectColumnsByFeatureAndGroup.groovy b/examples/groovy/selectColumnsByFeatureAndGroup.groovy
index 0a16391..aaa3405 100644 (file)
--- a/examples/groovy/selectColumnsByFeatureAndGroup.groovy
+++ b/examples/groovy/selectColumnsByFeatureAndGroup.groovy
@@ -1,9 +1,29 @@
+/*
+ * 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;
 import java.util.BitSet;
-import javax.swing.JOptionPane;
+import jalview.gui.JvOptionPane;
 import groovy.swing.SwingBuilder;
 def toselect = getFeatureInput(); // change this to select the desired feature type
 
@@ -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))
@@ -61,7 +81,7 @@ for (ala in Jalview.getAlignframes()) {
         cs.addElement(i);
         }
       ala.viewport.setColumnSelection(cs);
-      ala.alignPanel.paintAlignment(true);
+      ala.alignPanel.paintAlignment(true, true);
       ala.statusBar.setText("Marked "+bs.cardinality()+" columns containing features of type "+toselect)
       } else {
         ala.statusBar.setText("No features of type "+toselect+" found.");
@@ -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
+    }