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 3323d67..aaa3405 100644 (file)
--- a/examples/groovy/selectColumnsByFeatureAndGroup.groovy
+++ b/examples/groovy/selectColumnsByFeatureAndGroup.groovy
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,7 +23,7 @@ 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
 
@@ -81,7 +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.");
@@ -92,8 +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
+    }