X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FJsSelectionSender.java;h=c2a963e4997167126ce561e93386823d20cab0ce;hb=e1cb1f4ff4ae05504c806d99395358629c807956;hp=d9e1b98d4924099499c9c70530a006e6ed241bc9;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/javascript/JsSelectionSender.java b/src/jalview/javascript/JsSelectionSender.java
index d9e1b98..c2a963e 100644
--- a/src/jalview/javascript/JsSelectionSender.java
+++ b/src/jalview/javascript/JsSelectionSender.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
  * 
@@ -23,11 +23,12 @@ package jalview.javascript;
 import jalview.appletgui.AlignFrame;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.structure.SelectionSource;
 
-public class JsSelectionSender extends JSFunctionExec implements
-        jalview.structure.SelectionListener, JsCallBack
+public class JsSelectionSender extends JSFunctionExec
+        implements jalview.structure.SelectionListener, JsCallBack
 {
 
   AlignFrame _af;
@@ -44,13 +45,13 @@ public class JsSelectionSender extends JSFunctionExec implements
 
   @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
-          SelectionSource source)
+          HiddenColumns hidden, SelectionSource source)
   {
-    // System.err.println("Testing selection event relay to jsfunction:"+_listener);
+    // System.err.println("Testing selection event relay to
+    // jsfunction:"+_listener);
     try
     {
       String setid = "";
-      String viewid = "";
       AlignFrame src = _af;
       if (source != null)
       {
@@ -62,12 +63,10 @@ public class JsSelectionSender extends JSFunctionExec implements
 
         }
       }
-      String[] seqs = new String[]
-      {};
-      String[] cols = new String[]
-      {};
-      int strt = 0, end = (src == null) ? -1 : src.alignPanel.av
-              .getAlignment().getWidth();
+      String[] seqs = new String[] {};
+      String[] cols = new String[] {};
+      int strt = 0, end = (src == null) ? -1
+              : src.alignPanel.av.getAlignment().getWidth();
       if (seqsel != null && seqsel.getSize() > 0)
       {
         seqs = new String[seqsel.getSize()];
@@ -84,19 +83,16 @@ public class JsSelectionSender extends JSFunctionExec implements
           end = seqsel.getEndRes();
         }
       }
-      if (colsel != null && colsel.size() > 0)
+      if (colsel != null && !colsel.isEmpty())
       {
         if (end == -1)
         {
           end = colsel.getMax() + 1;
         }
         cols = new String[colsel.getSelected().size()];
-        int d = 0, r = -1;
         for (int i = 0; i < cols.length; i++)
         {
-          cols[i] = ""
-                  + (1 + ((Integer) colsel.getSelected().elementAt(i))
-                          .intValue());
+          cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
         }
       }
       else
@@ -111,15 +107,14 @@ public class JsSelectionSender extends JSFunctionExec implements
 
       }
       System.err.println("Relaying selection to jsfunction:" + _listener);
-      executeJavascriptFunction(
-              _listener,
+      executeJavascriptFunction(_listener,
               new Object[]
               { src, setid, jvlite.arrayToSeparatorList(seqs),
                   jvlite.arrayToSeparatorList(cols) });
     } catch (Exception ex)
     {
-      System.err
-              .println("Jalview Javascript exec error: Couldn't send selection message using function '"
+      System.err.println(
+              "Jalview Javascript exec error: Couldn't send selection message using function '"
                       + _listener + "'");
       ex.printStackTrace();
       if (ex instanceof netscape.javascript.JSException)