X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=d3dad58f982edccc05f422578f0e94b0eae4b445;hb=6b71746c98f7c1118b474b0b920db3bd7b2a15c0;hp=63c1ca74b42f54ee58be5392907cd99706933e21;hpb=e683768e084c5e2999846de881b3903f62417919;p=jalview.git
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 63c1ca7..d3dad58 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,3 +1,20 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
package jalview.appletgui;
import java.awt.Container;
@@ -16,15 +33,17 @@ import jalview.ext.jmol.JalviewJmolBinding;
/**
* bind an alignment view to an external Jmol instance.
+ *
* @author JimP
- *
+ *
*/
public class ExtJmol extends JalviewJmolBinding
{
private AlignmentPanel ap;
- protected ExtJmol(jalview.appletgui.AlignFrame alframe, PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
+ protected ExtJmol(jalview.appletgui.AlignFrame alframe,
+ PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
String protocol)
{
super(pdbentry, seq, chains, protocol);
@@ -41,7 +60,7 @@ public class ExtJmol extends JalviewJmolBinding
public void updateColours(Object source)
{
-
+
// TODO Auto-generated method stub
}
@@ -103,22 +122,23 @@ public class ExtJmol extends JalviewJmolBinding
Vector pdbe = new Vector();
Hashtable fileids = new Hashtable();
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
- for (int s=0;s