X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=5714ce9f5dc1dcb1478beffb7bf57d64614f3039;hb=9ff5fcbe6681e37c441656e2f704f8d9bab9179c;hp=4bee84c6de88606f49f23b410b23fd7fa0fcc943;hpb=1b5f1de68f3f4dadcd4eecc80a5db17441eb7ab6;p=jalview.git
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 4bee84c..5714ce9 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;
@@ -8,23 +25,27 @@ import java.util.Vector;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolViewer;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
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 +62,7 @@ public class ExtJmol extends JalviewJmolBinding
public void updateColours(Object source)
{
-
+
// TODO Auto-generated method stub
}
@@ -51,8 +72,9 @@ public class ExtJmol extends JalviewJmolBinding
showUrl(arg0, "jmol");
}
- public FeatureRenderer getFeatureRenderer()
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
+ AlignmentPanel ap = (AlignmentPanel)alignment;
if (ap.av.showSequenceFeatures)
{
return ap.getFeatureRenderer();
@@ -63,9 +85,9 @@ public class ExtJmol extends JalviewJmolBinding
}
}
- public SequenceRenderer getSequenceRenderer()
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
- return ap.getSequenceRenderer();
+ return ((AlignmentPanel)alignment).getSequenceRenderer();
}
public void notifyScriptTermination(String strStatus, int msWalltime)
@@ -103,22 +125,23 @@ public class ExtJmol extends JalviewJmolBinding
Vector pdbe = new Vector();
Hashtable fileids = new Hashtable();
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
- for (int s=0;s