X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=ae6b5ab385522fbc36bce17f1a3ae005ac991a9c;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=2c5da174bb38c206e0e1bd589da1d7027867e85b;hpb=cdb2c3afc153577cceb0d5c6a4b12532f6dde601;p=jalview.git
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 2c5da17..ae6b5ab 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,11 +1,32 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.appletgui;
+import java.awt.Container;
import java.util.BitSet;
import java.util.Hashtable;
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.PDBEntry;
@@ -14,24 +35,27 @@ 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);
+ super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
+ chains, protocol);
}
public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
- SequenceI[] seqs)
+ SequenceI[][] seqs)
{
- super(viewer);
+ super(alignPanel.getStructureSelectionManager(), viewer);
ap = alignPanel;
this.sequence = seqs;
notifyFileLoaded(null, null, null, null, 0);
@@ -39,7 +63,7 @@ public class ExtJmol extends JalviewJmolBinding
public void updateColours(Object source)
{
-
+
// TODO Auto-generated method stub
}
@@ -49,8 +73,9 @@ 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();
@@ -61,9 +86,9 @@ 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)
@@ -86,7 +111,7 @@ public class ExtJmol extends JalviewJmolBinding
ap.alignFrame.showURL(url, target);
}
- public void updateUI()
+ public void refreshGUI()
{
// ignore
}
@@ -101,24 +126,71 @@ public class ExtJmol extends JalviewJmolBinding
Vector pdbe = new Vector();
Hashtable fileids = new Hashtable();
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
- for (int s=0;s