X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=cb99f87127d59695c5f01b48757261635e2211b8;hb=c94c1390298db2e80abc04b371d3e7767f5e5968;hp=a854c6c1cae9f76ae325d9d19ee464db328ea35f;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index a854c6c..cb99f87 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,64 +1,71 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.
- *
+ * 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 .
+ * 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 jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+
import java.awt.Container;
+import java.util.ArrayList;
import java.util.BitSet;
-import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolViewer;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-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);
+ super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
+ chains, protocol);
}
public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
SequenceI[][] seqs)
{
- super(viewer);
+ super(alignPanel.getStructureSelectionManager(), seqs, viewer);
ap = alignPanel;
- this.sequence = seqs;
notifyFileLoaded(null, null, null, null, 0);
}
public void updateColours(Object source)
{
-
+
// TODO Auto-generated method stub
}
@@ -68,9 +75,10 @@ public class ExtJmol extends JalviewJmolBinding
showUrl(arg0, "jmol");
}
- public FeatureRenderer getFeatureRenderer()
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- if (ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
{
return ap.getFeatureRenderer();
}
@@ -80,9 +88,9 @@ 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)
@@ -117,35 +125,44 @@ public class ExtJmol extends JalviewJmolBinding
public void refreshPdbEntries()
{
- Vector pdbe = new Vector();
- Hashtable fileids = new Hashtable();
+ List pdbe = new ArrayList();
+ List fileids = new ArrayList();
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
- for (int s=0;s