X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=647929695d12be9b8d1dac815dccadd77de3ce9e;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=2c5da174bb38c206e0e1bd589da1d7027867e85b;hpb=cdb2c3afc153577cceb0d5c6a4b12532f6dde601;p=jalview.git
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 2c5da17..6479296 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,45 +1,72 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.util.BitSet;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.jmol.api.JmolViewer;
-
+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.List;
+import java.util.Map;
+import java.util.Vector;
+
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.java.BS;
+import org.jmol.viewer.Viewer;
+
/**
* 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)
+ public ExtJmol(Viewer 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
}
@@ -49,9 +76,11 @@ public class ExtJmol extends JalviewJmolBinding
showUrl(arg0, "jmol");
}
- public FeatureRenderer getFeatureRenderer()
+ @Override
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- if (ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
{
return ap.getFeatureRenderer();
}
@@ -61,64 +90,118 @@ public class ExtJmol extends JalviewJmolBinding
}
}
- public SequenceRenderer getSequenceRenderer()
+ @Override
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
- return ap.getSequenceRenderer();
+ return ((AlignmentPanel) alignment).getSequenceRenderer();
}
+ @Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// ignore
}
+ @Override
public void sendConsoleEcho(String strEcho)
{
// ignore
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
// ignore
}
+ @Override
public void showUrl(String url, String target)
{
ap.alignFrame.showURL(url, target);
}
- public void updateUI()
+ @Override
+ public void refreshGUI()
{
// ignore
}
- public void selectionChanged(BitSet arg0)
+ public void selectionChanged(BS arg0)
{
System.out.println(arg0);
}
+ @Override
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 pdbids = sq[s].getAllPDBEntries();
+ if (pdbids != null)
{
- for (int pe=0,peSize=pdbids.size(); pe getJSpecViewProperty(String arg0)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}