X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=929a871106b9c3c4888212175405efac1d13cc9f;hb=d82ec00f14199ef0ce21bd5bc70a59142b7c4b07;hp=aaab8bda6af2a4b3225686ef7c21eca5c16f3037;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index aaab8bd..929a871 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,30 +1,25 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 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;
@@ -32,6 +27,16 @@ 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.
*
@@ -51,12 +56,11 @@ public class ExtJmol extends JalviewJmolBinding
chains, protocol);
}
- public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
+ public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
SequenceI[][] seqs)
{
- super(alignPanel.getStructureSelectionManager(), viewer);
+ super(alignPanel.getStructureSelectionManager(), seqs, viewer);
ap = alignPanel;
- this.sequence = seqs;
notifyFileLoaded(null, null, null, null, 0);
}
@@ -72,10 +76,11 @@ public class ExtJmol extends JalviewJmolBinding
showUrl(arg0, "jmol");
}
+ @Override
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
AlignmentPanel ap = (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
+ if (ap.av.isShowSequenceFeatures())
{
return ap.getFeatureRenderer();
}
@@ -85,66 +90,78 @@ public class ExtJmol extends JalviewJmolBinding
}
}
+ @Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
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);
}
+ @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 < sq.length; s++)
{
- Vector pdbids = sq[s].getPDBId();
+ Vector pdbids = sq[s].getAllPDBEntries();
if (pdbids != null)
{
for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
{
- PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
- if (!fileids.containsKey(pentry.getId()))
+ PDBEntry pentry = pdbids.elementAt(pe);
+ if (!fileids.contains(pentry.getId()))
+ {
+ pdbe.add(pentry);
+ }
+ else
{
- pdbe.addElement(pentry);
+ fileids.add(pentry.getId());
}
}
}
}
- pdbentry = new PDBEntry[pdbe.size()];
+ PDBEntry[] newEntries = new PDBEntry[pdbe.size()];
for (int pe = 0; pe < pdbe.size(); pe++)
{
- pdbentry[pe] = (PDBEntry) pdbe.elementAt(pe);
+ newEntries[pe] = pdbe.get(pe);
}
+ setPdbentry(newEntries);
}
@Override
@@ -158,7 +175,7 @@ public class ExtJmol extends JalviewJmolBinding
}
@Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
// TODO Auto-generated method stub
@@ -169,19 +186,7 @@ public class ExtJmol extends JalviewJmolBinding
protected void releaseUIResources()
{
ap = null;
- if (console != null)
- {
- try
- {
- console.setVisible(false);
- } catch (Error e)
- {
- } catch (Exception x)
- {
- }
- ;
- console = null;
- }
+ closeConsole();
}
@@ -192,4 +197,11 @@ public class ExtJmol extends JalviewJmolBinding
}
+ @Override
+ public Map getJSpecViewProperty(String arg0)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}