X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=5a6d0d09d71cf0e4e5f0a635ae7e26bb2b947ce4;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=f73fb4156529ea378211dbc19c81fbb08cfac5ce;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index f73fb41..5a6d0d0 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,37 +1,42 @@
/*
- * 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;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
+
+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 javajs.util.BS;
+import org.jmol.viewer.Viewer;
/**
* bind an alignment view to an external Jmol instance.
@@ -44,41 +49,39 @@ public class ExtJmol extends JalviewJmolBinding
private AlignmentPanel ap;
- protected ExtJmol(jalview.appletgui.AlignFrame alframe,
- PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
- String protocol)
+ protected ExtJmol(AlignFrame alframe, PDBEntry[] pdbentry,
+ SequenceI[][] seq, DataSourceType protocol)
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
- chains, protocol);
+ 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);
}
+ @Override
public void updateColours(Object source)
{
-
- // TODO Auto-generated method stub
-
}
+ @Override
public void showUrl(String arg0)
{
showUrl(arg0, "jmol");
}
+ @Override
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
+ AlignmentPanel alignPanel = (AlignmentPanel) alignment;
+ if (alignPanel.av.isShowSequenceFeatures())
{
- return ap.getFeatureRenderer();
+ return alignPanel.getFeatureRenderer();
}
else
{
@@ -86,66 +89,80 @@ 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)
+ @Override
+ 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
@@ -153,16 +170,15 @@ public class ExtJmol extends JalviewJmolBinding
{
// This never gets called because we haven't overriden the associated Jmol's
// console
- System.err
- .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+ System.err.println(
+ "WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+ show);
}
@Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
- // TODO Auto-generated method stub
return null;
}
@@ -170,27 +186,19 @@ 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();
}
@Override
public void releaseReferences(Object svl)
{
- // TODO Auto-generated method stub
+ }
+ @Override
+ public Map getJSpecViewProperty(String arg0)
+ {
+ return null;
}
}