X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=cb99f87127d59695c5f01b48757261635e2211b8;hb=c94c1390298db2e80abc04b371d3e7767f5e5968;hp=b3d1a3cb2a944d0296030ddb9536ff185ae2ce8f;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index b3d1a3c..cb99f87 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,38 +1,41 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 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 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 java.awt.Container;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.List;
+import java.util.Vector;
+
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolViewer;
+
/**
* bind an alignment view to an external Jmol instance.
*
@@ -48,15 +51,15 @@ public class ExtJmol extends JalviewJmolBinding
PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
String protocol)
{
- super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq, chains, protocol);
+ super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
+ chains, protocol);
}
public ExtJmol(JmolViewer 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);
}
@@ -74,8 +77,8 @@ public class ExtJmol extends JalviewJmolBinding
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (AlignmentPanel)alignment;
- if (ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
{
return ap.getFeatureRenderer();
}
@@ -87,7 +90,7 @@ public class ExtJmol extends JalviewJmolBinding
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
- return ((AlignmentPanel)alignment).getSequenceRenderer();
+ return ((AlignmentPanel) alignment).getSequenceRenderer();
}
public void notifyScriptTermination(String strStatus, int msWalltime)
@@ -122,8 +125,8 @@ 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 < sq.length; s++)
{
@@ -133,18 +136,23 @@ public class ExtJmol extends JalviewJmolBinding
for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
{
PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
- if (!fileids.containsKey(pentry.getId()))
+ if (!fileids.contains(pentry.getId()))
{
- pdbe.addElement(pentry);
+ pdbe.add(pentry);
+ }
+ else
+ {
+ 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
@@ -169,19 +177,7 @@ 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();
}
@@ -189,7 +185,7 @@ public class ExtJmol extends JalviewJmolBinding
public void releaseReferences(Object svl)
{
// TODO Auto-generated method stub
-
+
}
}