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JAL-1780 JAL-653 JAL-1892 brackets in wrong place broke ‘add to file’ for splitframe...
[jalview.git]
/
src
/
jalview
/
appletgui
/
ExtJmol.java
diff --git
a/src/jalview/appletgui/ExtJmol.java
b/src/jalview/appletgui/ExtJmol.java
index
1efb971
..
cec77d2
100644
(file)
--- a/
src/jalview/appletgui/ExtJmol.java
+++ b/
src/jalview/appletgui/ExtJmol.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,14
+20,6
@@
*/
package jalview.appletgui;
*/
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.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
@@
-35,6
+27,15
@@
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
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.
*
/**
* bind an alignment view to an external Jmol instance.
*
@@
-57,9
+58,8
@@
public class ExtJmol extends JalviewJmolBinding
public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
SequenceI[][] seqs)
{
public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
SequenceI[][] seqs)
{
- super(alignPanel.getStructureSelectionManager(), viewer);
+ super(alignPanel.getStructureSelectionManager(), seqs, viewer);
ap = alignPanel;
ap = alignPanel;
- this.sequence = seqs;
notifyFileLoaded(null, null, null, null, 0);
}
notifyFileLoaded(null, null, null, null, 0);
}
@@
-125,8
+125,8
@@
public class ExtJmol extends JalviewJmolBinding
public void refreshPdbEntries()
{
public void refreshPdbEntries()
{
- Vector pdbe = new Vector();
- Hashtable fileids = new Hashtable();
+ List<PDBEntry> pdbe = new ArrayList<PDBEntry>();
+ List<String> fileids = new ArrayList<String>();
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
for (int s = 0; s < sq.length; s++)
{
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
for (int s = 0; s < sq.length; s++)
{
@@
-136,18
+136,23
@@
public class ExtJmol extends JalviewJmolBinding
for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
{
PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
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++)
{
for (int pe = 0; pe < pdbe.size(); pe++)
{
- pdbentry[pe] = (PDBEntry) pdbe.elementAt(pe);
+ newEntries[pe] = pdbe.get(pe);
}
}
+ setPdbentry(newEntries);
}
@Override
}
@Override
@@
-172,19
+177,7
@@
public class ExtJmol extends JalviewJmolBinding
protected void releaseUIResources()
{
ap = null;
protected void releaseUIResources()
{
ap = null;
- if (console != null)
- {
- try
- {
- console.setVisible(false);
- } catch (Error e)
- {
- } catch (Exception x)
- {
- }
- ;
- console = null;
- }
+ closeConsole();
}
}