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JAL-1859 removed unneeded dependency on package not in Jmol applet lib
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 3 Sep 2015 13:36:50 +0000
(14:36 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 3 Sep 2015 13:36:50 +0000
(14:36 +0100)
src/jalview/ext/jmol/PDBFileWithJmol.java
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diff --git
a/src/jalview/ext/jmol/PDBFileWithJmol.java
b/src/jalview/ext/jmol/PDBFileWithJmol.java
index
cb19769
..
ddfa1b0
100644
(file)
--- a/
src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/
src/jalview/ext/jmol/PDBFileWithJmol.java
@@
-45,7
+45,6
@@
import org.jmol.modelset.ModelSet;
import org.jmol.modelsetbio.BioModel;
import org.jmol.modelsetbio.BioPolymer;
import org.jmol.viewer.Viewer;
import org.jmol.modelsetbio.BioModel;
import org.jmol.modelsetbio.BioPolymer;
import org.jmol.viewer.Viewer;
-import org.openscience.jmol.app.JmolApp;
/**
* Import and process PDB files with Jmol
/**
* Import and process PDB files with Jmol
@@
-56,9
+55,6
@@
import org.openscience.jmol.app.JmolApp;
public class PDBFileWithJmol extends AlignFile implements
JmolStatusListener
{
public class PDBFileWithJmol extends AlignFile implements
JmolStatusListener
{
-
- JmolApp jmolApp = null;
-
Viewer viewer = null;
public PDBFileWithJmol(String inFile, String type) throws IOException
Viewer viewer = null;
public PDBFileWithJmol(String inFile, String type) throws IOException
@@
-73,7
+69,6
@@
public class PDBFileWithJmol extends AlignFile implements
public PDBFileWithJmol()
{
public PDBFileWithJmol()
{
- // TODO Auto-generated constructor stub
}
/**
}
/**
@@
-84,18
+79,11
@@
public class PDBFileWithJmol extends AlignFile implements
private Viewer getJmolData()
{
if (viewer == null)
private Viewer getJmolData()
{
if (viewer == null)
- { // note that -o -n -x are all implied // TODO check for Jmol 14.2
- jmolApp = new JmolApp();
- jmolApp.isDataOnly = true;
- jmolApp.haveConsole = false;
- jmolApp.haveDisplay = false;
+ {
try
{
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
null, "-x -o -n", this);
try
{
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
null, "-x -o -n", this);
- viewer.setScreenDimension(jmolApp.startupWidth,
- jmolApp.startupHeight);
- jmolApp.startViewer(viewer, null, false);
} catch (ClassCastException x)
{
throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}),
} catch (ClassCastException x)
{
throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}),