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patch for secondary issue in JAL-664 re parsing empty fields in description line
[jalview.git]
/
src
/
jalview
/
gui
/
AppJmol.java
diff --git
a/src/jalview/gui/AppJmol.java
b/src/jalview/gui/AppJmol.java
index
7af2cfb
..
041d6a2
100644
(file)
--- a/
src/jalview/gui/AppJmol.java
+++ b/
src/jalview/gui/AppJmol.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
@@
-49,7
+49,7
@@
public class AppJmol extends GStructureViewer implements Runnable,
AppJmolBinding jmb;
JPanel scriptWindow;
AppJmolBinding jmb;
JPanel scriptWindow;
-
+
JSplitPane splitPane;
RenderPanel renderPanel;
JSplitPane splitPane;
RenderPanel renderPanel;
@@
-255,12
+255,13
@@
public class AppJmol extends GStructureViewer implements Runnable,
* @param pdbentry
* @param seq
* @param chains
* @param pdbentry
* @param seq
* @param chains
- * @param alignFrame
+ * @param alignFrame
* @param align
* if true, new structure(s) will be align using associated alignment
*/
private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
* @param align
* if true, new structure(s) will be align using associated alignment
*/
private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
- final String[] chains, final boolean b, final IProgressIndicator alignFrame)
+ final String[] chains, final boolean b,
+ final IProgressIndicator alignFrame)
{
if (pdbentry.getFile() == null)
{
{
if (pdbentry.getFile() == null)
{
@@
-298,7
+299,7
@@
public class AppJmol extends GStructureViewer implements Runnable,
addingStructures = true;
_started = false;
alignAddedStructures = b;
addingStructures = true;
_started = false;
alignAddedStructures = b;
- progressBar = alignFrame; // visual indication happens on caller frame.
+ progressBar = alignFrame; // visual indication happens on caller frame.
(worker = new Thread(this)).start();
return;
}
(worker = new Thread(this)).start();
return;
}
@@
-340,8
+341,10
@@
public class AppJmol extends GStructureViewer implements Runnable,
bl.setVgap(0);
scriptWindow = new JPanel(bl);
scriptWindow.setVisible(false);
bl.setVgap(0);
scriptWindow = new JPanel(bl);
scriptWindow.setVisible(false);
- };
- jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null);
+ }
+ ;
+ jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
+ null);
jmb.newJmolPopup(true, "Jmol", true);
jmb.evalStateCommand(command);
jmb.setFinishedInit(true);
jmb.newJmolPopup(true, "Jmol", true);
jmb.evalStateCommand(command);
jmb.setFinishedInit(true);
@@
-414,7
+417,7
@@
public class AppJmol extends GStructureViewer implements Runnable,
void closeViewer()
{
jmb.closeViewer();
void closeViewer()
{
jmb.closeViewer();
-
+
// TODO: check for memory leaks where instance isn't finalised because jmb
// holds a reference to the window
jmb = null;
// TODO: check for memory leaks where instance isn't finalised because jmb
// holds a reference to the window
jmb = null;
@@
-445,11
+448,10
@@
public class AppJmol extends GStructureViewer implements Runnable,
// retrieve the pdb and store it locally
AlignmentI pdbseq = null;
pdbid = jmb.pdbentry[pi].getId();
// retrieve the pdb and store it locally
AlignmentI pdbseq = null;
pdbid = jmb.pdbentry[pi].getId();
- long hdl=pdbid.hashCode()-System.currentTimeMillis();
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
if (progressBar != null)
{
- progressBar.setProgressBar("Fetching PDB " + pdbid,
- hdl);
+ progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
}
try
{
}
try
{
@@
-557,23
+559,24
@@
public class AppJmol extends GStructureViewer implements Runnable,
{
Cache.log.error("Couldn't add files to Jmol viewer!", ex);
}
{
Cache.log.error("Couldn't add files to Jmol viewer!", ex);
}
- long lastnotify=jmb.getLoadNotifiesHandled();
- // need to wait around until script has finished
- while (lastnotify>=jmb.getLoadNotifiesHandled());
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ // need to wait around until script has finished
+ while (lastnotify >= jmb.getLoadNotifiesHandled())
+ ;
+ {
+ try
{
{
- try
- {
- Thread.sleep(35);
- } catch (Exception e)
- {
- }
- }
- // refresh the sequence colours for the new structure(s)
- jmb.updateColours(ap);
- // do superposition if asked to
- if (alignAddedStructures)
+ Thread.sleep(35);
+ } catch (Exception e)
{
{
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ }
+ }
+ // refresh the sequence colours for the new structure(s)
+ jmb.updateColours(ap);
+ // do superposition if asked to
+ if (alignAddedStructures)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
public void run()
{
{
public void run()
{
@@
-787,7
+790,8
@@
public class AppJmol extends GStructureViewer implements Runnable,
{
}
}
{
}
}
-public void showConsole(boolean showConsole)
+
+ public void showConsole(boolean showConsole)
{
if (showConsole)
{
if (showConsole)
@@
-808,9
+812,9
@@
public void showConsole(boolean showConsole)
else
{
if (splitPane != null)
else
{
if (splitPane != null)
- {
- splitPane.setVisible(false);
- }
+ {
+ splitPane.setVisible(false);
+ }
splitPane = null;
splitPane = null;
@@
-819,6
+823,7
@@
public void showConsole(boolean showConsole)
validate();
}
validate();
}
+
class RenderPanel extends JPanel
{
final Dimension currentSize = new Dimension();
class RenderPanel extends JPanel
{
final Dimension currentSize = new Dimension();