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JAL-1563 JAL-2071 Update and completed implementation for UniProt FTS support
[jalview.git]
/
src
/
jalview
/
gui
/
AppJmol.java
diff --git
a/src/jalview/gui/AppJmol.java
b/src/jalview/gui/AppJmol.java
index
dcd4f7d
..
a1846bc
100644
(file)
--- a/
src/jalview/gui/AppJmol.java
+++ b/
src/jalview/gui/AppJmol.java
@@
-174,7
+174,8
@@
public class AppJmol extends StructureViewerBase
_alignwith = new Vector<AlignmentPanel>();
}
_alignwith = new Vector<AlignmentPanel>();
}
- seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
+ seqColourBy = new ViewSelectionMenu(
+ MessageManager.getString("label.colour_by"), this, _colourwith,
new ItemListener()
{
new ItemListener()
{
@@
-194,7
+195,8
@@
public class AppJmol extends StructureViewerBase
});
viewMenu.add(seqColourBy);
final ItemListener handler;
});
viewMenu.add(seqColourBy);
final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
+ JMenu alpanels = new ViewSelectionMenu(
+ MessageManager.getString("label.superpose_with"), this,
_alignwith, handler = new ItemListener()
{
_alignwith, handler = new ItemListener()
{
@@
-205,8
+207,8
@@
public class AppJmol extends StructureViewerBase
alignStructs.setToolTipText(MessageManager
.formatMessage(
"label.align_structures_using_linked_alignment_views",
alignStructs.setToolTipText(MessageManager
.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new String[]
- { new Integer(_alignwith.size()).toString() }));
+ new String[] { new Integer(_alignwith
+ .size()).toString() }));
}
});
handler.itemStateChanged(null);
}
});
handler.itemStateChanged(null);
@@
-381,6
+383,7
@@
public class AppJmol extends StructureViewerBase
command = "";
}
jmb.evalStateCommand(command);
command = "";
}
jmb.evalStateCommand(command);
+ jmb.evalStateCommand("set hoverDelay=0.1");
jmb.setFinishedInit(true);
}
jmb.setFinishedInit(true);
}
@@
-395,6
+398,7
@@
public class AppJmol extends StructureViewerBase
MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
allChainsSelected = true;
public void actionPerformed(ActionEvent evt)
{
allChainsSelected = true;
@@
-417,6
+421,7
@@
public class AppJmol extends StructureViewerBase
menuItem = new JCheckBoxMenuItem(chain, true);
menuItem.addItemListener(new ItemListener()
{
menuItem = new JCheckBoxMenuItem(chain, true);
menuItem.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
@@
-449,6
+454,7
@@
public class AppJmol extends StructureViewerBase
jmb.centerViewer(toshow);
}
jmb.centerViewer(toshow);
}
+ @Override
public void closeViewer(boolean closeExternalViewer)
{
// Jmol does not use an external viewer
public void closeViewer(boolean closeExternalViewer)
{
// Jmol does not use an external viewer
@@
-465,6
+471,7
@@
public class AppJmol extends StructureViewerBase
jmb = null;
}
jmb = null;
}
+ @Override
public void run()
{
_started = true;
public void run()
{
_started = true;
@@
-488,7
+495,8
@@
public class AppJmol extends StructureViewerBase
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
- progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
+ progressBar.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_pdb", new String[] { pdbid }), hdl);
}
try
{
}
try
{
@@
-503,7
+511,8
@@
public class AppJmol extends StructureViewerBase
}
if (progressBar != null)
{
}
if (progressBar != null)
{
- progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
+ progressBar.setProgressBar(
+ MessageManager.getString("label.state_completed"), hdl);
}
if (pdbseq != null)
{
}
if (pdbseq != null)
{
@@
-554,9
+563,8
@@
public class AppJmol extends StructureViewerBase
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new String[]
- { errormsgs.toString() }), MessageManager
- .getString("label.couldnt_load_file"),
+ new String[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
JOptionPane.ERROR_MESSAGE);
}
JOptionPane.ERROR_MESSAGE);
}
@@
-623,10
+631,11
@@
public class AppJmol extends StructureViewerBase
jmb.updateColours(ap);
}
// do superposition if asked to
jmb.updateColours(ap);
}
// do superposition if asked to
- if (alignAddedStructures)
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
if (jmb.viewer.isScriptExecuting())
public void run()
{
if (jmb.viewer.isScriptExecuting())
@@
-674,8
+683,7
@@
public class AppJmol extends StructureViewerBase
try
{
// TODO: cope with multiple PDB files in view
try
{
// TODO: cope with multiple PDB files in view
- in = new BufferedReader(new FileReader(
- jmb.getPdbFile()[0]));
+ in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@
-749,22
+757,21
@@
public class AppJmol extends StructureViewerBase
if (type == jalview.util.ImageMaker.TYPE.PNG)
{
im = new jalview.util.ImageMaker(this,
if (type == jalview.util.ImageMaker.TYPE.PNG)
{
im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG,
- "Make PNG image from view", width, height, null, null);
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+ width, height, null, null, null, 0, false);
}
else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
im = new jalview.util.ImageMaker(this,
}
else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS,
- "Make EPS file from view", width, height, null,
- this.getTitle());
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+ width, height, null, this.getTitle(), null, 0, false);
}
else
{
im = new jalview.util.ImageMaker(this,
jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
}
else
{
im = new jalview.util.ImageMaker(this,
jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle());
+ width, height, null, this.getTitle(), null, 0, false);
}
if (im.getGraphics() != null)
}
if (im.getGraphics() != null)
@@
-889,8
+896,9
@@
public class AppJmol extends StructureViewerBase
@Override
public void backGround_actionPerformed(ActionEvent actionEvent)
{
@Override
public void backGround_actionPerformed(ActionEvent actionEvent)
{
- java.awt.Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_backgroud_colour"), null);
+ java.awt.Color col = JColorChooser
+ .showDialog(this, MessageManager
+ .getString("label.select_backgroud_colour"), null);
if (col != null)
{
jmb.setBackgroundColour(col);
if (col != null)
{
jmb.setBackgroundColour(col);
@@
-1067,6
+1075,7
@@
public class AppJmol extends StructureViewerBase
}
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);