_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()
{
});
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()
{
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);
command = "";
}
jmb.evalStateCommand(command);
+ jmb.evalStateCommand("set hoverDelay=0.1");
jmb.setFinishedInit(true);
}
MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
allChainsSelected = true;
menuItem = new JCheckBoxMenuItem(chain, true);
menuItem.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
jmb.centerViewer(toshow);
}
+ @Override
public void closeViewer(boolean closeExternalViewer)
{
// Jmol does not use an external viewer
jmb = null;
}
+ @Override
public void run()
{
_started = true;
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
{
}
if (progressBar != null)
{
- progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
+ progressBar.setProgressBar(
+ MessageManager.getString("label.state_completed"), hdl);
}
if (pdbseq != null)
{
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);
}
jmb.updateColours(ap);
}
// do superposition if asked to
- if (alignAddedStructures)
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
if (jmb.viewer.isScriptExecuting())
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));
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,
- 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",
- width, height, null, this.getTitle());
+ width, height, null, this.getTitle(), null, 0, false);
}
if (im.getGraphics() != null)
@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);
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);