alignStructs.setToolTipText(MessageManager
.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new Object[]
- { new Integer(_alignwith.size()).toString() }));
+ new Object[] { new Integer(_alignwith
+ .size()).toString() }));
}
});
handler.itemStateChanged(null);
this.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
String chain = null;
if (seq.getDatasetSequence() != null)
{
- Vector<PDBEntry> pdbrefs = seq.getDatasetSequence().getAllPDBEntries();
+ Vector<PDBEntry> pdbrefs = seq.getDatasetSequence()
+ .getAllPDBEntries();
if (pdbrefs != null && pdbrefs.size() > 0)
{
chain = pdbrefs.get(0).getChainCode();
* @param newViewId
*/
public ChimeraViewFrame(String chimeraSessionFile,
- AlignmentPanel alignPanel,
- PDBEntry[] pdbArray,
+ AlignmentPanel alignPanel, PDBEntry[] pdbArray,
SequenceI[][] seqsArray, boolean colourByChimera,
boolean colourBySequence, String newViewId)
{
void initChimera()
{
jmb.setFinishedInit(false);
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
- getBounds().width, getBounds().height);
+ jalview.gui.Desktop.addInternalFrame(this,
+ jmb.getViewerTitle("Chimera", true), getBounds().width,
+ getBounds().height);
if (!jmb.launchChimera())
{
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
+ JOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString("label.chimera_failed"),
MessageManager.getString("label.error_loading_file"),
JOptionPane.ERROR_MESSAGE);
MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
allChainsSelected = true;
menuItem = new JCheckBoxMenuItem(chainName, true);
menuItem.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
* @param closeChimera
* if true, close any linked Chimera process; if false, prompt first
*/
+ @Override
public void closeViewer(boolean closeChimera)
{
if (jmb != null && jmb.isChimeraRunning())
if (!closeChimera)
{
String prompt = MessageManager.formatMessage(
- "label.confirm_close_chimera", new Object[]
- { jmb.getViewerTitle("Chimera", false) });
+ "label.confirm_close_chimera",
+ new Object[] { jmb.getViewerTitle("Chimera", false) });
prompt = JvSwingUtils.wrapTooltip(true, prompt);
int confirm = JOptionPane.showConfirmDialog(this, prompt,
MessageManager.getString("label.close_viewer"),
* Open any newly added PDB structures in Chimera, having first fetched data
* from PDB (if not already saved).
*/
+ @Override
public void run()
{
_started = true;
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new Object[]
- { errormsgs.toString() }), MessageManager
- .getString("label.couldnt_load_file"),
+ new Object[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
JOptionPane.ERROR_MESSAGE);
}
}
// Explicitly map to the filename used by Chimera ;
jmb.getSsm().setMapping(jmb.getSequence()[pos],
- jmb.getChains()[pos],
- pe.getFile(),
- protocol);
+ jmb.getChains()[pos], pe.getFile(), protocol);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
alignStructs_withAllAlignPanels();
* Write 'fetching PDB' progress on AlignFrame as we are not yet visible
*/
String msg = MessageManager.formatMessage("status.fetching_pdb",
- new Object[]
- { pdbid });
+ new Object[] { pdbid });
getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
// long hdl = startProgressBar(MessageManager.formatMessage(
// "status.fetching_pdb", new Object[]
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} finally
{
- msg = pdbid + " "
- + MessageManager.getString("label.state_completed");
+ msg = pdbid + " " + MessageManager.getString("label.state_completed");
getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
// stopProgressBar(msg, hdl);
}
}
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);