*/
package jalview.ws.jws2;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.JvSwingUtils;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
+import java.util.Locale;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.ToolTipManager;
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
/**
* DOCUMENT ME!
if (!(sh.service instanceof MsaWS))
{
// redundant at mo - but may change
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.service_called_is_not_msa_service",
- new String[] { sh.serviceType }), MessageManager
- .getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.service_called_is_not_msa_service",
+ new String[]
+ { sh.serviceType }),
+ MessageManager.getString("label.internal_jalview_error"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
server = (MsaWS) sh.service;
if ((wsInfo = setWebService(sh, false)) == null)
{
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.msa_service_is_unknown",
- new String[] { sh.serviceType }), MessageManager
- .getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.msa_service_is_unknown", new String[]
+ { sh.serviceType }),
+ MessageManager.getString("label.internal_jalview_error"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
- String jobtitle = WebServiceName.toLowerCase();
+ String jobtitle = WebServiceName.toLowerCase(Locale.ROOT);
if (jobtitle.endsWith("alignment"))
{
- if (submitGaps
- && (!jobtitle.endsWith("realignment") || jobtitle
- .indexOf("profile") == -1))
+ if (submitGaps && (!jobtitle.endsWith("realignment")
+ || jobtitle.indexOf("profile") == -1))
{
int pos = jobtitle.indexOf("alignment");
jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
+ "alignment of " + altitle;
}
- MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
- WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
- submitGaps, preserveOrder, seqdataset);
+ MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL,
+ wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps,
+ preserveOrder, seqdataset);
if (msathread.hasValidInput())
{
wsInfo.setthisService(msathread);
}
else
{
- JOptionPane.showMessageDialog(alignFrame,
+ wsInfo.setVisible(false);
+ JvOptionPane.showMessageDialog(alignFrame,
MessageManager.getString("info.invalid_msa_input_mininfo"),
MessageManager.getString("info.invalid_msa_notenough"),
- JOptionPane.INFORMATION_MESSAGE);
- wsInfo.setVisible(false);
+ JvOptionPane.INFORMATION_MESSAGE);
}
}
- public static void main(String[] args)
- {
- System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*"));
- }
-
protected String getServiceActionKey()
{
return "MsaWS";
@Override
public void attachWSMenuEntry(JMenu rmsawsmenu,
- final Jws2Instance service, final AlignFrame alignFrame)
+ final Jws2Instance service, final AlignFrame af)
{
- if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+ if (registerAAConWSInstance(rmsawsmenu, service, af))
{
// Alignment dependent analysis calculation WS gui
return;
if (submitGaps == true)
{
action = "Realign ";
- msawsmenu = new JMenu(MessageManager.formatMessage(
- "label.realign_with_params", new String[] { svcname }));
+ msawsmenu = new JMenu(MessageManager
+ .formatMessage("label.realign_with_params", new String[]
+ { svcname }));
msawsmenu.setToolTipText(MessageManager
.getString("label.align_sequences_to_existing_alignment"));
rmsawsmenu.add(msawsmenu);
final boolean withGaps = submitGaps;
JMenuItem method = new JMenuItem(MessageManager.formatMessage(
- "label.calcname_with_default_settings",
- new String[] { calcName }));
- method.setToolTipText(MessageManager
- .formatMessage("label.action_with_default_settings",
- new String[] { action }));
+ "label.calcname_with_default_settings", new String[]
+ { calcName }));
+ method.setToolTipText(MessageManager.formatMessage(
+ "label.action_with_default_settings", new String[]
+ { action }));
method.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+ AlignmentView msa = af.gatherSequencesForAlignment();
if (msa != null)
{
- new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
- true, alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
+ new MsaWSClient(service, af.getTitle(), msa, withGaps,
+ true,
+ af.getViewport().getAlignment().getDataset(),
+ af);
}
}
// arguments
method = new JMenuItem(
MessageManager.getString("label.edit_settings_and_run"));
- method.setToolTipText(MessageManager
- .getString("label.view_and_change_parameters_before_alignment"));
+ method.setToolTipText(MessageManager.getString(
+ "label.view_and_change_parameters_before_alignment"));
method.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+ AlignmentView msa = af.gatherSequencesForAlignment();
if (msa != null)
{
- new MsaWSClient(service, null, null, true, alignFrame
- .getTitle(), msa, withGaps, true, alignFrame
- .getViewport().getAlignment().getDataset(),
- alignFrame);
+ startJob(service, af, withGaps, msa);
}
}
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu(
- MessageManager.formatMessage(
- "label.run_with_preset_params",
- new String[] { calcName }));
+ JMenu presetlist = new JMenu(MessageManager.formatMessage(
+ "label.run_with_preset_params", new String[]
+ { calcName }));
final int showToolTipFor = ToolTipManager.sharedInstance()
.getDismissDelay();
- for (final WsParamSetI preset : presets)
+ for (final WsParamSetI preSet : presets)
{
- final JMenuItem methodR = new JMenuItem(preset.getName());
+ final JMenuItem methodR = new JMenuItem(preSet.getName());
final int QUICK_TOOLTIP = 1500;
// JAL-1582 shorten tooltip display time in these menu items as
// they can obscure other options
@Override
public void mouseEntered(MouseEvent e)
{
- ToolTipManager.sharedInstance().setDismissDelay(
- QUICK_TOOLTIP);
+ ToolTipManager.sharedInstance()
+ .setDismissDelay(QUICK_TOOLTIP);
}
@Override
public void mouseExited(MouseEvent e)
{
- ToolTipManager.sharedInstance().setDismissDelay(
- showToolTipFor);
+ ToolTipManager.sharedInstance()
+ .setDismissDelay(showToolTipFor);
}
});
- String tooltip = JvSwingUtils
- .wrapTooltip(
- true,
- "<strong>"
- + (preset.isModifiable() ? MessageManager
- .getString("label.user_preset")
- : MessageManager
- .getString("label.service_preset"))
- + "</strong><br/>"
- + preset.getDescription());
+ String tooltip = JvSwingUtils.wrapTooltip(true, "<strong>"
+ + (preSet.isModifiable()
+ ? MessageManager.getString("label.user_preset")
+ : MessageManager
+ .getString("label.service_preset"))
+ + "</strong><br/>" + preSet.getDescription());
methodR.setToolTipText(tooltip);
methodR.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- AlignmentView msa = alignFrame
+ AlignmentView msa = af
.gatherSequencesForAlignment();
if (msa != null)
{
- MsaWSClient msac = new MsaWSClient(service, preset,
- alignFrame.getTitle(), msa, false, true,
- alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
+ MsaWSClient msac = new MsaWSClient(service, preSet,
+ af.getTitle(), msa, false, true,
+ af.getViewport().getAlignment()
+ .getDataset(),
+ af);
}
}
}
} while (!finished);
}
+
+ protected void startJob(final Jws2Instance service, final AlignFrame af,
+ final boolean withGaps, AlignmentView msa)
+ {
+ try {
+ new MsaWSClient(service, null, null, true,
+ af.getTitle(), msa, withGaps, true,
+ af.getViewport().getAlignment().getDataset(),
+ af);
+ } catch (Exception e) {
+ JvOptionPane.showMessageDialog(alignFrame, e.getMessage(),
+ MessageManager.getString("label.state_job_error"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ }
+ }
}