/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import jalview.api.AlignCalcWorkerI;
-import jalview.bin.Cache;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
-import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.util.MessageManager;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.List;
+import java.util.Locale;
+
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
/**
* @author jprocter
// TODO Auto-generated constructor stub
}
- public SequenceAnnotationWSClient(final Jws2Instance sh,
+ public SequenceAnnotationWSClient(final ServiceWithParameters sh,
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
super(alignFrame, preset, null);
initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
}
- // dan think. Do I need to change this method to run RNAalifold through the GUI
-
- public void initSequenceAnnotationWSClient(final Jws2Instance sh,
- AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
+ // dan think. Do I need to change this method to run RNAalifold through the
+ // GUI
+
+ private void initSequenceAnnotationWSClient(final ServiceWithParameters sh,
+ AlignFrame alignFrame, final WsParamSetI preset, boolean editParams)
{
- // dan changed! dan test. comment out if conditional
-// if (alignFrame.getViewport().getAlignment().isNucleotide())
-// {
-// JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
-// + " can only be used\nfor amino acid alignments.",
-// "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
-// return;
-//
-// }
+ // dan changed! dan test. comment out if conditional
+ // if (alignFrame.getViewport().getAlignment().isNucleotide())
+ // {
+ // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
+ // + " can only be used\nfor amino acid alignments.",
+ // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE);
+ // return;
+ //
+ // }
AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
- if (aaui!=null)
+ if (aaui != null)
{
Class clientClass = aaui.getClient();
-
+
// Build an AACon style client - take alignment, return annotation for
// columns
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(clientClass);
- JabawsAlignCalcWorker worker;
- if (clnts == null || clnts.size() == 0)
+ .getCalcManager()
+ .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
+
+ SeqAnnotationServiceCalcWorker tmpworker = null;
+ if (clnts != null)
{
- if (!processParams(sh, editParams))
+ for (AlignCalcWorkerI _worker : clnts)
{
- return;
- }
- try {
- worker = (JabawsAlignCalcWorker) (clientClass.getConstructor(
- new Class[] { Jws2Instance.class,
- AlignFrame.class, WsParamSetI.class,
- List.class }).newInstance(new Object[] { sh, alignFrame, this.preset, paramset}));
- } catch (Exception x)
- {
- x.printStackTrace();
- throw new Error("Implementation error",x);
+ tmpworker = (SeqAnnotationServiceCalcWorker) _worker;
+ if (tmpworker.hasService()
+ && tmpworker.getService().getClass().equals(clientClass))
+ {
+ break;
+ }
+ tmpworker = null;
}
- alignFrame
- .getViewport()
- .getCalcManager()
- .registerWorker(
- worker);
- alignFrame.getViewport().getCalcManager().startWorker(worker);
+ }
+ final var worker = tmpworker;
+ if (worker == null)
+ {
+ processParams(sh, editParams).thenAccept((startJob) -> {
+ if (startJob)
+ {
+ final SeqAnnotationServiceCalcWorker worker_;
+ try
+ {
+ worker_ = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset,
+ paramset);
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ throw new Error(
+ MessageManager.getString("error.implementation_error"),
+ x);
+ }
+ alignFrame.getViewport().getCalcManager().registerWorker(worker_);
+ // also starts the worker
+ startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
+ }
+ });
}
else
{
- worker = (JabawsAlignCalcWorker) clnts.get(0);
+ WsParamSetI preset_;
if (editParams)
{
paramset = worker.getArguments();
- preset = worker.getPreset();
+ preset_ = worker.getPreset();
+ }
+ else
+ {
+ preset_ = preset;
}
+ processParams(sh, editParams, true).thenAccept((startJob) -> {
+ if (startJob)
+ {
+ // reinstate worker if it was blacklisted (might have happened due
+ // to
+ // invalid parameters)
+ alignFrame.getViewport().getCalcManager().enableWorker(worker);
+ worker.updateParameters(this.preset, paramset);
+ startSeqAnnotationWorker(sh, alignFrame, preset_, editParams);
+ }
+ });
- if (!processParams(sh, editParams, true))
+ if (!processParams(sh, editParams, true).toCompletableFuture().join())
{
return;
}
- // reinstate worker if it was blacklisted (might have happened due to
- // invalid parameters)
- alignFrame.getViewport().getCalcManager().workerMayRun(worker);
- worker.updateParameters(this.preset, paramset);
}
}
- if (sh.action.toLowerCase().contains("disorder"))
+ if (sh.action.toLowerCase(Locale.ROOT).contains("disorder"))
{
// build IUPred style client. take sequences, returns annotation per
// sequence.
- if (!processParams(sh, editParams))
- {
- return;
- }
-
- alignFrame
- .getViewport()
- .getCalcManager()
- .startWorker(
- new AADisorderClient(sh, alignFrame, preset, paramset));
+ processParams(sh, editParams).thenAccept((startJob) -> {
+ if (startJob)
+ {
+ alignFrame.getViewport().getCalcManager().startWorker(
+ new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
+ }
+ });
}
}
- public SequenceAnnotationWSClient(AAConSettings fave,
+ public SequenceAnnotationWSClient(AutoCalcSetting fave,
AlignFrame alignFrame, boolean b)
{
- super(alignFrame, fave.getPreset(), fave.getJobArgset());
+ super(alignFrame, fave.getPreset(), fave.getArgumentSet());
initSequenceAnnotationWSClient(fave.getService(), alignFrame,
fave.getPreset(), b);
}
* @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
* jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
*/
- public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
+ @Override
+ public void attachWSMenuEntry(JMenu wsmenu,
+ final ServiceWithParameters service,
final AlignFrame alignFrame)
{
- if (registerAAConWSInstance(wsmenu, service, alignFrame)) {
+ if (Jws2ClientFactory.registerAAConWSInstance(wsmenu,
+ service, alignFrame))
+ {
// Alignment dependent analysis calculation WS gui
return;
}
boolean hasparams = service.hasParameters();
- // Assume name ends in WS
- String calcName = service.serviceType.substring(0,
- service.serviceType.length() - 2);
+ String calcName = service.getName();
+ if (calcName.endsWith("WS"))
+ {
+ // Remove "WS" suffix
+ calcName = calcName.substring(0, calcName.length() - 2);
+ }
- JMenuItem annotservice = new JMenuItem(calcName + " Defaults");
+ JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
+ "label.calcname_with_default_settings", new String[]
+ { calcName }));
annotservice.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- new SequenceAnnotationWSClient(service, alignFrame, null, false);
+ new SequenceAnnotationWSClient(service, alignFrame,
+ null, false);
}
});
wsmenu.add(annotservice);
{
// only add these menu options if the service has user-modifiable
// arguments
- annotservice = new JMenuItem("Edit settings and run ...");
- annotservice
- .setToolTipText("View and change parameters before running calculation");
+ annotservice = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ annotservice.setToolTipText(MessageManager.getString(
+ "label.view_and_change_parameters_before_running_calculation"));
annotservice.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- new SequenceAnnotationWSClient(service, alignFrame, null, true);
+ new SequenceAnnotationWSClient(service, alignFrame,
+ null, true);
}
});
wsmenu.add(annotservice);
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu("Run " + calcName + "with preset");
+ JMenu presetlist = new JMenu(MessageManager
+ .formatMessage("label.run_with_preset", new String[]
+ { calcName }));
for (final WsParamSetI preset : presets)
{
final JMenuItem methodR = new JMenuItem(preset.getName());
- methodR.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip("<strong>"
- + (preset.isModifiable() ? "User Preset"
- : "Service Preset") + "</strong><br/>"
- + preset.getDescription() + "</p>") + "</html>");
+ methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
+ + (preset.isModifiable()
+ ? MessageManager.getString("label.user_preset")
+ : MessageManager
+ .getString("label.service_preset"))
+ + "</strong><br/>" + preset.getDescription()));
methodR.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- new SequenceAnnotationWSClient(service, alignFrame, preset,
+ new SequenceAnnotationWSClient(service,
+ alignFrame, preset,
false);
}
}
else
{
- annotservice = new JMenuItem("View documentation");
- if (service.docUrl != null)
+ annotservice = new JMenuItem(
+ MessageManager.getString("label.view_documentation"));
+ if (service != null && service.hasDocumentationUrl())
{
annotservice.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent arg0)
{
- Desktop.instance.showUrl(service.docUrl);
+ Desktop.getInstance().showUrl(service.getDocumentationUrl());
}
});
- annotservice.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("View <a href=\""
- + service.docUrl + "\">" + service.docUrl + "</a>")
- + "</html>");
+ annotservice.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
+ "label.view_service_doc_url", new String[]
+ { service.getDocumentationUrl(),
+ service.getDocumentationUrl() })));
wsmenu.add(annotservice);
}
}
}
-
-
- private boolean registerAAConWSInstance(final JMenu wsmenu,
- final Jws2Instance service, final AlignFrame alignFrame)
- {
- final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString());
- if (aaui==null)
- {
- // not an instantaneous calculation GUI type service
- return false;
- }
- // create the instaneous calculation GUI bits and update state if existing GUI elements already present
-
- JCheckBoxMenuItem _aaConEnabled = null;
- for (int i = 0; i < wsmenu.getItemCount(); i++)
- {
- JMenuItem item = wsmenu.getItem(i);
- if (item instanceof JCheckBoxMenuItem
- && item.getText().equals(aaui.getAAconToggle()))
- {
- _aaConEnabled = (JCheckBoxMenuItem) item;
- }
- }
- // is there an aaCon worker already present - if so, set it to use the
- // given service handle
- {
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- JabawsAlignCalcWorker worker = (JabawsAlignCalcWorker) aaconClient.get(0);
- if (!worker.service.hosturl.equals(service.hosturl))
- {
- // javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- // @Override
- // public void run()
- {
- removeCurrentAAConWorkerFor(aaui, alignFrame);
- buildCurrentAAConWorkerFor(aaui, alignFrame, service);
- }
- }// );
- }
- }
- }
-
- // is there a service already registered ? there shouldn't be if we are
- // being called correctly
- if (_aaConEnabled == null)
- {
- final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
- aaui.getAAconToggle());
-
- aaConEnabled.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(aaui.getAAconToggleTooltip() + "</p>")
- + "</html>");
- aaConEnabled.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- removeCurrentAAConWorkerFor(aaui, alignFrame);
- }
- else
- {
- buildCurrentAAConWorkerFor(aaui, alignFrame);
-
- }
- }
-
- });
- wsmenu.add(aaConEnabled);
- final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
- modifyParams.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(aaui.getAAeditSettingsTooltip() + "</p>")
- + "</html>");
- modifyParams.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- showAAConAnnotationSettingsFor(aaui, alignFrame);
- }
- });
- wsmenu.add(modifyParams);
- wsmenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent arg0)
- {
- // TODO: refactor to the implementing class.
- if (alignFrame.getViewport().getAlignment()
- .isNucleotide() ? aaui.isNa() : aaui.isPr()) {
- aaConEnabled.setEnabled(true);
- modifyParams.setEnabled(true);
- }
- else {
- aaConEnabled.setEnabled(false);
- modifyParams.setEnabled(false);
- }
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- aaConEnabled.setSelected(true);
- }
- else
- {
- aaConEnabled.setSelected(false);
- }
- }
-
- @Override
- public void menuDeselected(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void menuCanceled(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
- });
-
- }
- return true;
- }
-
- private static void showAAConAnnotationSettingsFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame)
- {
- /*
- * preferred settings Whether AACon is automatically recalculated Which
- * AACon server to use What parameters to use
- */
- // could actually do a class search for this too
- AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(aaui.getCalcId());
- if (fave == null)
- {
- fave = createDefaultAAConSettings(aaui);
- }
- new SequenceAnnotationWSClient(fave, alignFrame, true);
-
- }
-
- private static void buildCurrentAAConWorkerFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame)
- {
- buildCurrentAAConWorkerFor(aaui, alignFrame, null);
- }
-
- private static void buildCurrentAAConWorkerFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame,
- Jws2Instance service)
- {
- /*
- * preferred settings Whether AACon is automatically recalculated Which
- * AACon server to use What parameters to use
- */
- AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(aaui.getCalcId());
- if (fave == null)
- {
- fave = createDefaultAAConSettings(aaui, service);
- }
- else
- {
- if (service != null
- && !fave.getService().hosturl.equals(service.hosturl))
- {
- Cache.log.debug("Changing AACon service to " + service.hosturl
- + " from " + fave.getService().hosturl);
- fave.setService(service);
- }
- }
- new SequenceAnnotationWSClient(fave, alignFrame, false);
- }
-
- private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui)
- {
- return createDefaultAAConSettings(aaui, null);
- }
-
- private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui,
- Jws2Instance service)
- {
- if (service != null)
- {
- if (!service.serviceType.toString().equals(
- compbio.ws.client.Services.AAConWS.toString()))
- {
- Cache.log
- .warn("Ignoring invalid preferred service for AACon calculations (service type was "
- + service.serviceType + ")");
- service = null;
- }
- else
- {
- // check service is actually in the list of currently avaialable
- // services
- if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
- {
- // it isn't ..
- service = null;
- }
- }
- }
- if (service == null)
- {
- // get the default service for AACon
- service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
- aaui.getServiceType());
- }
- if (service == null)
- {
- // TODO raise dialog box explaining error, and/or open the JABA
- // preferences menu.
- throw new Error("No AACon service found.");
- }
- return new AAConSettings(true, service, null, null);
- }
-
- private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui, AlignFrame alignFrame)
- {
- alignFrame.getViewport().getCalcManager()
- .removeRegisteredWorkersOfClass(aaui.getClient());
- }
}
git://source.jalview.org / jalview.git / blobdiff