-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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/>.
*/
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.util.MessageManager;
+import jalview.ws.jws2.dm.AAConSettings;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+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 javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
-import javax.swing.event.AncestorEvent;
-import javax.swing.event.AncestorListener;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
-import compbio.metadata.Argument;
-
-import jalview.api.AlignCalcWorkerI;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.JalviewDialog;
-import jalview.gui.JvSwingUtils;
-import jalview.ws.jws2.dm.AAConsSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
-
/**
- * @author jimp
+ * @author jprocter
*
*/
public class SequenceAnnotationWSClient extends Jws2Client
{
-
/**
* initialise a client so its attachWSMenuEntry method can be called.
*/
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)
{
- if (alignFrame.getViewport().getAlignment().isNucleotide())
+ // 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;
+//
+// }
+ AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
+ if (aaui!=null)
{
- JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
- + " can only be used\nfor amino acid alignments.",
- "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
- return;
-
- }
- if (sh.action.toLowerCase().contains("conservation"))
- {
- // Build an AACons style client - take alignment, return annotation for
+ Class clientClass = aaui.getClient();
+
+ // Build an AACon style client - take alignment, return annotation for
// columns
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
.getCalcManager()
- .getRegisteredWorkersOfClass(AAConsClient.class);
+ .getRegisteredWorkersOfClass(clientClass);
+ JabawsAlignCalcWorker worker;
if (clnts == null || clnts.size() == 0)
{
if (!processParams(sh, editParams))
{
return;
}
- AAConsClient worker;
+ 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);
+ }
alignFrame
.getViewport()
.getCalcManager()
.registerWorker(
- worker = new AAConsClient(sh, alignFrame, this.preset,
- paramset));
- alignFrame.getViewport().setPreferredAAConsSettings(new AAConsSettings(true, sh, this.preset, paramset));
+ worker);
alignFrame.getViewport().getCalcManager().startWorker(worker);
}
else
{
- AAConsClient worker = (AAConsClient) clnts.get(0);
+ worker = (JabawsAlignCalcWorker) clnts.get(0);
if (editParams)
{
paramset = worker.getArguments();
{
return;
}
- alignFrame.getViewport().setPreferredAAConsSettings(new AAConsSettings(true, sh, preset, paramset));
// reinstate worker if it was blacklisted (might have happened due to
// invalid parameters)
alignFrame.getViewport().getCalcManager().workerMayRun(worker);
- worker.updateParameters(preset, paramset);
-
+ worker.updateParameters(this.preset, paramset);
}
}
if (sh.action.toLowerCase().contains("disorder"))
.startWorker(
new AADisorderClient(sh, alignFrame, preset, paramset));
}
-
}
- public SequenceAnnotationWSClient(AAConsSettings fave,
+ public SequenceAnnotationWSClient(AAConSettings fave,
AlignFrame alignFrame, boolean b)
{
super(alignFrame, fave.getPreset(), fave.getJobArgset());
- initSequenceAnnotationWSClient(fave.getService(), alignFrame, fave.getPreset(), b);
+ initSequenceAnnotationWSClient(fave.getService(), alignFrame,
+ fave.getPreset(), b);
}
/*
public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
final AlignFrame alignFrame)
{
- if (service.serviceType.equals(compbio.ws.client.Services.AAConWS
- .toString()))
- {
- registerAAConsWSInstance(wsmenu, service, alignFrame);
+ if (registerAAConWSInstance(wsmenu, service, alignFrame)) {
+ // Alignment dependent analysis calculation WS gui
return;
}
boolean hasparams = service.hasParameters();
String calcName = service.serviceType.substring(0,
service.serviceType.length() - 2);
- JMenuItem aacons = new JMenuItem(calcName + " Defaults");
- aacons.addActionListener(new ActionListener()
+ JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage("label.calcname_with_default_settings", new String[]{calcName}));
+ annotservice.addActionListener(new ActionListener()
{
@Override
new SequenceAnnotationWSClient(service, alignFrame, null, false);
}
});
- wsmenu.add(aacons);
+ wsmenu.add(annotservice);
if (hasparams)
{
// only add these menu options if the service has user-modifiable
// arguments
- aacons = new JMenuItem("Edit settings and run ...");
- aacons.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"));
- aacons.addActionListener(new ActionListener()
+ annotservice.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
new SequenceAnnotationWSClient(service, alignFrame, null, true);
}
});
- wsmenu.add(aacons);
+ wsmenu.add(annotservice);
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
}
}
- }
-
- private final String AAconsToggle = "AACons Calculations",
- AAconsToggleTooltip = "When checked, AACons calculations are updated automatically.",
- AAeditSettings = "Change AACons Settings...",
- AAeditSettingsTooltip = "Modify settings for AACons calculations.";
+ else
+ {
+ annotservice = new JMenuItem(MessageManager.getString("label.view_documentation"));
+ if (service.docUrl != null)
+ {
+ annotservice.addActionListener(new ActionListener()
+ {
- private SequenceAnnotationWSClient preferredAAConsClient = null;
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ Desktop.instance.showUrl(service.docUrl);
+ }
+ });
+ annotservice.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("View <a href=\""
+ + service.docUrl + "\">" + service.docUrl + "</a>")
+ + "</html>");
+ wsmenu.add(annotservice);
+ }
+ }
+ }
- // private final enableAAConsCalculation(final AlignFrame alignFrame, )
- private void registerAAConsWSInstance(final JMenu wsmenu,
+
+ private boolean registerAAConWSInstance(final JMenu wsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{
- // register this in the AACons settings set
- JCheckBoxMenuItem _aaConsEnabled = null;
+ 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(AAconsToggle))
+ && item.getText().equals(aaui.getAAconToggle()))
{
- _aaConsEnabled = (JCheckBoxMenuItem) item;
+ _aaConEnabled = (JCheckBoxMenuItem) item;
}
}
-
- // is there a service already registered ?
- if (_aaConsEnabled == null)
+ // is there an aaCon worker already present - if so, set it to use the
+ // given service handle
{
- final JCheckBoxMenuItem aaConsEnabled = new JCheckBoxMenuItem(
- AAconsToggle);
- wsmenu.addMenuListener(new MenuListener()
+ 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 menuSelected(MenuEvent arg0)
+ public void actionPerformed(ActionEvent arg0)
{
- wsmenu.setEnabled(!alignFrame.getViewport().getAlignment()
- .isNucleotide());
- List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
.getCalcManager()
- .getRegisteredWorkersOfClass(AAConsClient.class);
- if (aaconsClient != null && aaconsClient.size() > 0)
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
{
- aaConsEnabled.setSelected(true);
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
}
else
{
- aaConsEnabled.setSelected(false);
+ buildCurrentAAConWorkerFor(aaui, alignFrame);
+
}
}
- @Override
- public void menuDeselected(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
+ });
+ 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 menuCanceled(MenuEvent arg0)
+ public void actionPerformed(ActionEvent arg0)
{
- // TODO Auto-generated method stub
-
+ showAAConAnnotationSettingsFor(aaui, alignFrame);
}
});
- aaConsEnabled.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(AAconsToggleTooltip + "</p>")
- + "</html>");
- aaConsEnabled.addActionListener(new ActionListener()
+ wsmenu.add(modifyParams);
+ wsmenu.addMenuListener(new MenuListener()
{
+
@Override
- public void actionPerformed(ActionEvent arg0)
+ public void menuSelected(MenuEvent arg0)
{
- // aaConsEnabled.setSelected(!aaConsEnabled.isSelected());
- List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
+ // 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(AAConsClient.class);
- if (aaconsClient != null && aaconsClient.size() > 0)
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
{
- removeCurrentAAConsWorkerFor(alignFrame);
+ aaConEnabled.setSelected(true);
}
else
{
- buildCurrentAAConsWorkerFor(alignFrame);
-
+ aaConEnabled.setSelected(false);
}
}
- });
- wsmenu.add(aaConsEnabled);
- JMenuItem modifyParams = new JMenuItem(AAeditSettings);
- modifyParams.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "</p>")
- + "</html>");
- modifyParams.addActionListener(new ActionListener()
- {
+ @Override
+ public void menuDeselected(MenuEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
@Override
- public void actionPerformed(ActionEvent arg0)
+ public void menuCanceled(MenuEvent arg0)
{
- showAAConsAnnotationSettingsFor(alignFrame);
+ // TODO Auto-generated method stub
+
}
});
- wsmenu.add(modifyParams);
}
-
+ return true;
}
- private static void showAAConsAnnotationSettingsFor(AlignFrame alignFrame)
+ private static void showAAConAnnotationSettingsFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame)
{
/*
- * preferred settings
- * Whether AACons is automatically recalculated
- * Which AACons server to use
- * What parameters to use
+ * preferred settings Whether AACon is automatically recalculated Which
+ * AACon server to use What parameters to use
*/
- AAConsSettings fave= alignFrame.getViewport().getPreferredAAConsSettings();
- if (fave==null)
+ // could actually do a class search for this too
+ AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(aaui.getCalcId());
+ if (fave == null)
{
- fave = createDefaultAAConsSettings();
+ fave = createDefaultAAConSettings(aaui);
}
new SequenceAnnotationWSClient(fave, alignFrame, true);
}
- private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame)
+
+ 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 AACons is automatically recalculated
- * Which AACons server to use
- * What parameters to use
+ * preferred settings Whether AACon is automatically recalculated Which
+ * AACon server to use What parameters to use
*/
- AAConsSettings fave= alignFrame.getViewport().getPreferredAAConsSettings();
- if (fave==null)
+ AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(aaui.getCalcId());
+ if (fave == null)
+ {
+ fave = createDefaultAAConSettings(aaui, service);
+ }
+ else
{
- fave = createDefaultAAConsSettings();
+ 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 AAConsSettings createDefaultAAConsSettings()
+ private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui)
+ {
+ return createDefaultAAConSettings(aaui, null);
+ }
+
+ private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui,
+ Jws2Instance service)
{
- Jws2Instance service=null;
- // set sensible defaults
- for (Jws2Instance sv: Jws2Discoverer.getDiscoverer().getServices()) {
- if (sv.serviceType.toString().equals(compbio.ws.client.Services.AAConWS.toString()))
+ if (service != null)
+ {
+ if (!service.serviceType.toString().equals(
+ compbio.ws.client.Services.AAConWS.toString()))
{
- service = sv;
- break;
+ 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)
+ if (service == null)
{
- // TODO raise dialog box explaining error, and/or open the JABA preferences menu.
- throw new Error("No AACons service found.");
+ // get the default service for AACon
+ service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
+ aaui.getServiceType());
}
- return new AAConsSettings(true, service, null, null);
+ 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 removeCurrentAAConsWorkerFor(AlignFrame alignFrame)
+ private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui, AlignFrame alignFrame)
{
alignFrame.getViewport().getCalcManager()
- .removeRegisteredWorkersOfClass(AAConsClient.class);
- // AAConsClient.removeAAConsAnnotation(alignFrame.alignPanel);
-
+ .removeRegisteredWorkersOfClass(aaui.getClient());
}
}
git://source.jalview.org / jalview.git / blobdiff