-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
-import jalview.ws.jws2.dm.AAConsSettings;
+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 javax.swing.event.MenuListener;
/**
- * @author jprocter
+ * @author jprocter
*
*/
-public class SequenceAnnotationWSClient extends Jws2Client
+public class SequenceAnnotationWSClient extends Jws2Client
{
-
- public static final String AAConsCalcId = "jabaws2.AACons";
-
/**
* initialise a client so its attachWSMenuEntry method can be called.
*/
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())
- {
- 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"))
+ // 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)
{
- // 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));
+ worker);
alignFrame.getViewport().getCalcManager().startWorker(worker);
}
else
{
- AAConsClient worker = (AAConsClient) clnts.get(0);
+ worker = (JabawsAlignCalcWorker) clnts.get(0);
if (editParams)
{
paramset = worker.getArguments();
// invalid parameters)
alignFrame.getViewport().getCalcManager().workerMayRun(worker);
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());
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)
{
wsmenu.add(presetlist);
}
- } else {
- aacons = new JMenuItem("View documentation");
- if (service.docUrl!=null)
+ }
+ else
+ {
+ annotservice = new JMenuItem(MessageManager.getString("label.view_documentation"));
+ if (service.docUrl != null)
{
- aacons.addActionListener(new ActionListener()
+ annotservice.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent arg0)
{
Desktop.instance.showUrl(service.docUrl);
}
});
- aacons.setToolTipText("<html>"+JvSwingUtils.wrapTooltip("View <a href=\""+service.docUrl+"\">"+service.docUrl+"</a>")+"</html>");
- wsmenu.add(aacons);
+ annotservice.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("View <a href=\""
+ + service.docUrl + "\">" + service.docUrl + "</a>")
+ + "</html>");
+ wsmenu.add(annotservice);
}
}
}
- private final String AAconsToggle = "AACons Calculations",
- AAconsToggleTooltip = "When checked, AACons calculations are updated automatically.",
- AAeditSettings = "Change AACons Settings...",
- AAeditSettingsTooltip = "Modify settings for AACons calculations.";
-
- // 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 an aaCons worker already present - if so, set it to use the
+ // is there an aaCon worker already present - if so, set it to use the
// given service handle
{
- 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)
{
- AAConsClient worker = (AAConsClient) aaconsClient.get(0);
+ JabawsAlignCalcWorker worker = (JabawsAlignCalcWorker) aaconClient.get(0);
if (!worker.service.hosturl.equals(service.hosturl))
{
- // javax.swing.SwingUtilities.invokeLater(new Runnable()
+ // javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- // @Override
- // public void run()
+ // @Override
+ // public void run()
{
- removeCurrentAAConsWorkerFor(alignFrame);
- buildCurrentAAConsWorkerFor(alignFrame, service);
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
+ buildCurrentAAConWorkerFor(aaui, alignFrame, service);
}
- }//);
+ }// );
}
}
}
// is there a service already registered ? there shouldn't be if we are
// being called correctly
- if (_aaConsEnabled == null)
+ if (_aaConEnabled == null)
{
- final JCheckBoxMenuItem aaConsEnabled = new JCheckBoxMenuItem(
- AAconsToggle);
- wsmenu.addMenuListener(new MenuListener()
- {
+ 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
*/
// could actually do a class search for this too
- AAConsSettings fave = (AAConsSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(AAConsCalcId);
+ 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)
{
- buildCurrentAAConsWorkerFor(alignFrame, null);
+ buildCurrentAAConWorkerFor(aaui, alignFrame, null);
}
- private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame,
+ 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 = (AAConsSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(AAConsCalcId);
+ AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(aaui.getCalcId());
if (fave == null)
{
- fave = createDefaultAAConsSettings(service);
+ fave = createDefaultAAConSettings(aaui, service);
}
else
{
if (service != null
&& !fave.getService().hosturl.equals(service.hosturl))
{
- Cache.log.debug("Changing AACons service to " + 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 createDefaultAAConsSettings(null);
+ return createDefaultAAConSettings(aaui, null);
}
- private static AAConsSettings createDefaultAAConsSettings(
+ private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui,
Jws2Instance service)
{
if (service != null)
compbio.ws.client.Services.AAConWS.toString()))
{
Cache.log
- .warn("Ignoring invalid preferred service for AACons calculations (service type was "
+ .warn("Ignoring invalid preferred service for AACon calculations (service type was "
+ service.serviceType + ")");
service = null;
}
}
if (service == null)
{
- // get the default service for AACons
+ // get the default service for AACon
service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
- compbio.ws.client.Services.AAConWS.toString());
- /*
- * for (Jws2Instance sv : Jws2Discoverer.getDiscoverer().getServices()) {
- * if (sv.serviceType.toString().equals(
- * compbio.ws.client.Services.AAConWS.toString())) { service = sv; break;
- * } }
- */
+ aaui.getServiceType());
}
if (service == null)
{
// TODO raise dialog box explaining error, and/or open the JABA
// preferences menu.
- throw new Error("No AACons service found.");
+ throw new Error("No AACon service found.");
}
- return new AAConsSettings(true, service, null, null);
+ 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