import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
-import jalview.ws.jws2.dm.AAConsSettings;
+import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
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";
+ public static final String AAConCalcId = "jabaws2.AACon";
/**
* initialise a client so its attachWSMenuEntry method can be called.
}
if (sh.action.toLowerCase().contains("conservation"))
{
- // Build an AACons style client - take alignment, return annotation for
+ // Build an AACon style client - take alignment, return annotation for
// columns
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
.getCalcManager()
- .getRegisteredWorkersOfClass(AAConsClient.class);
+ .getRegisteredWorkersOfClass(AAConClient.class);
if (clnts == null || clnts.size() == 0)
{
if (!processParams(sh, editParams))
{
return;
}
- AAConsClient worker;
+ AAConClient worker;
alignFrame
.getViewport()
.getCalcManager()
.registerWorker(
- worker = new AAConsClient(sh, alignFrame,
+ worker = new AAConClient(sh, alignFrame,
this.preset, paramset));
alignFrame.getViewport().getCalcManager().startWorker(worker);
}
else
{
- AAConsClient worker = (AAConsClient) clnts.get(0);
+ AAConClient worker = (AAConClient) clnts.get(0);
if (editParams)
{
paramset = worker.getArguments();
}
- public SequenceAnnotationWSClient(AAConsSettings fave,
+ public SequenceAnnotationWSClient(AAConSettings fave,
AlignFrame alignFrame, boolean b)
{
super(alignFrame, fave.getPreset(), fave.getJobArgset());
if (service.serviceType.equals(compbio.ws.client.Services.AAConWS
.toString()))
{
- registerAAConsWSInstance(wsmenu, service, alignFrame);
+ registerAAConWSInstance(wsmenu, service, alignFrame);
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(calcName + " Defaults");
+ 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("Edit settings and run ...");
+ annotservice
+ .setToolTipText("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("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 String AAconToggle = "AACon Calculations",
+ AAconToggleTooltip = "When checked, AACon calculations are updated automatically.",
+ AAeditSettings = "Change AACon Settings...",
+ AAeditSettingsTooltip = "Modify settings for AACon calculations.";
- // private final enableAAConsCalculation(final AlignFrame alignFrame, )
- private void registerAAConsWSInstance(final JMenu wsmenu,
+ private void registerAAConWSInstance(final JMenu wsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{
- // register this in the AACons settings set
- JCheckBoxMenuItem _aaConsEnabled = null;
+ // register this in the AACon settings set
+ 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(AAconToggle))
{
- _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(AAConClient.class);
+ if (aaconClient != null && aaconClient.size() > 0)
{
- AAConsClient worker = (AAConsClient) aaconsClient.get(0);
+ AAConClient worker = (AAConClient) 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(alignFrame);
+ buildCurrentAAConWorkerFor(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);
+ final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
+ AAconToggle);
wsmenu.addMenuListener(new MenuListener()
{
{
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(AAConClient.class);
+ if (aaconClient != null && aaconClient.size() > 0)
{
- aaConsEnabled.setSelected(true);
+ aaConEnabled.setSelected(true);
}
else
{
- aaConsEnabled.setSelected(false);
+ aaConEnabled.setSelected(false);
}
}
}
});
- aaConsEnabled.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(AAconsToggleTooltip + "</p>")
+ aaConEnabled.setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip(AAconToggleTooltip + "</p>")
+ "</html>");
- aaConsEnabled.addActionListener(new ActionListener()
+ aaConEnabled.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent arg0)
{
- // aaConsEnabled.setSelected(!aaConsEnabled.isSelected());
- List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
.getCalcManager()
- .getRegisteredWorkersOfClass(AAConsClient.class);
- if (aaconsClient != null && aaconsClient.size() > 0)
+ .getRegisteredWorkersOfClass(AAConClient.class);
+ if (aaconClient != null && aaconClient.size() > 0)
{
- removeCurrentAAConsWorkerFor(alignFrame);
+ removeCurrentAAConWorkerFor(alignFrame);
}
else
{
- buildCurrentAAConsWorkerFor(alignFrame);
+ buildCurrentAAConWorkerFor(alignFrame);
}
}
});
- wsmenu.add(aaConsEnabled);
+ wsmenu.add(aaConEnabled);
JMenuItem modifyParams = new JMenuItem(AAeditSettings);
modifyParams.setToolTipText("<html><p>"
+ JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "</p>")
@Override
public void actionPerformed(ActionEvent arg0)
{
- showAAConsAnnotationSettingsFor(alignFrame);
+ showAAConAnnotationSettingsFor(alignFrame);
}
});
wsmenu.add(modifyParams);
}
}
- private static void showAAConsAnnotationSettingsFor(AlignFrame alignFrame)
+ private static void showAAConAnnotationSettingsFor(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(AAConCalcId);
if (fave == null)
{
- fave = createDefaultAAConsSettings();
+ fave = createDefaultAAConSettings();
}
new SequenceAnnotationWSClient(fave, alignFrame, true);
}
- private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame)
+ private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame)
{
- buildCurrentAAConsWorkerFor(alignFrame, null);
+ buildCurrentAAConWorkerFor(alignFrame, null);
}
- private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame,
+ private static void buildCurrentAAConWorkerFor(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(AAConCalcId);
if (fave == null)
{
- fave = createDefaultAAConsSettings(service);
+ fave = createDefaultAAConSettings(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()
{
- return createDefaultAAConsSettings(null);
+ return createDefaultAAConSettings(null);
}
- private static AAConsSettings createDefaultAAConsSettings(
+ private static AAConSettings createDefaultAAConSettings(
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;
- * } }
- */
}
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(AlignFrame alignFrame)
{
alignFrame.getViewport().getCalcManager()
- .removeRegisteredWorkersOfClass(AAConsClient.class);
- // AAConsClient.removeAAConsAnnotation(alignFrame.alignPanel);
-
+ .removeRegisteredWorkersOfClass(AAConClient.class);
}
}
git://source.jalview.org / jalview.git / blobdiff