X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Client.java;h=0f1a25e6fc1e8907c51e3093346d026483a5d894;hb=15a0e4b34d301c187569de8cb429d5d380bdaf0f;hp=1a755995b24a7ee1c0bfa094fab376dce0103c27;hpb=185dc2485e575e598330cda1e380d9d1d1c82ed8;p=jalview.git
diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java
index 1a75599..0f1a25e 100644
--- a/src/jalview/ws/jws2/Jws2Client.java
+++ b/src/jalview/ws/jws2/Jws2Client.java
@@ -1,54 +1,431 @@
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.jws2;
-import javax.swing.JMenu;
-
+import jalview.api.AlignCalcWorkerI;
+import jalview.bin.Cache;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
import jalview.gui.WebserviceInfo;
-import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
+import jalview.gui.WsJobParameters;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.dm.AAConSettings;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+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.JCheckBoxMenuItem;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+import compbio.metadata.Argument;
/**
- * provides metadata for a jws2 service instance - resolves names, etc.
+ * provides metadata for a jabaws2 service instance - resolves names, etc.
*
* @author JimP
*
*/
public abstract class Jws2Client extends jalview.ws.WSClient
{
+ protected AlignFrame alignFrame;
+
+ protected WsParamSetI preset;
+
+ protected List paramset;
+
+ public Jws2Client(AlignFrame _alignFrame, WsParamSetI preset,
+ List arguments)
+ {
+ alignFrame = _alignFrame;
+ this.preset = preset;
+ if (preset != null)
+ {
+ if (!((preset instanceof JabaPreset)
+ || preset instanceof JabaWsParamSet))
+ {
+ /*
+ * { this.preset = ((JabaPreset) preset).p; } else if (preset instanceof
+ * JabaWsParamSet) { List newargs = new ArrayList();
+ * JabaWsParamSet pset = ((JabaWsParamSet) preset); for (Option opt :
+ * pset.getjabaArguments()) { newargs.add(opt); } if (arguments != null
+ * && arguments.size() > 0) { // merge arguments with preset's own
+ * arguments. for (Argument opt : arguments) { newargs.add(opt); } }
+ * paramset = newargs; } else {
+ */
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_can_only_instantiate_jaba_param_sets"));
+ }
+ }
+ else
+ {
+ // just provided with a bunch of arguments
+ this.paramset = arguments;
+ }
+ }
+
+ boolean processParams(Jws2Instance sh, boolean editParams)
+ {
+ return processParams(sh, editParams, false);
+ }
+
+ protected boolean processParams(Jws2Instance sh, boolean editParams,
+ boolean adjustingExisting)
+ {
+
+ if (editParams)
+ {
+ if (sh.paramStore == null)
+ {
+ sh.paramStore = new JabaParamStore(sh,
+ Desktop.getUserParameterStore());
+ }
+ WsJobParameters jobParams = (preset == null && paramset != null
+ && paramset.size() > 0)
+ ? new WsJobParameters(null, sh, null, paramset)
+ : new WsJobParameters(sh, preset);
+ if (adjustingExisting)
+ {
+ jobParams.setName(MessageManager
+ .getString("label.adjusting_parameters_for_calculation"));
+ }
+ if (!jobParams.showRunDialog())
+ {
+ return false;
+ }
+ WsParamSetI prset = jobParams.getPreset();
+ if (prset == null)
+ {
+ paramset = jobParams.isServiceDefaults() ? null
+ : JabaParamStore
+ .getJabafromJwsArgs(jobParams.getJobParams());
+ this.preset = null;
+ }
+ else
+ {
+ this.preset = prset; // ((JabaPreset) prset).p;
+ paramset = null; // no user supplied parameters.
+ }
+ }
+ return true;
+
+ }
+
+ public Jws2Client()
+ {
+ // anonymous constructor - used for headless method calls only
+ }
+
protected WebserviceInfo setWebService(Jws2Instance serv, boolean b)
{
// serviceHandle = serv;
- String serviceInstance = serv.service.getClass().getName();
+ String serviceInstance = serv.action; // serv.service.getClass().getName();
WebServiceName = serv.serviceType;
WebServiceJobTitle = serv.getActionText();
WsURL = serv.hosturl;
if (!b)
{
- return new WebserviceInfo(WebServiceJobTitle, WebServiceJobTitle
- + " using service hosted at " + serv.hosturl);
+ return new WebserviceInfo(WebServiceJobTitle,
+ WebServiceJobTitle + " using service hosted at "
+ + serv.hosturl + "\n"
+ + (serv.description != null ? serv.description : ""),
+ false);
}
return null;
}
+
/*
- Jws2Instance serviceHandle;
- * (non-Javadoc)
- * @see jalview.ws.WSMenuEntryProviderI#attachWSMenuEntry(javax.swing.JMenu, jalview.gui.AlignFrame)
- *
- @Override
- public void attachWSMenuEntry(JMenu wsmenu, AlignFrame alignFrame)
- {
- if (serviceHandle==null)
- {
- throw new Error("Implementation error: No service handle for this Jws2 service.");
- }
- attachWSMenuEntry(wsmenu, serviceHandle, alignFrame);
- }*/
+ * Jws2Instance serviceHandle; (non-Javadoc)
+ *
+ * @see jalview.ws.WSMenuEntryProviderI#attachWSMenuEntry(javax.swing.JMenu,
+ * jalview.gui.AlignFrame)
+ *
+ * @Override public void attachWSMenuEntry(JMenu wsmenu, AlignFrame
+ * alignFrame) { if (serviceHandle==null) { throw new
+ * Error("Implementation error: No service handle for this Jws2 service."); }
+ * attachWSMenuEntry(wsmenu, serviceHandle, alignFrame); }
+ */
/**
* add the menu item for a particular jws2 service instance
+ *
* @param wsmenu
* @param service
* @param alignFrame
*/
- abstract void attachWSMenuEntry(JMenu wsmenu,
- final Jws2Instance service, final AlignFrame alignFrame);
+ abstract void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
+ final AlignFrame alignFrame);
+
+ protected 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 aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ AbstractJabaCalcWorker worker = (AbstractJabaCalcWorker) 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(
+ JvSwingUtils.wrapTooltip(true, aaui.getAAconToggleTooltip()));
+ aaConEnabled.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ List 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(JvSwingUtils.wrapTooltip(true,
+ aaui.getAAeditSettingsTooltip()));
+ 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 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(
+ MessageManager.getString("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());
+ }
}