/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) * Copyright (C) 2015 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 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.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 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.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 + "\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); } */ /** * 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); 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(false, 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()); } }