X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=2af31bb83f71ca848ab577545ab091e56a62ceea;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=06c54709f1d2a19fed74908217eb99dc221fbac4;hpb=27d1490bba5753b3f9c8fac0647cfe8148c53310;p=jalview.git diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index 06c5470..2af31bb 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -1,37 +1,48 @@ -/** +/* + * 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 jalview.api.AlignCalcWorkerI; -import jalview.bin.Cache; 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 java.util.List; -import javax.swing.JCheckBoxMenuItem; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.event.MenuEvent; -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. */ @@ -47,44 +58,58 @@ public class SequenceAnnotationWSClient extends Jws2Client 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; + Class clientClass = aaui.getClient(); - } - 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 clnts = alignFrame.getViewport() - .getCalcManager() - .getRegisteredWorkersOfClass(AAConsClient.class); + .getCalcManager().getRegisteredWorkersOfClass(clientClass); + AbstractJabaCalcWorker worker; if (clnts == null || clnts.size() == 0) { if (!processParams(sh, editParams)) { return; } - AAConsClient worker; - alignFrame - .getViewport() - .getCalcManager() - .registerWorker( - worker = new AAConsClient(sh, alignFrame, - this.preset, paramset)); + try + { + worker = (AbstractJabaCalcWorker) (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( + MessageManager.getString("error.implementation_error"), x); + } + alignFrame.getViewport().getCalcManager().registerWorker(worker); alignFrame.getViewport().getCalcManager().startWorker(worker); } else { - AAConsClient worker = (AAConsClient) clnts.get(0); + worker = (AbstractJabaCalcWorker) clnts.get(0); if (editParams) { paramset = worker.getArguments(); @@ -97,9 +122,8 @@ public class SequenceAnnotationWSClient extends Jws2Client } // reinstate worker if it was blacklisted (might have happened due to // invalid parameters) - alignFrame.getViewport().getCalcManager().workerMayRun(worker); + alignFrame.getViewport().getCalcManager().enableWorker(worker); worker.updateParameters(this.preset, paramset); - } } if (sh.action.toLowerCase().contains("disorder")) @@ -117,10 +141,9 @@ public class SequenceAnnotationWSClient extends Jws2Client .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()); @@ -137,10 +160,9 @@ public class SequenceAnnotationWSClient extends Jws2Client public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service, final AlignFrame alignFrame) { - if (service.serviceType.equals(compbio.ws.client.Services.AAConWS - .toString())) + if (registerAAConWSInstance(wsmenu, service, alignFrame)) { - registerAAConsWSInstance(wsmenu, service, alignFrame); + // Alignment dependent analysis calculation WS gui return; } boolean hasparams = service.hasParameters(); @@ -148,8 +170,10 @@ public class SequenceAnnotationWSClient extends Jws2Client 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 @@ -158,35 +182,42 @@ public class SequenceAnnotationWSClient extends Jws2Client 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 presets = service.getParamStore().getPresets(); if (presets != null && presets.size() > 0) { - JMenu presetlist = new JMenu("Run " + calcName + "with preset"); + JMenu presetlist = new JMenu(MessageManager.formatMessage( + "label.run_with_preset", new String[] { calcName })); for (final WsParamSetI preset : presets) { final JMenuItem methodR = new JMenuItem(preset.getName()); - methodR.setToolTipText("

" - + JvSwingUtils.wrapTooltip("" - + (preset.isModifiable() ? "User Preset" - : "Service Preset") + "
" - + preset.getDescription() + "

") + ""); + methodR.setToolTipText(JvSwingUtils.wrapTooltip( + true, + "" + + (preset.isModifiable() ? MessageManager + .getString("label.user_preset") + : MessageManager + .getString("label.service_preset")) + + "
" + preset.getDescription())); methodR.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -202,239 +233,26 @@ public class SequenceAnnotationWSClient extends Jws2Client } } - } - - 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, - final Jws2Instance service, final AlignFrame alignFrame) - { - // register this in the AACons settings set - JCheckBoxMenuItem _aaConsEnabled = null; - for (int i = 0; i < wsmenu.getItemCount(); i++) - { - JMenuItem item = wsmenu.getItem(i); - if (item instanceof JCheckBoxMenuItem - && item.getText().equals(AAconsToggle)) - { - _aaConsEnabled = (JCheckBoxMenuItem) item; - } - } - // is there an aaCons worker already present - if so, set it to use the - // given service handle - { - List aaconsClient = alignFrame.getViewport() - .getCalcManager() - .getRegisteredWorkersOfClass(AAConsClient.class); - if (aaconsClient != null && aaconsClient.size() > 0) - { - AAConsClient worker = (AAConsClient) aaconsClient.get(0); - if (!worker.service.hosturl.equals(service.hosturl)) - { - // javax.swing.SwingUtilities.invokeLater(new Runnable() - { - // @Override - // public void run() - { - removeCurrentAAConsWorkerFor(alignFrame); - buildCurrentAAConsWorkerFor(alignFrame, service); - } - }//); - } - } - } - - // is there a service already registered ? there shouldn't be if we are - // being called correctly - if (_aaConsEnabled == null) + else { - final JCheckBoxMenuItem aaConsEnabled = new JCheckBoxMenuItem( - AAconsToggle); - wsmenu.addMenuListener(new MenuListener() + annotservice = new JMenuItem( + MessageManager.getString("label.view_documentation")); + if (service.docUrl != null) { - - @Override - public void menuSelected(MenuEvent arg0) - { - wsmenu.setEnabled(!alignFrame.getViewport().getAlignment() - .isNucleotide()); - List aaconsClient = alignFrame.getViewport() - .getCalcManager() - .getRegisteredWorkersOfClass(AAConsClient.class); - if (aaconsClient != null && aaconsClient.size() > 0) - { - aaConsEnabled.setSelected(true); - } - else - { - aaConsEnabled.setSelected(false); - } - } - - @Override - public void menuDeselected(MenuEvent arg0) + annotservice.addActionListener(new ActionListener() { - // TODO Auto-generated method stub - } - - @Override - public void menuCanceled(MenuEvent arg0) - { - // TODO Auto-generated method stub - - } - }); - aaConsEnabled.setToolTipText("

" - + JvSwingUtils.wrapTooltip(AAconsToggleTooltip + "

") - + ""); - aaConsEnabled.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent arg0) - { - // aaConsEnabled.setSelected(!aaConsEnabled.isSelected()); - List aaconsClient = alignFrame.getViewport() - .getCalcManager() - .getRegisteredWorkersOfClass(AAConsClient.class); - if (aaconsClient != null && aaconsClient.size() > 0) - { - removeCurrentAAConsWorkerFor(alignFrame); - } - else + @Override + public void actionPerformed(ActionEvent arg0) { - buildCurrentAAConsWorkerFor(alignFrame); - + Desktop.instance.showUrl(service.docUrl); } - } - - }); - wsmenu.add(aaConsEnabled); - JMenuItem modifyParams = new JMenuItem(AAeditSettings); - modifyParams.setToolTipText("

" - + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "

") - + ""); - modifyParams.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent arg0) - { - showAAConsAnnotationSettingsFor(alignFrame); - } - }); - wsmenu.add(modifyParams); - - } - } - - private static void showAAConsAnnotationSettingsFor(AlignFrame alignFrame) - { - /* - * preferred settings Whether AACons is automatically recalculated Which - * AACons server to use What parameters to use - */ - // could actually do a class search for this too - AAConsSettings fave = (AAConsSettings) alignFrame.getViewport() - .getCalcIdSettingsFor(AAConsCalcId); - if (fave == null) - { - fave = createDefaultAAConsSettings(); - } - new SequenceAnnotationWSClient(fave, alignFrame, true); - - } - - private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame) - { - buildCurrentAAConsWorkerFor(alignFrame, null); - } - - private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame, - Jws2Instance service) - { - /* - * preferred settings Whether AACons is automatically recalculated Which - * AACons server to use What parameters to use - */ - AAConsSettings fave = (AAConsSettings) alignFrame.getViewport() - .getCalcIdSettingsFor(AAConsCalcId); - if (fave == null) - { - fave = createDefaultAAConsSettings(service); - } - else - { - if (service != null - && !fave.getService().hosturl.equals(service.hosturl)) - { - Cache.log.debug("Changing AACons service to " + service.hosturl - + " from " + fave.getService().hosturl); - fave.setService(service); - } - } - new SequenceAnnotationWSClient(fave, alignFrame, false); - } - - private static AAConsSettings createDefaultAAConsSettings() - { - return createDefaultAAConsSettings(null); - } - - private static AAConsSettings createDefaultAAConsSettings( - Jws2Instance service) - { - if (service != null) - { - if (!service.serviceType.toString().equals( - compbio.ws.client.Services.AAConWS.toString())) - { - Cache.log - .warn("Ignoring invalid preferred service for AACons calculations (service type was " - + service.serviceType + ")"); - service = null; + }); + annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage("label.view_service_doc_url", + new String[] { service.docUrl, service.docUrl }))); + wsmenu.add(annotservice); } - 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 AACons - 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."); - } - return new AAConsSettings(true, service, null, null); - } - - private static void removeCurrentAAConsWorkerFor(AlignFrame alignFrame) - { - alignFrame.getViewport().getCalcManager() - .removeRegisteredWorkersOfClass(AAConsClient.class); - // AAConsClient.removeAAConsAnnotation(alignFrame.alignPanel); - } }