X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=2af31bb83f71ca848ab577545ab091e56a62ceea;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=e985f41260c6bf09c93e63b8b0dad51c6c126563;hpb=9daf267d40a67e589a92d3d8fe14f9e535d10ee2;p=jalview.git diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index e985f41..2af31bb 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -1,41 +1,41 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * 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. + * 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 . + * 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.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 @@ -43,9 +43,6 @@ import javax.swing.event.MenuListener; */ public class SequenceAnnotationWSClient extends Jws2Client { - - public static final String AAConCalcId = "jabaws2.AACon"; - /** * initialise a client so its attachWSMenuEntry method can be called. */ @@ -61,47 +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 - + // 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) { - // 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; -// -// } - 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) { + Class clientClass = aaui.getClient(); + // Build an AACon style client - take alignment, return annotation for // columns List clnts = alignFrame.getViewport() - .getCalcManager() - .getRegisteredWorkersOfClass(AAConClient.class); + .getCalcManager().getRegisteredWorkersOfClass(clientClass); + AbstractJabaCalcWorker worker; if (clnts == null || clnts.size() == 0) { if (!processParams(sh, editParams)) { return; } - AAConClient worker; - alignFrame - .getViewport() - .getCalcManager() - .registerWorker( - worker = new AAConClient(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 { - AAConClient worker = (AAConClient) clnts.get(0); + worker = (AbstractJabaCalcWorker) clnts.get(0); if (editParams) { paramset = worker.getArguments(); @@ -114,9 +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")) @@ -134,65 +141,6 @@ public class SequenceAnnotationWSClient extends Jws2Client .startWorker( new AADisorderClient(sh, alignFrame, preset, paramset)); } - - - // dan test dan changed! - if (sh.action.toLowerCase().contains("rna structure prediction")) - { - - List clnts = alignFrame.getViewport() - .getCalcManager() - .getRegisteredWorkersOfClass(RNAalifoldClient.class); - if (clnts == null || clnts.size() == 0) - { - if (!processParams(sh, editParams)) - { - return; - } - RNAalifoldClient worker; - alignFrame - .getViewport() - .getCalcManager() - .registerWorker( - worker = new RNAalifoldClient(sh, alignFrame, - this.preset, paramset)); - alignFrame.getViewport().getCalcManager().startWorker(worker); - } - else - { - RNAalifoldClient worker = (RNAalifoldClient) clnts.get(0); - if (editParams) - { - paramset = worker.getArguments(); - preset = worker.getPreset(); - } - - if (!processParams(sh, editParams, true)) - { - return; - } - - // reinstate worker if it was blacklisted (might have happened due to - // invalid parameters) - alignFrame.getViewport().getCalcManager().workerMayRun(worker); - worker.updateParameters(this.preset, paramset); - } - - } - -// -// if (!processParams(sh, editParams, true)) -// { -// return; -// } -// -// alignFrame -// .getViewport() -// .getCalcManager() -// .startWorker( -// new RNAalifoldClient(sh, alignFrame, preset, paramset)); -// - } public SequenceAnnotationWSClient(AAConSettings fave, @@ -212,10 +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)) { - registerAAConWSInstance(wsmenu, service, alignFrame); + // Alignment dependent analysis calculation WS gui return; } boolean hasparams = service.hasParameters(); @@ -223,7 +170,9 @@ public class SequenceAnnotationWSClient extends Jws2Client String calcName = service.serviceType.substring(0, service.serviceType.length() - 2); - JMenuItem annotservice = new JMenuItem(calcName + " Defaults"); + JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage( + "label.calcname_with_default_settings", + new String[] { calcName })); annotservice.addActionListener(new ActionListener() { @@ -238,9 +187,11 @@ public class SequenceAnnotationWSClient extends Jws2Client { // only add these menu options if the service has user-modifiable // arguments - annotservice = new JMenuItem("Edit settings and run ..."); + annotservice = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); annotservice - .setToolTipText("View and change parameters before running calculation"); + .setToolTipText(MessageManager + .getString("label.view_and_change_parameters_before_running_calculation")); annotservice.addActionListener(new ActionListener() { @@ -253,16 +204,20 @@ public class SequenceAnnotationWSClient extends Jws2Client 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) @@ -280,7 +235,8 @@ public class SequenceAnnotationWSClient extends Jws2Client } else { - annotservice = new JMenuItem("View documentation"); + annotservice = new JMenuItem( + MessageManager.getString("label.view_documentation")); if (service.docUrl != null) { annotservice.addActionListener(new ActionListener() @@ -292,236 +248,11 @@ public class SequenceAnnotationWSClient extends Jws2Client Desktop.instance.showUrl(service.docUrl); } }); - annotservice.setToolTipText("" - + JvSwingUtils.wrapTooltip("View " + service.docUrl + "") - + ""); + annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage("label.view_service_doc_url", + new String[] { service.docUrl, service.docUrl }))); wsmenu.add(annotservice); } } } - - 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 void registerAAConWSInstance(final JMenu wsmenu, - final Jws2Instance service, final AlignFrame alignFrame) - { - // 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(AAconToggle)) - { - _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(AAConClient.class); - if (aaconClient != null && aaconClient.size() > 0) - { - AAConClient worker = (AAConClient) aaconClient.get(0); - if (!worker.service.hosturl.equals(service.hosturl)) - { - // javax.swing.SwingUtilities.invokeLater(new Runnable() - { - // @Override - // public void run() - { - removeCurrentAAConWorkerFor(alignFrame); - buildCurrentAAConWorkerFor(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( - AAconToggle); - wsmenu.addMenuListener(new MenuListener() - { - - @Override - public void menuSelected(MenuEvent arg0) - { - wsmenu.setEnabled(!alignFrame.getViewport().getAlignment() - .isNucleotide()); - List aaconClient = alignFrame.getViewport() - .getCalcManager() - .getRegisteredWorkersOfClass(AAConClient.class); - 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 - - } - }); - aaConEnabled.setToolTipText("

" - + JvSwingUtils.wrapTooltip(AAconToggleTooltip + "

") - + ""); - aaConEnabled.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent arg0) - { - List aaconClient = alignFrame.getViewport() - .getCalcManager() - .getRegisteredWorkersOfClass(AAConClient.class); - if (aaconClient != null && aaconClient.size() > 0) - { - removeCurrentAAConWorkerFor(alignFrame); - } - else - { - buildCurrentAAConWorkerFor(alignFrame); - - } - } - - }); - wsmenu.add(aaConEnabled); - JMenuItem modifyParams = new JMenuItem(AAeditSettings); - modifyParams.setToolTipText("

" - + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "

") - + ""); - modifyParams.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent arg0) - { - showAAConAnnotationSettingsFor(alignFrame); - } - }); - wsmenu.add(modifyParams); - - } - } - - private static void showAAConAnnotationSettingsFor(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(AAConCalcId); - if (fave == null) - { - fave = createDefaultAAConSettings(); - } - new SequenceAnnotationWSClient(fave, alignFrame, true); - - } - - private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame) - { - buildCurrentAAConWorkerFor(alignFrame, null); - } - - private static void buildCurrentAAConWorkerFor(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(AAConCalcId); - if (fave == null) - { - fave = createDefaultAAConSettings(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() - { - return createDefaultAAConSettings(null); - } - - private static AAConSettings createDefaultAAConSettings( - 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, - compbio.ws.client.Services.AAConWS.toString()); - } - if (service == null) - { - // TODO raise dialog box explaining error, and/or open the JABA - // preferences menu. - throw new Error("No AACon service found."); - } - return new AAConSettings(true, service, null, null); - } - - private static void removeCurrentAAConWorkerFor(AlignFrame alignFrame) - { - alignFrame.getViewport().getCalcManager() - .removeRegisteredWorkersOfClass(AAConClient.class); - } }