X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=6939db46493e89be334e61acdb3b13b3aae57db0;hb=4898f0ae429e0c61ddba72ca46be89b34bb4df8b;hp=c78ed98deffdc8f1da701cf6aa66d2a91a0d58bb;hpb=85c7ac5fb01ae254b336a6d5e743e004799a05ce;p=jalview.git diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index c78ed98..6939db4 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -1,34 +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.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.JvSwingUtils; +import jalview.util.MessageManager; +import jalview.ws.api.ServiceWithParameters; +import jalview.ws.params.AutoCalcSetting; +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.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; - -import compbio.metadata.Argument; - -import jalview.api.AlignCalcWorkerI; -import jalview.datamodel.AlignmentView; -import jalview.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.gui.JalviewDialog; -import jalview.gui.JvSwingUtils; -import jalview.ws.jws2.jabaws2.Jws2Instance; -import jalview.ws.params.WsParamSetI; /** - * @author jimp + * @author jprocter * */ public class SequenceAnnotationWSClient extends Jws2Client { - /** * initialise a client so its attachWSMenuEntry method can be called. */ @@ -37,45 +51,78 @@ public class SequenceAnnotationWSClient extends Jws2Client // TODO Auto-generated constructor stub } - public SequenceAnnotationWSClient(final Jws2Instance sh, + public SequenceAnnotationWSClient(final ServiceWithParameters sh, AlignFrame alignFrame, WsParamSetI preset, boolean editParams) { super(alignFrame, preset, null); - 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; + initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams); + } - } - if (sh.action.toLowerCase().contains("conservation")) + // dan think. Do I need to change this method to run RNAalifold through the + // GUI + + public void initSequenceAnnotationWSClient(final ServiceWithParameters sh, + AlignFrame alignFrame, WsParamSetI preset, boolean editParams) + { + // dan changed! dan test. comment out if conditional + // if (alignFrame.getViewport().getAlignment().isNucleotide()) + // { + // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType + // + " can only be used\nfor amino acid alignments.", + // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE); + // return; + // + // } + AlignAnalysisUIText aaui = sh.getAlignAnalysisUI(); + if (aaui != null) { - // Build an AACons style client - take alignment, return annotation for + Class clientClass = aaui.getClient(); + + // Build an AACon style client - take alignment, return annotation for // columns List clnts = alignFrame.getViewport() .getCalcManager() - .getRegisteredWorkersOfClass(AAConsClient.class); - if (clnts == null || clnts.size() == 0) + .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class); + + SeqAnnotationServiceCalcWorker worker = null; + if (clnts != null) + { + for (AlignCalcWorkerI _worker : clnts) + { + worker = (SeqAnnotationServiceCalcWorker) _worker; + if (worker.hasService() + && worker.getService().getClass().equals(clientClass)) + { + break; + } + worker = null; + } + } + if (worker == null) { if (!processParams(sh, editParams)) { return; } - AAConsClient worker; - alignFrame - .getViewport() - .getCalcManager() - .registerWorker( - worker = new AAConsClient(sh, alignFrame, preset, - paramset)); - alignFrame.getViewport().getCalcManager().startWorker(worker); - + try + { + worker = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset, + paramset); + } catch (Exception x) + { + x.printStackTrace(); + throw new Error( + MessageManager.getString("error.implementation_error"), + x); + } + alignFrame.getViewport().getCalcManager().registerWorker(worker); // also + // starts + // the + // worker } else { - AAConsClient worker = (AAConsClient) clnts.get(0); if (editParams) { paramset = worker.getArguments(); @@ -83,15 +130,16 @@ public class SequenceAnnotationWSClient extends Jws2Client } 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(preset, paramset); - + alignFrame.getViewport().getCalcManager().enableWorker(worker); + worker.updateParameters(this.preset, paramset); } } - if (sh.action.toLowerCase().contains("disorder")) + if (!sh.isInteractiveUpdate()) { // build IUPred style client. take sequences, returns annotation per // sequence. @@ -100,13 +148,17 @@ public class SequenceAnnotationWSClient extends Jws2Client return; } - alignFrame - .getViewport() - .getCalcManager() - .startWorker( - new AADisorderClient(sh, alignFrame, preset, paramset)); + alignFrame.getViewport().getCalcManager().startWorker( + new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset)); } + } + public SequenceAnnotationWSClient(AutoCalcSetting fave, + AlignFrame alignFrame, boolean b) + { + super(alignFrame, fave.getPreset(), fave.getArgumentSet()); + initSequenceAnnotationWSClient(fave.getService(), alignFrame, + fave.getPreset(), b); } /* @@ -115,58 +167,81 @@ public class SequenceAnnotationWSClient extends Jws2Client * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu, * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame) */ - public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service, + @Override + public void attachWSMenuEntry(JMenu wsmenu, + final ServiceWithParameters service, final AlignFrame alignFrame) { + if (Jws2ClientFactory.registerAAConWSInstance(wsmenu, + service, alignFrame)) + { + // Alignment dependent analysis calculation WS gui + return; + } boolean hasparams = service.hasParameters(); - // Assume name ends in WS - String calcName = service.serviceType.substring(0, - service.serviceType.length() - 2); + String calcName = service.getName(); + if (calcName.endsWith("WS")) + { + // Remove "WS" suffix + calcName = calcName.substring(0, calcName.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 public void actionPerformed(ActionEvent e) { - new SequenceAnnotationWSClient(service, alignFrame, null, false); + 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() { + @Override public void actionPerformed(ActionEvent e) { - new SequenceAnnotationWSClient(service, alignFrame, null, true); + 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() { + @Override public void actionPerformed(ActionEvent e) { - new SequenceAnnotationWSClient(service, alignFrame, preset, + new SequenceAnnotationWSClient(service, + alignFrame, preset, false); } @@ -177,5 +252,28 @@ public class SequenceAnnotationWSClient extends Jws2Client } } + else + { + annotservice = new JMenuItem( + MessageManager.getString("label.view_documentation")); + if (service != null && service.hasDocumentationUrl()) + { + annotservice.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent arg0) + { + Desktop.getInstance().showUrl(service.getDocumentationUrl()); + } + }); + annotservice.setToolTipText( + JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage( + "label.view_service_doc_url", new String[] + { service.getDocumentationUrl(), + service.getDocumentationUrl() }))); + wsmenu.add(annotservice); + } + } } }