X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=29343f2bf66f7ed6e2c1ad1e6d831a720c938537;hb=c41398473f1493a06f28da53be50630a0f6e6f6d;hp=e7e5a6f575a0d2c73c19bfb63ad8afe621c24caa;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index e7e5a6f..29343f2 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -25,14 +25,16 @@ 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.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 java.util.Locale; + import javax.swing.JMenu; import javax.swing.JMenuItem; @@ -51,7 +53,7 @@ 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); @@ -61,15 +63,15 @@ public class SequenceAnnotationWSClient extends Jws2Client // 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) + private void initSequenceAnnotationWSClient(final ServiceWithParameters sh, + AlignFrame alignFrame, final WsParamSetI preset, boolean editParams) { // dan changed! dan test. comment out if conditional // if (alignFrame.getViewport().getAlignment().isNucleotide()) // { - // JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType + // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType // + " can only be used\nfor amino acid alignments.", - // "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE); + // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE); // return; // // } @@ -82,71 +84,100 @@ public class SequenceAnnotationWSClient extends Jws2Client // columns List clnts = alignFrame.getViewport() - .getCalcManager().getRegisteredWorkersOfClass(clientClass); - AbstractJabaCalcWorker worker; - if (clnts == null || clnts.size() == 0) + .getCalcManager() + .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class); + + SeqAnnotationServiceCalcWorker tmpworker = null; + if (clnts != null) { - if (!processParams(sh, editParams)) - { - return; - } - try + for (AlignCalcWorkerI _worker : clnts) { - 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); + tmpworker = (SeqAnnotationServiceCalcWorker) _worker; + if (tmpworker.hasService() + && tmpworker.getService().getClass().equals(clientClass)) + { + break; + } + tmpworker = null; } - alignFrame.getViewport().getCalcManager().registerWorker(worker); - alignFrame.getViewport().getCalcManager().startWorker(worker); + } + final var worker = tmpworker; + if (worker == null) + { + processParams(sh, editParams).thenAccept((startJob) -> { + if (startJob) + { + final SeqAnnotationServiceCalcWorker 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 + startSeqAnnotationWorker(sh, alignFrame, preset, editParams); + } + }); } else { - worker = (AbstractJabaCalcWorker) clnts.get(0); + WsParamSetI preset_; if (editParams) { paramset = worker.getArguments(); - preset = worker.getPreset(); + preset_ = worker.getPreset(); } - - if (!processParams(sh, editParams, true)) + else { - return; + preset_ = preset; } - // reinstate worker if it was blacklisted (might have happened due to - // invalid parameters) - alignFrame.getViewport().getCalcManager().workerMayRun(worker); - worker.updateParameters(this.preset, paramset); + processParams(sh, editParams, true).thenAccept((startJob) -> { + if (startJob) + { + // reinstate worker if it was blacklisted (might have happened due + // to + // invalid parameters) + alignFrame.getViewport().getCalcManager().enableWorker(worker); + worker.updateParameters(this.preset, paramset); + startSeqAnnotationWorker(sh, alignFrame, preset_, editParams); + } + }); } } - if (sh.action.toLowerCase().contains("disorder")) + else + { + startSeqAnnotationWorker(sh, alignFrame, preset, editParams); + } + } + + private void startSeqAnnotationWorker(ServiceWithParameters sh, + AlignFrame alignFrame, WsParamSetI preset, boolean editParams) + { + if (!sh.isInteractiveUpdate()) { // build IUPred style client. take sequences, returns annotation per // sequence. - if (!processParams(sh, editParams)) - { - return; - } - - alignFrame - .getViewport() - .getCalcManager() - .startWorker( - new AADisorderClient(sh, alignFrame, preset, paramset)); + processParams(sh, editParams).thenAccept((startJob) -> { + if (startJob) + { + alignFrame.getViewport().getCalcManager().startWorker( + new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset)); + } + }); } } - public SequenceAnnotationWSClient(AAConSettings fave, + public SequenceAnnotationWSClient(AutoCalcSetting fave, AlignFrame alignFrame, boolean b) { - super(alignFrame, fave.getPreset(), fave.getJobArgset()); + super(alignFrame, fave.getPreset(), fave.getArgumentSet()); initSequenceAnnotationWSClient(fave.getService(), alignFrame, fave.getPreset(), b); } @@ -157,29 +188,36 @@ 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 (registerAAConWSInstance(wsmenu, service, 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 annotservice = new JMenuItem(MessageManager.formatMessage( - "label.calcname_with_default_settings", - new String[] { calcName })); + "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(annotservice); @@ -189,40 +227,42 @@ public class SequenceAnnotationWSClient extends Jws2Client // arguments annotservice = new JMenuItem( MessageManager.getString("label.edit_settings_and_run")); - annotservice - .setToolTipText(MessageManager - .getString("label.view_and_change_parameters_before_running_calculation")); + annotservice.setToolTipText(MessageManager.getString( + "label.view_and_change_parameters_before_running_calculation")); annotservice.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - new SequenceAnnotationWSClient(service, alignFrame, null, true); + new SequenceAnnotationWSClient(service, alignFrame, + null, true); } }); wsmenu.add(annotservice); List presets = service.getParamStore().getPresets(); if (presets != null && presets.size() > 0) { - JMenu presetlist = new JMenu(MessageManager.formatMessage( - "label.run_with_preset", new String[] { calcName })); + 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( - true, - "" - + (preset.isModifiable() ? MessageManager - .getString("label.user_preset") - : MessageManager - .getString("label.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); } @@ -237,7 +277,7 @@ public class SequenceAnnotationWSClient extends Jws2Client { annotservice = new JMenuItem( MessageManager.getString("label.view_documentation")); - if (service.docUrl != null) + if (service != null && service.hasDocumentationUrl()) { annotservice.addActionListener(new ActionListener() { @@ -245,12 +285,14 @@ public class SequenceAnnotationWSClient extends Jws2Client @Override public void actionPerformed(ActionEvent arg0) { - Desktop.instance.showUrl(service.docUrl); + Desktop.getInstance().showUrl(service.getDocumentationUrl()); } }); - annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true, - MessageManager.formatMessage("label.view_service_doc_url", - new String[] { service.docUrl, service.docUrl }))); + annotservice.setToolTipText( + JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage( + "label.view_service_doc_url", new String[] + { service.getDocumentationUrl(), + service.getDocumentationUrl() }))); wsmenu.add(annotservice); } }