X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=aae6f7954858a6245bf70a44f3ceeabb94bf6964;hb=66a0dd08260a7ded38e4437f6d75af9fc6189f1c;hp=1ddc02d2fb435246af39eeb9b8a095c8d2a601b9;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index 1ddc02d..aae6f79 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -21,13 +21,12 @@ 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.api.ServiceWithParameters; +import jalview.ws.params.AutoCalcSetting; import jalview.ws.params.WsParamSetI; import jalview.ws.uimodel.AlignAnalysisUIText; @@ -35,12 +34,8 @@ 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 @@ -56,7 +51,7 @@ 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); @@ -66,15 +61,15 @@ 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; // // } @@ -87,71 +82,99 @@ 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 - { - 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) + for (AlignCalcWorkerI _worker : clnts) { - 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); } @@ -162,18 +185,24 @@ 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[] @@ -184,7 +213,8 @@ public class SequenceAnnotationWSClient extends Jws2Client @Override public void actionPerformed(ActionEvent e) { - new SequenceAnnotationWSClient(service, alignFrame, null, false); + new SequenceAnnotationWSClient(service, alignFrame, + null, false); } }); wsmenu.add(annotservice); @@ -194,35 +224,42 @@ 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())); + + (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 +274,7 @@ 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() { @@ -245,10 +282,14 @@ 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); } }