X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=d72681df9da50a17efc4fc1a1cb3fcfadc167b16;hb=23a5ed32b702d4d3682b8cdc8fd8e3f238202f7d;hp=fea8f2a72e74c3236e6d4c4759061a5a986f5a84;hpb=b2c4d6c467255b5e30caf4cac1be372b89db0eea;p=jalview.git diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index fea8f2a..d72681d 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -7,28 +7,37 @@ 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.AncestorEvent; +import javax.swing.event.AncestorListener; +import javax.swing.event.MenuEvent; +import javax.swing.event.MenuListener; import compbio.metadata.Argument; import jalview.api.AlignCalcWorkerI; +import jalview.bin.Cache; import jalview.datamodel.AlignmentView; import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.JalviewDialog; import jalview.gui.JvSwingUtils; +import jalview.ws.jws2.dm.AAConsSettings; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.WsParamSetI; /** - * @author jimp + * @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. */ @@ -41,20 +50,25 @@ public class SequenceAnnotationWSClient extends Jws2Client AlignFrame alignFrame, WsParamSetI preset, boolean editParams) { super(alignFrame, preset, null); - if (sh.serviceType.toLowerCase().contains("aaconws")) + initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams); + } + + public void initSequenceAnnotationWSClient(final Jws2Instance sh, + AlignFrame alignFrame, WsParamSetI preset, boolean editParams) + { + if (alignFrame.getViewport().getAlignment().isNucleotide()) { - // Build an AACons client - if (alignFrame.getViewport().getAlignment().isNucleotide()) - { - JOptionPane - .showMessageDialog( - Desktop.desktop, - "AACons can only be used\nfor amino acid alignments.\nSorry about that!", - "Wrong type of sequences!", - JOptionPane.WARNING_MESSAGE); - return; + 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")) + { + // Build an AACons style client - take alignment, return annotation for + // columns - } List clnts = alignFrame.getViewport() .getCalcManager() .getRegisteredWorkersOfClass(AAConsClient.class); @@ -64,11 +78,15 @@ public class SequenceAnnotationWSClient extends Jws2Client { return; } + AAConsClient worker; alignFrame .getViewport() .getCalcManager() .registerWorker( - new AAConsClient(sh, alignFrame, preset, paramset)); + worker = new AAConsClient(sh, alignFrame, + this.preset, paramset)); + alignFrame.getViewport().getCalcManager().startWorker(worker); + } else { @@ -80,15 +98,40 @@ 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); + worker.updateParameters(this.preset, paramset); } } - + if (sh.action.toLowerCase().contains("disorder")) + { + // 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)); + } + + } + + public SequenceAnnotationWSClient(AAConsSettings fave, + AlignFrame alignFrame, boolean b) + { + super(alignFrame, fave.getPreset(), fave.getJobArgset()); + initSequenceAnnotationWSClient(fave.getService(), alignFrame, + fave.getPreset(), b); } /* @@ -100,64 +143,304 @@ public class SequenceAnnotationWSClient extends Jws2Client public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service, final AlignFrame alignFrame) { - if (service.serviceType.toLowerCase().contains("aaconws")) + if (service.serviceType.equals(compbio.ws.client.Services.AAConWS + .toString())) { - boolean hasparams = service.hasParameters(); - String calcName = "AACons"; - JMenuItem aacons = new JMenuItem("AACons Defaults"); - aacons.addActionListener(new ActionListener() + registerAAConsWSInstance(wsmenu, service, alignFrame); + return; + } + boolean hasparams = service.hasParameters(); + // Assume name ends in WS + String calcName = service.serviceType.substring(0, + service.serviceType.length() - 2); + + JMenuItem aacons = new JMenuItem(calcName + " Defaults"); + aacons.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) { + new SequenceAnnotationWSClient(service, alignFrame, null, false); + } + }); + wsmenu.add(aacons); + 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"); - @Override + aacons.addActionListener(new ActionListener() + { public void actionPerformed(ActionEvent e) { - new SequenceAnnotationWSClient(service, alignFrame, null, false); + new SequenceAnnotationWSClient(service, alignFrame, null, true); } }); wsmenu.add(aacons); - if (hasparams) + List presets = service.getParamStore().getPresets(); + if (presets != null && presets.size() > 0) { - // only add these menu options if the service has user-modifiable - // arguments - aacons = new JMenuItem("Edit settings and run ..."); - aacons.setToolTipText("View and change the parameters before alignment."); + JMenu presetlist = new JMenu("Run " + calcName + "with preset"); - aacons.addActionListener(new ActionListener() + for (final WsParamSetI preset : presets) { - public void actionPerformed(ActionEvent e) + final JMenuItem methodR = new JMenuItem(preset.getName()); + methodR.setToolTipText("

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

") + ""); + methodR.addActionListener(new ActionListener() { - new SequenceAnnotationWSClient(service, alignFrame, null, true); + public void actionPerformed(ActionEvent e) + { + new SequenceAnnotationWSClient(service, alignFrame, preset, + false); + } + + }); + presetlist.add(methodR); + } + wsmenu.add(presetlist); + } + + } + } + + 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) + { + final JCheckBoxMenuItem aaConsEnabled = new JCheckBoxMenuItem( + AAconsToggle); + wsmenu.addMenuListener(new MenuListener() + { + + @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); } - }); - wsmenu.add(aacons); - List presets = service.getParamStore().getPresets(); - if (presets != null && presets.size() > 0) + else + { + aaConsEnabled.setSelected(false); + } + } + + @Override + public void menuDeselected(MenuEvent arg0) + { + // TODO Auto-generated method stub + + } + + @Override + public void menuCanceled(MenuEvent arg0) { - JMenu presetlist = new JMenu("Run " + calcName + "with preset"); + // TODO Auto-generated method stub - for (final WsParamSetI preset : presets) + } + }); + 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) { - final JMenuItem methodR = new JMenuItem(preset.getName()); - methodR.setToolTipText("

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

") + ""); - methodR.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - new SequenceAnnotationWSClient(service, alignFrame, preset, - false); - } - - }); - presetlist.add(methodR); + removeCurrentAAConsWorkerFor(alignFrame); } - wsmenu.add(presetlist); + else + { + buildCurrentAAConsWorkerFor(alignFrame); + + } + } + + }); + 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; + } + 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); + } }