X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=bf20cd4d0073b1f5bc929ac3c766110e445f5150;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=46c04e50d39817afe4aad171789fa352edea52e7;hpb=b421ac29c2a40f7eb0dce7a50cfa1dd2ea7bb7ef;p=jalview.git diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index 46c04e5..bf20cd4 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -8,7 +8,7 @@ import jalview.bin.Cache; import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.JvSwingUtils; -import jalview.ws.jws2.dm.AAConsSettings; +import jalview.ws.jws2.dm.AAConSettings; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.WsParamSetI; @@ -24,13 +24,13 @@ import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; /** - * @author jprocter + * @author jprocter * */ -public class SequenceAnnotationWSClient extends Jws2Client +public class SequenceAnnotationWSClient extends Jws2Client { - public static final String AAConsCalcId = "jabaws2.AACons"; + public static final String AAConCalcId = "jabaws2.AACon"; /** * initialise a client so its attachWSMenuEntry method can be called. @@ -60,31 +60,31 @@ public class SequenceAnnotationWSClient extends Jws2Client } if (sh.action.toLowerCase().contains("conservation")) { - // Build an AACons style client - take alignment, return annotation for + // Build an AACon style client - take alignment, return annotation for // columns List clnts = alignFrame.getViewport() .getCalcManager() - .getRegisteredWorkersOfClass(AAConsClient.class); + .getRegisteredWorkersOfClass(AAConClient.class); if (clnts == null || clnts.size() == 0) { if (!processParams(sh, editParams)) { return; } - AAConsClient worker; + AAConClient worker; alignFrame .getViewport() .getCalcManager() .registerWorker( - worker = new AAConsClient(sh, alignFrame, + worker = new AAConClient(sh, alignFrame, this.preset, paramset)); alignFrame.getViewport().getCalcManager().startWorker(worker); } else { - AAConsClient worker = (AAConsClient) clnts.get(0); + AAConClient worker = (AAConClient) clnts.get(0); if (editParams) { paramset = worker.getArguments(); @@ -120,7 +120,7 @@ public class SequenceAnnotationWSClient extends Jws2Client } - public SequenceAnnotationWSClient(AAConsSettings fave, + public SequenceAnnotationWSClient(AAConSettings fave, AlignFrame alignFrame, boolean b) { super(alignFrame, fave.getPreset(), fave.getJobArgset()); @@ -140,7 +140,7 @@ public class SequenceAnnotationWSClient extends Jws2Client if (service.serviceType.equals(compbio.ws.client.Services.AAConWS .toString())) { - registerAAConsWSInstance(wsmenu, service, alignFrame); + registerAAConWSInstance(wsmenu, service, alignFrame); return; } boolean hasparams = service.hasParameters(); @@ -148,8 +148,8 @@ public class SequenceAnnotationWSClient extends Jws2Client String calcName = service.serviceType.substring(0, service.serviceType.length() - 2); - JMenuItem aacons = new JMenuItem(calcName + " Defaults"); - aacons.addActionListener(new ActionListener() + JMenuItem annotservice = new JMenuItem(calcName + " Defaults"); + annotservice.addActionListener(new ActionListener() { @Override @@ -158,22 +158,23 @@ public class SequenceAnnotationWSClient extends Jws2Client 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("Edit settings and run ..."); + annotservice + .setToolTipText("View and change parameters before running calculation"); - aacons.addActionListener(new ActionListener() + annotservice.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { new SequenceAnnotationWSClient(service, alignFrame, null, true); } }); - wsmenu.add(aacons); + wsmenu.add(annotservice); List presets = service.getParamStore().getPresets(); if (presets != null && presets.size() > 0) { @@ -201,75 +202,79 @@ public class SequenceAnnotationWSClient extends Jws2Client wsmenu.add(presetlist); } - } else { - aacons = new JMenuItem("View documentation"); - if (service.docUrl!=null) + } + else + { + annotservice = new JMenuItem("View documentation"); + if (service.docUrl != null) { - aacons.addActionListener(new ActionListener() + annotservice.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent arg0) { Desktop.instance.showUrl(service.docUrl); } }); - aacons.setToolTipText(""+JvSwingUtils.wrapTooltip("View "+service.docUrl+"")+""); - wsmenu.add(aacons); + annotservice.setToolTipText("" + + JvSwingUtils.wrapTooltip("View " + service.docUrl + "") + + ""); + wsmenu.add(annotservice); } } } - 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 String AAconToggle = "AACon Calculations", + AAconToggleTooltip = "When checked, AACon calculations are updated automatically.", + AAeditSettings = "Change AACon Settings...", + AAeditSettingsTooltip = "Modify settings for AACon calculations."; - // private final enableAAConsCalculation(final AlignFrame alignFrame, ) - private void registerAAConsWSInstance(final JMenu wsmenu, + private void registerAAConWSInstance(final JMenu wsmenu, final Jws2Instance service, final AlignFrame alignFrame) { - // register this in the AACons settings set - JCheckBoxMenuItem _aaConsEnabled = null; + // 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(AAconsToggle)) + && item.getText().equals(AAconToggle)) { - _aaConsEnabled = (JCheckBoxMenuItem) item; + _aaConEnabled = (JCheckBoxMenuItem) item; } } - // is there an aaCons worker already present - if so, set it to use the + // is there an aaCon worker already present - if so, set it to use the // given service handle { - List aaconsClient = alignFrame.getViewport() + List aaconClient = alignFrame.getViewport() .getCalcManager() - .getRegisteredWorkersOfClass(AAConsClient.class); - if (aaconsClient != null && aaconsClient.size() > 0) + .getRegisteredWorkersOfClass(AAConClient.class); + if (aaconClient != null && aaconClient.size() > 0) { - AAConsClient worker = (AAConsClient) aaconsClient.get(0); + AAConClient worker = (AAConClient) aaconClient.get(0); if (!worker.service.hosturl.equals(service.hosturl)) { - // javax.swing.SwingUtilities.invokeLater(new Runnable() + // javax.swing.SwingUtilities.invokeLater(new Runnable() { - // @Override - // public void run() + // @Override + // public void run() { - removeCurrentAAConsWorkerFor(alignFrame); - buildCurrentAAConsWorkerFor(alignFrame, service); + removeCurrentAAConWorkerFor(alignFrame); + buildCurrentAAConWorkerFor(alignFrame, service); } - }//); + }// ); } } } // is there a service already registered ? there shouldn't be if we are // being called correctly - if (_aaConsEnabled == null) + if (_aaConEnabled == null) { - final JCheckBoxMenuItem aaConsEnabled = new JCheckBoxMenuItem( - AAconsToggle); + final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem( + AAconToggle); wsmenu.addMenuListener(new MenuListener() { @@ -278,16 +283,16 @@ public class SequenceAnnotationWSClient extends Jws2Client { wsmenu.setEnabled(!alignFrame.getViewport().getAlignment() .isNucleotide()); - List aaconsClient = alignFrame.getViewport() + List aaconClient = alignFrame.getViewport() .getCalcManager() - .getRegisteredWorkersOfClass(AAConsClient.class); - if (aaconsClient != null && aaconsClient.size() > 0) + .getRegisteredWorkersOfClass(AAConClient.class); + if (aaconClient != null && aaconClient.size() > 0) { - aaConsEnabled.setSelected(true); + aaConEnabled.setSelected(true); } else { - aaConsEnabled.setSelected(false); + aaConEnabled.setSelected(false); } } @@ -305,31 +310,30 @@ public class SequenceAnnotationWSClient extends Jws2Client } }); - aaConsEnabled.setToolTipText("

" - + JvSwingUtils.wrapTooltip(AAconsToggleTooltip + "

") + aaConEnabled.setToolTipText("

" + + JvSwingUtils.wrapTooltip(AAconToggleTooltip + "

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

" + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "

") @@ -340,7 +344,7 @@ public class SequenceAnnotationWSClient extends Jws2Client @Override public void actionPerformed(ActionEvent arg0) { - showAAConsAnnotationSettingsFor(alignFrame); + showAAConAnnotationSettingsFor(alignFrame); } }); wsmenu.add(modifyParams); @@ -348,47 +352,47 @@ public class SequenceAnnotationWSClient extends Jws2Client } } - private static void showAAConsAnnotationSettingsFor(AlignFrame alignFrame) + private static void showAAConAnnotationSettingsFor(AlignFrame alignFrame) { /* - * preferred settings Whether AACons is automatically recalculated Which - * AACons server to use What parameters to use + * 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 - AAConsSettings fave = (AAConsSettings) alignFrame.getViewport() - .getCalcIdSettingsFor(AAConsCalcId); + AAConSettings fave = (AAConSettings) alignFrame.getViewport() + .getCalcIdSettingsFor(AAConCalcId); if (fave == null) { - fave = createDefaultAAConsSettings(); + fave = createDefaultAAConSettings(); } new SequenceAnnotationWSClient(fave, alignFrame, true); } - private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame) + private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame) { - buildCurrentAAConsWorkerFor(alignFrame, null); + buildCurrentAAConWorkerFor(alignFrame, null); } - private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame, + private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame, Jws2Instance service) { /* - * preferred settings Whether AACons is automatically recalculated Which - * AACons server to use What parameters to use + * preferred settings Whether AACon is automatically recalculated Which + * AACon server to use What parameters to use */ - AAConsSettings fave = (AAConsSettings) alignFrame.getViewport() - .getCalcIdSettingsFor(AAConsCalcId); + AAConSettings fave = (AAConSettings) alignFrame.getViewport() + .getCalcIdSettingsFor(AAConCalcId); if (fave == null) { - fave = createDefaultAAConsSettings(service); + fave = createDefaultAAConSettings(service); } else { if (service != null && !fave.getService().hosturl.equals(service.hosturl)) { - Cache.log.debug("Changing AACons service to " + service.hosturl + Cache.log.debug("Changing AACon service to " + service.hosturl + " from " + fave.getService().hosturl); fave.setService(service); } @@ -396,12 +400,12 @@ public class SequenceAnnotationWSClient extends Jws2Client new SequenceAnnotationWSClient(fave, alignFrame, false); } - private static AAConsSettings createDefaultAAConsSettings() + private static AAConSettings createDefaultAAConSettings() { - return createDefaultAAConsSettings(null); + return createDefaultAAConSettings(null); } - private static AAConsSettings createDefaultAAConsSettings( + private static AAConSettings createDefaultAAConSettings( Jws2Instance service) { if (service != null) @@ -410,7 +414,7 @@ public class SequenceAnnotationWSClient extends Jws2Client compbio.ws.client.Services.AAConWS.toString())) { Cache.log - .warn("Ignoring invalid preferred service for AACons calculations (service type was " + .warn("Ignoring invalid preferred service for AACon calculations (service type was " + service.serviceType + ")"); service = null; } @@ -427,30 +431,22 @@ public class SequenceAnnotationWSClient extends Jws2Client } if (service == null) { - // get the default service for AACons + // get the default service for AACon 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."); + throw new Error("No AACon service found."); } - return new AAConsSettings(true, service, null, null); + return new AAConSettings(true, service, null, null); } - private static void removeCurrentAAConsWorkerFor(AlignFrame alignFrame) + private static void removeCurrentAAConWorkerFor(AlignFrame alignFrame) { alignFrame.getViewport().getCalcManager() - .removeRegisteredWorkersOfClass(AAConsClient.class); - // AAConsClient.removeAAConsAnnotation(alignFrame.alignPanel); - + .removeRegisteredWorkersOfClass(AAConClient.class); } }