X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=187540c3138cb14df61c52c2f30031528861dab3;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=77ba3002bbade76666403cc7c4af9531271e85c9;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index 77ba300..187540c 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 2.8.2) - * Copyright (C) 2014 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. * @@ -21,7 +21,6 @@ package jalview.ws.jws2; import jalview.api.AlignCalcWorkerI; -import jalview.bin.Cache; import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.JvSwingUtils; @@ -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 @@ -88,7 +83,7 @@ public class SequenceAnnotationWSClient extends Jws2Client List clnts = alignFrame.getViewport() .getCalcManager().getRegisteredWorkersOfClass(clientClass); - JabawsAlignCalcWorker worker; + AbstractJabaCalcWorker worker; if (clnts == null || clnts.size() == 0) { if (!processParams(sh, editParams)) @@ -97,16 +92,16 @@ public class SequenceAnnotationWSClient extends Jws2Client } try { - worker = (JabawsAlignCalcWorker) (clientClass - .getConstructor(new Class[] - { Jws2Instance.class, AlignFrame.class, - WsParamSetI.class, List.class }) - .newInstance(new Object[] - { sh, alignFrame, this.preset, paramset })); + 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("Implementation error", x); + throw new Error( + MessageManager.getString("error.implementation_error"), x); } alignFrame.getViewport().getCalcManager().registerWorker(worker); alignFrame.getViewport().getCalcManager().startWorker(worker); @@ -114,7 +109,7 @@ public class SequenceAnnotationWSClient extends Jws2Client } else { - worker = (JabawsAlignCalcWorker) clnts.get(0); + worker = (AbstractJabaCalcWorker) clnts.get(0); if (editParams) { paramset = worker.getArguments(); @@ -176,8 +171,8 @@ public class SequenceAnnotationWSClient extends Jws2Client service.serviceType.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() { @@ -209,16 +204,20 @@ public class SequenceAnnotationWSClient extends Jws2Client 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() { public void actionPerformed(ActionEvent e) @@ -249,258 +248,11 @@ public class SequenceAnnotationWSClient extends Jws2Client Desktop.instance.showUrl(service.docUrl); } }); - annotservice.setToolTipText("" - + JvSwingUtils.wrapTooltip("View " + service.docUrl + "") - + ""); + annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.formatMessage("label.view_service_doc_url", + new String[] { service.docUrl, service.docUrl }))); wsmenu.add(annotservice); } } } - - private boolean registerAAConWSInstance(final JMenu wsmenu, - final Jws2Instance service, final AlignFrame alignFrame) - { - final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; // - // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString()); - if (aaui == null) - { - // not an instantaneous calculation GUI type service - return false; - } - // create the instaneous calculation GUI bits and update state if existing - // GUI elements already present - - JCheckBoxMenuItem _aaConEnabled = null; - for (int i = 0; i < wsmenu.getItemCount(); i++) - { - JMenuItem item = wsmenu.getItem(i); - if (item instanceof JCheckBoxMenuItem - && item.getText().equals(aaui.getAAconToggle())) - { - _aaConEnabled = (JCheckBoxMenuItem) item; - } - } - // is there an aaCon worker already present - if so, set it to use the - // given service handle - { - List aaconClient = alignFrame.getViewport() - .getCalcManager() - .getRegisteredWorkersOfClass(aaui.getClient()); - if (aaconClient != null && aaconClient.size() > 0) - { - JabawsAlignCalcWorker worker = (JabawsAlignCalcWorker) aaconClient - .get(0); - if (!worker.service.hosturl.equals(service.hosturl)) - { - // javax.swing.SwingUtilities.invokeLater(new Runnable() - { - // @Override - // public void run() - { - removeCurrentAAConWorkerFor(aaui, alignFrame); - buildCurrentAAConWorkerFor(aaui, alignFrame, service); - } - }// ); - } - } - } - - // is there a service already registered ? there shouldn't be if we are - // being called correctly - if (_aaConEnabled == null) - { - final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem( - aaui.getAAconToggle()); - - aaConEnabled.setToolTipText("

" - + JvSwingUtils.wrapTooltip(aaui.getAAconToggleTooltip() - + "

") + ""); - aaConEnabled.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent arg0) - { - List aaconClient = alignFrame.getViewport() - .getCalcManager() - .getRegisteredWorkersOfClass(aaui.getClient()); - if (aaconClient != null && aaconClient.size() > 0) - { - removeCurrentAAConWorkerFor(aaui, alignFrame); - } - else - { - buildCurrentAAConWorkerFor(aaui, alignFrame); - - } - } - - }); - wsmenu.add(aaConEnabled); - final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings()); - modifyParams.setToolTipText("

" - + JvSwingUtils.wrapTooltip(aaui.getAAeditSettingsTooltip() - + "

") + ""); - modifyParams.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent arg0) - { - showAAConAnnotationSettingsFor(aaui, alignFrame); - } - }); - wsmenu.add(modifyParams); - wsmenu.addMenuListener(new MenuListener() - { - - @Override - public void menuSelected(MenuEvent arg0) - { - // TODO: refactor to the implementing class. - if (alignFrame.getViewport().getAlignment().isNucleotide() ? aaui - .isNa() : aaui.isPr()) - { - aaConEnabled.setEnabled(true); - modifyParams.setEnabled(true); - } - else - { - aaConEnabled.setEnabled(false); - modifyParams.setEnabled(false); - } - List aaconClient = alignFrame.getViewport() - .getCalcManager() - .getRegisteredWorkersOfClass(aaui.getClient()); - if (aaconClient != null && aaconClient.size() > 0) - { - aaConEnabled.setSelected(true); - } - else - { - aaConEnabled.setSelected(false); - } - } - - @Override - public void menuDeselected(MenuEvent arg0) - { - // TODO Auto-generated method stub - - } - - @Override - public void menuCanceled(MenuEvent arg0) - { - // TODO Auto-generated method stub - - } - }); - - } - return true; - } - - private static void showAAConAnnotationSettingsFor( - final AlignAnalysisUIText aaui, AlignFrame alignFrame) - { - /* - * 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 - AAConSettings fave = (AAConSettings) alignFrame.getViewport() - .getCalcIdSettingsFor(aaui.getCalcId()); - if (fave == null) - { - fave = createDefaultAAConSettings(aaui); - } - new SequenceAnnotationWSClient(fave, alignFrame, true); - - } - - private static void buildCurrentAAConWorkerFor( - final AlignAnalysisUIText aaui, AlignFrame alignFrame) - { - buildCurrentAAConWorkerFor(aaui, alignFrame, null); - } - - private static void buildCurrentAAConWorkerFor( - final AlignAnalysisUIText aaui, AlignFrame alignFrame, - Jws2Instance service) - { - /* - * preferred settings Whether AACon is automatically recalculated Which - * AACon server to use What parameters to use - */ - AAConSettings fave = (AAConSettings) alignFrame.getViewport() - .getCalcIdSettingsFor(aaui.getCalcId()); - if (fave == null) - { - fave = createDefaultAAConSettings(aaui, service); - } - else - { - if (service != null - && !fave.getService().hosturl.equals(service.hosturl)) - { - Cache.log.debug("Changing AACon service to " + service.hosturl - + " from " + fave.getService().hosturl); - fave.setService(service); - } - } - new SequenceAnnotationWSClient(fave, alignFrame, false); - } - - private static AAConSettings createDefaultAAConSettings( - AlignAnalysisUIText aaui) - { - return createDefaultAAConSettings(aaui, null); - } - - private static AAConSettings createDefaultAAConSettings( - AlignAnalysisUIText aaui, Jws2Instance service) - { - if (service != null) - { - if (!service.serviceType.toString().equals( - compbio.ws.client.Services.AAConWS.toString())) - { - Cache.log - .warn("Ignoring invalid preferred service for AACon 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 AACon - service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null, - aaui.getServiceType()); - } - if (service == null) - { - // TODO raise dialog box explaining error, and/or open the JABA - // preferences menu. - throw new Error("No AACon service found."); - } - return new AAConSettings(true, service, null, null); - } - - private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui, - AlignFrame alignFrame) - { - alignFrame.getViewport().getCalcManager() - .removeRegisteredWorkersOfClass(aaui.getClient()); - } }