4 package jalview.ws.jws2;
6 import java.awt.event.ActionEvent;
7 import java.awt.event.ActionListener;
10 import javax.swing.JCheckBoxMenuItem;
11 import javax.swing.JMenu;
12 import javax.swing.JMenuItem;
13 import javax.swing.JOptionPane;
14 import javax.swing.event.AncestorEvent;
15 import javax.swing.event.AncestorListener;
16 import javax.swing.event.MenuEvent;
17 import javax.swing.event.MenuListener;
19 import compbio.metadata.Argument;
21 import jalview.api.AlignCalcWorkerI;
22 import jalview.datamodel.AlignmentView;
23 import jalview.gui.AlignFrame;
24 import jalview.gui.Desktop;
25 import jalview.gui.JalviewDialog;
26 import jalview.gui.JvSwingUtils;
27 import jalview.ws.jws2.dm.AAConsSettings;
28 import jalview.ws.jws2.jabaws2.Jws2Instance;
29 import jalview.ws.params.WsParamSetI;
35 public class SequenceAnnotationWSClient extends Jws2Client
38 public static final String AAConsCalcId = "jabaws2.AACons";
41 * initialise a client so its attachWSMenuEntry method can be called.
43 public SequenceAnnotationWSClient()
45 // TODO Auto-generated constructor stub
48 public SequenceAnnotationWSClient(final Jws2Instance sh,
49 AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
51 super(alignFrame, preset, null);
52 initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
55 public void initSequenceAnnotationWSClient(final Jws2Instance sh,
56 AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
58 if (alignFrame.getViewport().getAlignment().isNucleotide())
60 JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
61 + " can only be used\nfor amino acid alignments.",
62 "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
66 if (sh.action.toLowerCase().contains("conservation"))
68 // Build an AACons style client - take alignment, return annotation for
71 List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
73 .getRegisteredWorkersOfClass(AAConsClient.class);
74 if (clnts == null || clnts.size() == 0)
76 if (!processParams(sh, editParams))
85 worker = new AAConsClient(sh, alignFrame, this.preset,
87 alignFrame.getViewport().getCalcManager().startWorker(worker);
92 AAConsClient worker = (AAConsClient) clnts.get(0);
95 paramset = worker.getArguments();
96 preset = worker.getPreset();
99 if (!processParams(sh, editParams, true))
103 alignFrame.getViewport().setPreferredAAConsSettings(new AAConsSettings(true, sh, preset, paramset));
104 // reinstate worker if it was blacklisted (might have happened due to
105 // invalid parameters)
106 alignFrame.getViewport().getCalcManager().workerMayRun(worker);
107 worker.updateParameters(preset, paramset);
111 if (sh.action.toLowerCase().contains("disorder"))
113 // build IUPred style client. take sequences, returns annotation per
115 if (!processParams(sh, editParams))
124 new AADisorderClient(sh, alignFrame, preset, paramset));
129 public SequenceAnnotationWSClient(AAConsSettings fave,
130 AlignFrame alignFrame, boolean b)
132 super(alignFrame, fave.getPreset(), fave.getJobArgset());
133 initSequenceAnnotationWSClient(fave.getService(), alignFrame, fave.getPreset(), b);
139 * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
140 * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
142 public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
143 final AlignFrame alignFrame)
145 if (service.serviceType.equals(compbio.ws.client.Services.AAConWS
148 registerAAConsWSInstance(wsmenu, service, alignFrame);
151 boolean hasparams = service.hasParameters();
152 // Assume name ends in WS
153 String calcName = service.serviceType.substring(0,
154 service.serviceType.length() - 2);
156 JMenuItem aacons = new JMenuItem(calcName + " Defaults");
157 aacons.addActionListener(new ActionListener()
161 public void actionPerformed(ActionEvent e)
163 new SequenceAnnotationWSClient(service, alignFrame, null, false);
169 // only add these menu options if the service has user-modifiable
171 aacons = new JMenuItem("Edit settings and run ...");
172 aacons.setToolTipText("View and change parameters before running calculation");
174 aacons.addActionListener(new ActionListener()
176 public void actionPerformed(ActionEvent e)
178 new SequenceAnnotationWSClient(service, alignFrame, null, true);
182 List<WsParamSetI> presets = service.getParamStore().getPresets();
183 if (presets != null && presets.size() > 0)
185 JMenu presetlist = new JMenu("Run " + calcName + "with preset");
187 for (final WsParamSetI preset : presets)
189 final JMenuItem methodR = new JMenuItem(preset.getName());
190 methodR.setToolTipText("<html><p>"
191 + JvSwingUtils.wrapTooltip("<strong>"
192 + (preset.isModifiable() ? "User Preset"
193 : "Service Preset") + "</strong><br/>"
194 + preset.getDescription() + "</p>") + "</html>");
195 methodR.addActionListener(new ActionListener()
197 public void actionPerformed(ActionEvent e)
199 new SequenceAnnotationWSClient(service, alignFrame, preset,
204 presetlist.add(methodR);
206 wsmenu.add(presetlist);
212 private final String AAconsToggle = "AACons Calculations",
213 AAconsToggleTooltip = "When checked, AACons calculations are updated automatically.",
214 AAeditSettings = "Change AACons Settings...",
215 AAeditSettingsTooltip = "Modify settings for AACons calculations.";
217 private SequenceAnnotationWSClient preferredAAConsClient = null;
219 // private final enableAAConsCalculation(final AlignFrame alignFrame, )
220 private void registerAAConsWSInstance(final JMenu wsmenu,
221 final Jws2Instance service, final AlignFrame alignFrame)
223 // register this in the AACons settings set
224 JCheckBoxMenuItem _aaConsEnabled = null;
225 for (int i = 0; i < wsmenu.getItemCount(); i++)
227 JMenuItem item = wsmenu.getItem(i);
228 if (item instanceof JCheckBoxMenuItem
229 && item.getText().equals(AAconsToggle))
231 _aaConsEnabled = (JCheckBoxMenuItem) item;
235 // is there a service already registered ?
236 if (_aaConsEnabled == null)
238 final JCheckBoxMenuItem aaConsEnabled = new JCheckBoxMenuItem(
240 wsmenu.addMenuListener(new MenuListener()
244 public void menuSelected(MenuEvent arg0)
246 wsmenu.setEnabled(!alignFrame.getViewport().getAlignment()
248 List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
250 .getRegisteredWorkersOfClass(AAConsClient.class);
251 if (aaconsClient != null && aaconsClient.size() > 0)
253 aaConsEnabled.setSelected(true);
257 aaConsEnabled.setSelected(false);
262 public void menuDeselected(MenuEvent arg0)
264 // TODO Auto-generated method stub
269 public void menuCanceled(MenuEvent arg0)
271 // TODO Auto-generated method stub
275 aaConsEnabled.setToolTipText("<html><p>"
276 + JvSwingUtils.wrapTooltip(AAconsToggleTooltip + "</p>")
278 aaConsEnabled.addActionListener(new ActionListener()
281 public void actionPerformed(ActionEvent arg0)
283 // aaConsEnabled.setSelected(!aaConsEnabled.isSelected());
284 List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
286 .getRegisteredWorkersOfClass(AAConsClient.class);
287 if (aaconsClient != null && aaconsClient.size() > 0)
289 removeCurrentAAConsWorkerFor(alignFrame);
293 buildCurrentAAConsWorkerFor(alignFrame);
299 wsmenu.add(aaConsEnabled);
300 JMenuItem modifyParams = new JMenuItem(AAeditSettings);
301 modifyParams.setToolTipText("<html><p>"
302 + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "</p>")
304 modifyParams.addActionListener(new ActionListener()
308 public void actionPerformed(ActionEvent arg0)
310 showAAConsAnnotationSettingsFor(alignFrame);
313 wsmenu.add(modifyParams);
319 private static void showAAConsAnnotationSettingsFor(AlignFrame alignFrame)
323 * Whether AACons is automatically recalculated
324 * Which AACons server to use
325 * What parameters to use
327 // could actually do a class search for this too
328 AAConsSettings fave= (AAConsSettings) alignFrame.getViewport().getCalcIdSettingsFor(AAConsCalcId);
331 fave = createDefaultAAConsSettings();
333 new SequenceAnnotationWSClient(fave, alignFrame, true);
336 private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame)
340 * Whether AACons is automatically recalculated
341 * Which AACons server to use
342 * What parameters to use
344 AAConsSettings fave= (AAConsSettings) alignFrame.getViewport().getCalcIdSettingsFor(AAConsCalcId);
347 fave = createDefaultAAConsSettings();
349 new SequenceAnnotationWSClient(fave, alignFrame, false);
352 private static AAConsSettings createDefaultAAConsSettings()
354 Jws2Instance service=null;
355 // set sensible defaults
356 for (Jws2Instance sv: Jws2Discoverer.getDiscoverer().getServices()) {
357 if (sv.serviceType.toString().equals(compbio.ws.client.Services.AAConWS.toString()))
365 // TODO raise dialog box explaining error, and/or open the JABA preferences menu.
366 throw new Error("No AACons service found.");
368 return new AAConsSettings(true, service, null, null);
371 private static void removeCurrentAAConsWorkerFor(AlignFrame alignFrame)
373 alignFrame.getViewport().getCalcManager()
374 .removeRegisteredWorkersOfClass(AAConsClient.class);
375 // AAConsClient.removeAAConsAnnotation(alignFrame.alignPanel);