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 // reinstate worker if it was blacklisted (might have happened due to
104 // invalid parameters)
105 alignFrame.getViewport().getCalcManager().workerMayRun(worker);
106 worker.updateParameters(this.preset, paramset);
110 if (sh.action.toLowerCase().contains("disorder"))
112 // build IUPred style client. take sequences, returns annotation per
114 if (!processParams(sh, editParams))
123 new AADisorderClient(sh, alignFrame, preset, paramset));
128 public SequenceAnnotationWSClient(AAConsSettings fave,
129 AlignFrame alignFrame, boolean b)
131 super(alignFrame, fave.getPreset(), fave.getJobArgset());
132 initSequenceAnnotationWSClient(fave.getService(), alignFrame, fave.getPreset(), b);
138 * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
139 * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
141 public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
142 final AlignFrame alignFrame)
144 if (service.serviceType.equals(compbio.ws.client.Services.AAConWS
147 registerAAConsWSInstance(wsmenu, service, alignFrame);
150 boolean hasparams = service.hasParameters();
151 // Assume name ends in WS
152 String calcName = service.serviceType.substring(0,
153 service.serviceType.length() - 2);
155 JMenuItem aacons = new JMenuItem(calcName + " Defaults");
156 aacons.addActionListener(new ActionListener()
160 public void actionPerformed(ActionEvent e)
162 new SequenceAnnotationWSClient(service, alignFrame, null, false);
168 // only add these menu options if the service has user-modifiable
170 aacons = new JMenuItem("Edit settings and run ...");
171 aacons.setToolTipText("View and change parameters before running calculation");
173 aacons.addActionListener(new ActionListener()
175 public void actionPerformed(ActionEvent e)
177 new SequenceAnnotationWSClient(service, alignFrame, null, true);
181 List<WsParamSetI> presets = service.getParamStore().getPresets();
182 if (presets != null && presets.size() > 0)
184 JMenu presetlist = new JMenu("Run " + calcName + "with preset");
186 for (final WsParamSetI preset : presets)
188 final JMenuItem methodR = new JMenuItem(preset.getName());
189 methodR.setToolTipText("<html><p>"
190 + JvSwingUtils.wrapTooltip("<strong>"
191 + (preset.isModifiable() ? "User Preset"
192 : "Service Preset") + "</strong><br/>"
193 + preset.getDescription() + "</p>") + "</html>");
194 methodR.addActionListener(new ActionListener()
196 public void actionPerformed(ActionEvent e)
198 new SequenceAnnotationWSClient(service, alignFrame, preset,
203 presetlist.add(methodR);
205 wsmenu.add(presetlist);
211 private final String AAconsToggle = "AACons Calculations",
212 AAconsToggleTooltip = "When checked, AACons calculations are updated automatically.",
213 AAeditSettings = "Change AACons Settings...",
214 AAeditSettingsTooltip = "Modify settings for AACons calculations.";
216 private SequenceAnnotationWSClient preferredAAConsClient = null;
218 // private final enableAAConsCalculation(final AlignFrame alignFrame, )
219 private void registerAAConsWSInstance(final JMenu wsmenu,
220 final Jws2Instance service, final AlignFrame alignFrame)
222 // register this in the AACons settings set
223 JCheckBoxMenuItem _aaConsEnabled = null;
224 for (int i = 0; i < wsmenu.getItemCount(); i++)
226 JMenuItem item = wsmenu.getItem(i);
227 if (item instanceof JCheckBoxMenuItem
228 && item.getText().equals(AAconsToggle))
230 _aaConsEnabled = (JCheckBoxMenuItem) item;
234 // is there a service already registered ?
235 if (_aaConsEnabled == null)
237 final JCheckBoxMenuItem aaConsEnabled = new JCheckBoxMenuItem(
239 wsmenu.addMenuListener(new MenuListener()
243 public void menuSelected(MenuEvent arg0)
245 wsmenu.setEnabled(!alignFrame.getViewport().getAlignment()
247 List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
249 .getRegisteredWorkersOfClass(AAConsClient.class);
250 if (aaconsClient != null && aaconsClient.size() > 0)
252 aaConsEnabled.setSelected(true);
256 aaConsEnabled.setSelected(false);
261 public void menuDeselected(MenuEvent arg0)
263 // TODO Auto-generated method stub
268 public void menuCanceled(MenuEvent arg0)
270 // TODO Auto-generated method stub
274 aaConsEnabled.setToolTipText("<html><p>"
275 + JvSwingUtils.wrapTooltip(AAconsToggleTooltip + "</p>")
277 aaConsEnabled.addActionListener(new ActionListener()
280 public void actionPerformed(ActionEvent arg0)
282 // aaConsEnabled.setSelected(!aaConsEnabled.isSelected());
283 List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
285 .getRegisteredWorkersOfClass(AAConsClient.class);
286 if (aaconsClient != null && aaconsClient.size() > 0)
288 removeCurrentAAConsWorkerFor(alignFrame);
292 buildCurrentAAConsWorkerFor(alignFrame);
298 wsmenu.add(aaConsEnabled);
299 JMenuItem modifyParams = new JMenuItem(AAeditSettings);
300 modifyParams.setToolTipText("<html><p>"
301 + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "</p>")
303 modifyParams.addActionListener(new ActionListener()
307 public void actionPerformed(ActionEvent arg0)
309 showAAConsAnnotationSettingsFor(alignFrame);
312 wsmenu.add(modifyParams);
318 private static void showAAConsAnnotationSettingsFor(AlignFrame alignFrame)
322 * Whether AACons is automatically recalculated
323 * Which AACons server to use
324 * What parameters to use
326 // could actually do a class search for this too
327 AAConsSettings fave= (AAConsSettings) alignFrame.getViewport().getCalcIdSettingsFor(AAConsCalcId);
330 fave = createDefaultAAConsSettings();
332 new SequenceAnnotationWSClient(fave, alignFrame, true);
335 private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame)
339 * Whether AACons is automatically recalculated
340 * Which AACons server to use
341 * What parameters to use
343 AAConsSettings fave= (AAConsSettings) alignFrame.getViewport().getCalcIdSettingsFor(AAConsCalcId);
346 fave = createDefaultAAConsSettings();
348 new SequenceAnnotationWSClient(fave, alignFrame, false);
351 private static AAConsSettings createDefaultAAConsSettings()
353 Jws2Instance service=null;
354 // set sensible defaults
355 for (Jws2Instance sv: Jws2Discoverer.getDiscoverer().getServices()) {
356 if (sv.serviceType.toString().equals(compbio.ws.client.Services.AAConWS.toString()))
364 // TODO raise dialog box explaining error, and/or open the JABA preferences menu.
365 throw new Error("No AACons service found.");
367 return new AAConsSettings(true, service, null, null);
370 private static void removeCurrentAAConsWorkerFor(AlignFrame alignFrame)
372 alignFrame.getViewport().getCalcManager()
373 .removeRegisteredWorkersOfClass(AAConsClient.class);
374 // AAConsClient.removeAAConsAnnotation(alignFrame.alignPanel);