Coverage Report
File Jws2ClientFactory.java
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52% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| Jws2ClientFactory | 26 | 71 | 37 |
Contributing tests
This file is covered by 134 tests.
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Source view
| 1 | package jalview.ws.jws2; | |
| 2 | ||
| 3 | import jalview.api.AlignCalcManagerI2; | |
| 4 | import jalview.api.AlignCalcWorkerI; | |
| 5 | import jalview.bin.Cache; | |
| 6 | import jalview.bin.Console; | |
| 7 | import jalview.gui.AlignFrame; | |
| 8 | import jalview.gui.JvSwingUtils; | |
| 9 | import jalview.util.MessageManager; | |
| 10 | import jalview.ws.api.ServiceWithParameters; | |
| 11 | import jalview.ws.jws2.dm.AAConSettings; | |
| 12 | import jalview.ws.jws2.jabaws2.Jws2Instance; | |
| 13 | import jalview.ws.params.AutoCalcSetting; | |
| 14 | import jalview.ws.uimodel.AlignAnalysisUIText; | |
| 15 | ||
| 16 | import java.awt.event.ActionEvent; | |
| 17 | import java.awt.event.ActionListener; | |
| 18 | import java.util.List; | |
| 19 | ||
| 20 | import javax.swing.JCheckBoxMenuItem; | |
| 21 | import javax.swing.JMenu; | |
| 22 | import javax.swing.JMenuItem; | |
| 23 | import javax.swing.event.MenuEvent; | |
| 24 | import javax.swing.event.MenuListener; | |
| 25 | ||
| 26 | public class Jws2ClientFactory | |
| 27 | { | |
| 28 | 18167 |  static boolean registerAAConWSInstance(final JMenu wsmenu, |
| 29 | final ServiceWithParameters service, final AlignFrame alignFrame) | |
| 30 | { | |
| 31 | 18167 | final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null |
| 32 | // ; // | |
| 33 | // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString()); | |
| 34 | 18167 | if (aaui == null) |
| 35 | { | |
| 36 | // not an instantaneous calculation GUI type service | |
| 37 | 16284 | return false; |
| 38 | } | |
| 39 | // create the instaneous calculation GUI bits and update state if existing | |
| 40 | // GUI elements already present | |
| 41 | ||
| 42 | 1883 | JCheckBoxMenuItem _aaConEnabled = null; |
| 43 | 4722 | for (int i = 0; i < wsmenu.getItemCount(); i++) |
| 44 | { | |
| 45 | 2839 | JMenuItem item = wsmenu.getItem(i); |
| 46 | 2839 | if (item instanceof JCheckBoxMenuItem |
| 47 | && item.getText().equals(aaui.getAAconToggle())) | |
| 48 | { | |
| 49 | 0 | _aaConEnabled = (JCheckBoxMenuItem) item; |
| 50 | } | |
| 51 | } | |
| 52 | // is there an aaCon worker already present - if so, set it to use the | |
| 53 | // given service handle | |
| 54 | { | |
| 55 | 1883 | AlignCalcManagerI2 mger = alignFrame.getViewport() |
| 56 | .getCalcManager(); | |
| 57 | 1883 | if (mger != null) |
| 58 | { | |
| 59 | 1859 | List<AlignCalcWorkerI> aaconClient = mger |
| 60 | .getWorkersOfClass(aaui.getClient()); | |
| 61 | 1859 | if (aaconClient != null && aaconClient.size() > 0) |
| 62 | { | |
| 63 | 0 | SeqAnnotationServiceCalcWorker worker = (SeqAnnotationServiceCalcWorker) aaconClient |
| 64 | .get(0); | |
| 65 | 0 | if (!worker.service.getHostURL().equals(service.getHostURL())) |
| 66 | { | |
| 67 | // javax.swing.SwingUtilities.invokeLater(new Runnable() | |
| 68 | { | |
| 69 | // @Override | |
| 70 | // public void run() | |
| 71 | { | |
| 72 | 0 | removeCurrentAAConWorkerFor(aaui, alignFrame); |
| 73 | 0 | buildCurrentAAConWorkerFor(aaui, alignFrame, service); |
| 74 | } | |
| 75 | } // ); | |
| 76 | } | |
| 77 | } | |
| 78 | } | |
| 79 | } | |
| 80 | ||
| 81 | // is there a service already registered ? there shouldn't be if we are | |
| 82 | // being called correctly | |
| 83 | 1883 | if (_aaConEnabled == null) |
| 84 | { | |
| 85 | 1883 | final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem( |
| 86 | aaui.getAAconToggle()); | |
| 87 | ||
| 88 | 1883 | aaConEnabled.setToolTipText( |
| 89 | JvSwingUtils.wrapTooltip(true, aaui.getAAconToggleTooltip())); | |
| 90 | 1883 | aaConEnabled.addActionListener(new ActionListener() |
| 91 | { | |
| 92 | 0 | @Override |
| 93 | public void actionPerformed(ActionEvent arg0) | |
| 94 | { | |
| 95 | ||
| 96 | 0 | List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport() |
| 97 | .getCalcManager() | |
| 98 | .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class); | |
| 99 | 0 | if (aaconClient != null) |
| 100 | { | |
| 101 | 0 | for (AlignCalcWorkerI worker : aaconClient) |
| 102 | { | |
| 103 | 0 | if (((SeqAnnotationServiceCalcWorker) worker).getService() |
| 104 | .getClass().equals(aaui.getClient())) | |
| 105 | { | |
| 106 | 0 | removeCurrentAAConWorkerFor(aaui, alignFrame); |
| 107 | 0 | return; |
| 108 | } | |
| 109 | } | |
| 110 | } | |
| 111 | 0 | buildCurrentAAConWorkerFor(aaui, alignFrame); |
| 112 | } | |
| 113 | ||
| 114 | }); | |
| 115 | 1883 | wsmenu.add(aaConEnabled); |
| 116 | 1883 | final JMenuItem modifyParams = new JMenuItem( |
| 117 | aaui.getAAeditSettings()); | |
| 118 | 1883 | modifyParams.setToolTipText(JvSwingUtils.wrapTooltip(true, |
| 119 | aaui.getAAeditSettingsTooltip())); | |
| 120 | 1883 | modifyParams.addActionListener(new ActionListener() |
| 121 | { | |
| 122 | ||
| 123 | 0 | @Override |
| 124 | public void actionPerformed(ActionEvent arg0) | |
| 125 | { | |
| 126 | 0 | showAAConAnnotationSettingsFor(aaui, alignFrame); |
| 127 | } | |
| 128 | }); | |
| 129 | 1883 | wsmenu.add(modifyParams); |
| 130 | 1883 | wsmenu.addMenuListener(new MenuListener() |
| 131 | { | |
| 132 | ||
| 133 | 0 | @Override |
| 134 | public void menuSelected(MenuEvent arg0) | |
| 135 | { | |
| 136 | // TODO: refactor to the implementing class. | |
| 137 | 0 | if (alignFrame.getViewport().getAlignment().isNucleotide() |
| 138 | ? aaui.isNa() | |
| 139 | : aaui.isPr()) | |
| 140 | { | |
| 141 | 0 | aaConEnabled.setEnabled(true); |
| 142 | 0 | modifyParams.setEnabled(true); |
| 143 | } | |
| 144 | else | |
| 145 | { | |
| 146 | 0 | aaConEnabled.setEnabled(false); |
| 147 | 0 | modifyParams.setEnabled(false); |
| 148 | 0 | return; |
| 149 | } | |
| 150 | 0 | List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport() |
| 151 | .getCalcManager() | |
| 152 | .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class); | |
| 153 | ||
| 154 | 0 | boolean serviceEnabled = false; |
| 155 | 0 | if (aaconClient != null) |
| 156 | { | |
| 157 | // NB code duplicatino again! | |
| 158 | 0 | for (AlignCalcWorkerI _worker : aaconClient) |
| 159 | { | |
| 160 | 0 | SeqAnnotationServiceCalcWorker worker = (SeqAnnotationServiceCalcWorker) _worker; |
| 161 | // this could be cleaner ? | |
| 162 | 0 | if (worker.hasService() |
| 163 | && aaui.getClient() | |
| 164 | .equals(worker.getService().getClass())) | |
| 165 | { | |
| 166 | 0 | serviceEnabled = true; |
| 167 | } | |
| 168 | } | |
| 169 | } | |
| 170 | 0 | aaConEnabled.setSelected(serviceEnabled); |
| 171 | } | |
| 172 | ||
| 173 | 0 | @Override |
| 174 | public void menuDeselected(MenuEvent arg0) | |
| 175 | { | |
| 176 | // TODO Auto-generated method stub | |
| 177 | ||
| 178 | } | |
| 179 | ||
| 180 | 0 | @Override |
| 181 | public void menuCanceled(MenuEvent arg0) | |
| 182 | { | |
| 183 | // TODO Auto-generated method stub | |
| 184 | ||
| 185 | } | |
| 186 | }); | |
| 187 | ||
| 188 | } | |
| 189 | 1883 | return true; |
| 190 | } | |
| 191 | ||
| 192 | 0 | private static void showAAConAnnotationSettingsFor( |
| 193 | final AlignAnalysisUIText aaui, AlignFrame alignFrame) | |
| 194 | { | |
| 195 | /* | |
| 196 | * preferred settings Whether AACon is automatically recalculated Which | |
| 197 | * AACon server to use What parameters to use | |
| 198 | */ | |
| 199 | // could actually do a class search for this too | |
| 200 | 0 | AutoCalcSetting fave = alignFrame.getViewport() |
| 201 | .getCalcIdSettingsFor(aaui.getCalcId()); | |
| 202 | 0 | if (fave == null) |
| 203 | { | |
| 204 | 0 | fave = createDefaultAAConSettings(aaui); |
| 205 | } | |
| 206 | 0 | new SequenceAnnotationWSClient(fave, alignFrame, true); |
| 207 | ||
| 208 | } | |
| 209 | ||
| 210 | 0 | private static void buildCurrentAAConWorkerFor( |
| 211 | final AlignAnalysisUIText aaui, AlignFrame alignFrame) | |
| 212 | { | |
| 213 | 0 | buildCurrentAAConWorkerFor(aaui, alignFrame, null); |
| 214 | } | |
| 215 | ||
| 216 | 0 | private static void buildCurrentAAConWorkerFor( |
| 217 | final AlignAnalysisUIText aaui, AlignFrame alignFrame, | |
| 218 | ServiceWithParameters service) | |
| 219 | { | |
| 220 | /* | |
| 221 | * preferred settings Whether AACon is automatically recalculated Which | |
| 222 | * AACon server to use What parameters to use | |
| 223 | */ | |
| 224 | 0 | AutoCalcSetting fave = alignFrame.getViewport() |
| 225 | .getCalcIdSettingsFor(aaui.getCalcId()); | |
| 226 | 0 | if (fave == null) |
| 227 | { | |
| 228 | 0 | fave = createDefaultAAConSettings(aaui, service); |
| 229 | } | |
| 230 | else | |
| 231 | { | |
| 232 | 0 | if (service != null && !fave.getService().getHostURL() |
| 233 | .equals(service.getHostURL())) | |
| 234 | { | |
| 235 | 0 | Console.debug("Changing AACon service to " + service.getHostURL() |
| 236 | + " from " + fave.getService().getHostURL()); | |
| 237 | 0 | fave.setService(service); |
| 238 | } | |
| 239 | } | |
| 240 | 0 | new SequenceAnnotationWSClient(fave, alignFrame, false); |
| 241 | } | |
| 242 | ||
| 243 | 0 | private static AutoCalcSetting createDefaultAAConSettings( |
| 244 | AlignAnalysisUIText aaui) | |
| 245 | { | |
| 246 | 0 | return createDefaultAAConSettings(aaui, null); |
| 247 | } | |
| 248 | ||
| 249 | 0 | private static AutoCalcSetting createDefaultAAConSettings( |
| 250 | AlignAnalysisUIText aaui, ServiceWithParameters service) | |
| 251 | { | |
| 252 | 0 | if (service != null) |
| 253 | { | |
| 254 | // if (!service.getServiceType() | |
| 255 | // .equals(compbio.ws.client.Services.AAConWS.toString())) | |
| 256 | // { | |
| 257 | // Console.warn( | |
| 258 | // "Ignoring invalid preferred service for AACon calculations (service | |
| 259 | // type was " | |
| 260 | // + service.getServiceType() + ")"); | |
| 261 | // service = null; | |
| 262 | // } | |
| 263 | // else | |
| 264 | { | |
| 265 | // check service is actually in the list of currently avaialable | |
| 266 | // services | |
| 267 | 0 | if (!PreferredServiceRegistry.getRegistry().contains(service)) |
| 268 | { | |
| 269 | // it isn't .. | |
| 270 | 0 | service = null; |
| 271 | } | |
| 272 | } | |
| 273 | } | |
| 274 | 0 | if (service == null) |
| 275 | { | |
| 276 | // get the default service for AACon | |
| 277 | 0 | service = PreferredServiceRegistry.getRegistry().getPreferredServiceFor(null, |
| 278 | aaui.getServiceType()); | |
| 279 | } | |
| 280 | 0 | if (service == null) |
| 281 | { | |
| 282 | // TODO raise dialog box explaining error, and/or open the JABA | |
| 283 | // preferences menu. | |
| 284 | 0 | throw new Error( |
| 285 | MessageManager.getString("error.no_aacon_service_found")); | |
| 286 | } | |
| 287 | 0 | return service instanceof Jws2Instance |
| 288 | ? new AAConSettings(true, service, null, null) | |
| 289 | : new AutoCalcSetting(service, null, null, true); | |
| 290 | } | |
| 291 | ||
| 292 | 0 | private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui, |
| 293 | AlignFrame alignFrame) | |
| 294 | { | |
| 295 | 0 | alignFrame.getViewport().getCalcManager() |
| 296 | .removeWorkersOfClass(aaui.getClient()); | |
| 297 | } | |
| 298 | } |