Coverage Report
File SequenceAnnotationWSClient.java
Coverage histogram
52% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| SequenceAnnotationWSClient | 46 | 60 | 24 |
Contributing tests
This file is covered by 18 tests.
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| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 7 | * Jalview is free software: you can redistribute it and/or | |
| 8 | * modify it under the terms of the GNU General Public License | |
| 9 | * as published by the Free Software Foundation, either version 3 | |
| 10 | * of the License, or (at your option) any later version. | |
| 11 | * | |
| 12 | * Jalview is distributed in the hope that it will be useful, but | |
| 13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
| 14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
| 15 | * PURPOSE. See the GNU General Public License for more details. | |
| 16 | * | |
| 17 | * You should have received a copy of the GNU General Public License | |
| 18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
| 19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
| 20 | */ | |
| 21 | package jalview.ws.jws2; | |
| 22 | ||
| 23 | import java.util.Locale; | |
| 24 | ||
| 25 | import jalview.api.AlignCalcWorkerI; | |
| 26 | import jalview.gui.AlignFrame; | |
| 27 | import jalview.gui.Desktop; | |
| 28 | import jalview.gui.JvSwingUtils; | |
| 29 | import jalview.util.MessageManager; | |
| 30 | import jalview.ws.jws2.dm.AAConSettings; | |
| 31 | import jalview.ws.jws2.jabaws2.Jws2Instance; | |
| 32 | import jalview.ws.params.WsParamSetI; | |
| 33 | import jalview.ws.uimodel.AlignAnalysisUIText; | |
| 34 | ||
| 35 | import java.awt.event.ActionEvent; | |
| 36 | import java.awt.event.ActionListener; | |
| 37 | import java.util.List; | |
| 38 | ||
| 39 | import javax.swing.JMenu; | |
| 40 | import javax.swing.JMenuItem; | |
| 41 | ||
| 42 | /** | |
| 43 | * @author jprocter | |
| 44 | * | |
| 45 | */ | |
| 46 | public class SequenceAnnotationWSClient extends Jws2Client | |
| 47 | { | |
| 48 | /** | |
| 49 | * initialise a client so its attachWSMenuEntry method can be called. | |
| 50 | */ | |
| 51 | 153 |  public SequenceAnnotationWSClient() |
| 52 | { | |
| 53 | // TODO Auto-generated constructor stub | |
| 54 | } | |
| 55 | ||
| 56 | 0 | public SequenceAnnotationWSClient(final Jws2Instance sh, |
| 57 | AlignFrame alignFrame, WsParamSetI preset, boolean editParams) | |
| 58 | { | |
| 59 | 0 | super(alignFrame, preset, null); |
| 60 | 0 | initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams); |
| 61 | } | |
| 62 | ||
| 63 | // dan think. Do I need to change this method to run RNAalifold through the | |
| 64 | // GUI | |
| 65 | ||
| 66 | 0 | public void initSequenceAnnotationWSClient(final Jws2Instance sh, |
| 67 | AlignFrame alignFrame, WsParamSetI preset, boolean editParams) | |
| 68 | { | |
| 69 | // dan changed! dan test. comment out if conditional | |
| 70 | // if (alignFrame.getViewport().getAlignment().isNucleotide()) | |
| 71 | // { | |
| 72 | // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType | |
| 73 | // + " can only be used\nfor amino acid alignments.", | |
| 74 | // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE); | |
| 75 | // return; | |
| 76 | // | |
| 77 | // } | |
| 78 | 0 | AlignAnalysisUIText aaui = sh.getAlignAnalysisUI(); |
| 79 | 0 | if (aaui != null) |
| 80 | { | |
| 81 | 0 | Class clientClass = aaui.getClient(); |
| 82 | ||
| 83 | // Build an AACon style client - take alignment, return annotation for | |
| 84 | // columns | |
| 85 | ||
| 86 | 0 | List<AlignCalcWorkerI> clnts = alignFrame.getViewport() |
| 87 | .getCalcManager().getRegisteredWorkersOfClass(clientClass); | |
| 88 | 0 | AbstractJabaCalcWorker worker; |
| 89 | 0 | if (clnts == null || clnts.size() == 0) |
| 90 | { | |
| 91 | 0 | if (!processParams(sh, editParams)) |
| 92 | { | |
| 93 | 0 | return; |
| 94 | } | |
| 95 | 0 | try |
| 96 | { | |
| 97 | 0 | worker = (AbstractJabaCalcWorker) (clientClass |
| 98 | .getConstructor(new Class[] | |
| 99 | { Jws2Instance.class, AlignFrame.class, WsParamSetI.class, | |
| 100 | List.class }) | |
| 101 | .newInstance(new Object[] | |
| 102 | { sh, alignFrame, this.preset, paramset })); | |
| 103 | } catch (Exception x) | |
| 104 | { | |
| 105 | 0 | x.printStackTrace(); |
| 106 | 0 | throw new Error( |
| 107 | MessageManager.getString("error.implementation_error"), | |
| 108 | x); | |
| 109 | } | |
| 110 | 0 | alignFrame.getViewport().getCalcManager().registerWorker(worker); |
| 111 | 0 | alignFrame.getViewport().getCalcManager().startWorker(worker); |
| 112 | ||
| 113 | } | |
| 114 | else | |
| 115 | { | |
| 116 | 0 | worker = (AbstractJabaCalcWorker) clnts.get(0); |
| 117 | 0 | if (editParams) |
| 118 | { | |
| 119 | 0 | paramset = worker.getArguments(); |
| 120 | 0 | preset = worker.getPreset(); |
| 121 | } | |
| 122 | ||
| 123 | 0 | if (!processParams(sh, editParams, true)) |
| 124 | { | |
| 125 | 0 | return; |
| 126 | } | |
| 127 | // reinstate worker if it was blacklisted (might have happened due to | |
| 128 | // invalid parameters) | |
| 129 | 0 | alignFrame.getViewport().getCalcManager().enableWorker(worker); |
| 130 | 0 | worker.updateParameters(this.preset, paramset); |
| 131 | } | |
| 132 | } | |
| 133 | 0 | if (sh.action.toLowerCase(Locale.ROOT).contains("disorder")) |
| 134 | { | |
| 135 | // build IUPred style client. take sequences, returns annotation per | |
| 136 | // sequence. | |
| 137 | 0 | if (!processParams(sh, editParams)) |
| 138 | { | |
| 139 | 0 | return; |
| 140 | } | |
| 141 | ||
| 142 | 0 | alignFrame.getViewport().getCalcManager().startWorker( |
| 143 | new AADisorderClient(sh, alignFrame, preset, paramset)); | |
| 144 | } | |
| 145 | } | |
| 146 | ||
| 147 | 0 | public SequenceAnnotationWSClient(AAConSettings fave, |
| 148 | AlignFrame alignFrame, boolean b) | |
| 149 | { | |
| 150 | 0 | super(alignFrame, fave.getPreset(), fave.getJobArgset()); |
| 151 | 0 | initSequenceAnnotationWSClient(fave.getService(), alignFrame, |
| 152 | fave.getPreset(), b); | |
| 153 | } | |
| 154 | ||
| 155 | /* | |
| 156 | * (non-Javadoc) | |
| 157 | * | |
| 158 | * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu, | |
| 159 | * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame) | |
| 160 | */ | |
| 161 | 153 | public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service, |
| 162 | final AlignFrame alignFrame) | |
| 163 | { | |
| 164 | 149 | if (registerAAConWSInstance(wsmenu, service, alignFrame)) |
| 165 | { | |
| 166 | // Alignment dependent analysis calculation WS gui | |
| 167 | 53 | return; |
| 168 | } | |
| 169 | 96 | boolean hasparams = service.hasParameters(); |
| 170 | // Assume name ends in WS | |
| 171 | 96 | String calcName = service.serviceType.substring(0, |
| 172 | service.serviceType.length() - 2); | |
| 173 | ||
| 174 | 96 | JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage( |
| 175 | "label.calcname_with_default_settings", new String[] | |
| 176 | { calcName })); | |
| 177 | 96 | annotservice.addActionListener(new ActionListener() |
| 178 | { | |
| 179 | ||
| 180 | 0 | @Override |
| 181 | public void actionPerformed(ActionEvent e) | |
| 182 | { | |
| 183 | 0 | new SequenceAnnotationWSClient(service, alignFrame, null, false); |
| 184 | } | |
| 185 | }); | |
| 186 | 96 | wsmenu.add(annotservice); |
| 187 | 96 | if (hasparams) |
| 188 | { | |
| 189 | // only add these menu options if the service has user-modifiable | |
| 190 | // arguments | |
| 191 | 24 | annotservice = new JMenuItem( |
| 192 | MessageManager.getString("label.edit_settings_and_run")); | |
| 193 | 24 | annotservice.setToolTipText(MessageManager.getString( |
| 194 | "label.view_and_change_parameters_before_running_calculation")); | |
| 195 | ||
| 196 | 24 | annotservice.addActionListener(new ActionListener() |
| 197 | { | |
| 198 | 0 | public void actionPerformed(ActionEvent e) |
| 199 | { | |
| 200 | 0 | new SequenceAnnotationWSClient(service, alignFrame, null, true); |
| 201 | } | |
| 202 | }); | |
| 203 | 24 | wsmenu.add(annotservice); |
| 204 | 24 | List<WsParamSetI> presets = service.getParamStore().getPresets(); |
| 205 | 24 | if (presets != null && presets.size() > 0) |
| 206 | { | |
| 207 | 0 | JMenu presetlist = new JMenu(MessageManager |
| 208 | .formatMessage("label.run_with_preset", new String[] | |
| 209 | { calcName })); | |
| 210 | ||
| 211 | 0 | for (final WsParamSetI preset : presets) |
| 212 | { | |
| 213 | 0 | final JMenuItem methodR = new JMenuItem(preset.getName()); |
| 214 | 0 | methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>" |
| 215 | 0 | + (preset.isModifiable() |
| 216 | ? MessageManager.getString("label.user_preset") | |
| 217 | : MessageManager | |
| 218 | .getString("label.service_preset")) | |
| 219 | + "</strong><br/>" + preset.getDescription())); | |
| 220 | 0 | methodR.addActionListener(new ActionListener() |
| 221 | { | |
| 222 | 0 | public void actionPerformed(ActionEvent e) |
| 223 | { | |
| 224 | 0 | new SequenceAnnotationWSClient(service, alignFrame, preset, |
| 225 | false); | |
| 226 | } | |
| 227 | ||
| 228 | }); | |
| 229 | 0 | presetlist.add(methodR); |
| 230 | } | |
| 231 | 0 | wsmenu.add(presetlist); |
| 232 | } | |
| 233 | ||
| 234 | } | |
| 235 | else | |
| 236 | { | |
| 237 | 72 | annotservice = new JMenuItem( |
| 238 | MessageManager.getString("label.view_documentation")); | |
| 239 | 72 | if (service.docUrl != null) |
| 240 | { | |
| 241 | 72 | annotservice.addActionListener(new ActionListener() |
| 242 | { | |
| 243 | ||
| 244 | 0 | @Override |
| 245 | public void actionPerformed(ActionEvent arg0) | |
| 246 | { | |
| 247 | 0 | Desktop.instance.showUrl(service.docUrl); |
| 248 | } | |
| 249 | }); | |
| 250 | 72 | annotservice.setToolTipText( |
| 251 | JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage( | |
| 252 | "label.view_service_doc_url", new String[] | |
| 253 | { service.docUrl, service.docUrl }))); | |
| 254 | 72 | wsmenu.add(annotservice); |
| 255 | } | |
| 256 | } | |
| 257 | } | |
| 258 | } |