src/jalview/ws/jws2/SequenceAnnotationWSClient.java

   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 jalview.api.AlignCalcWorkerI;
  24 import jalview.gui.AlignFrame;
  25 import jalview.gui.Desktop;
  26 import jalview.gui.JvSwingUtils;
  27 import jalview.util.MessageManager;
  28 import jalview.ws.api.ServiceWithParameters;
  29 import jalview.ws.params.AutoCalcSetting;
  30 import jalview.ws.params.WsParamSetI;
  31 import jalview.ws.uimodel.AlignAnalysisUIText;
  32
  33 import java.awt.event.ActionEvent;
  34 import java.awt.event.ActionListener;
  35 import java.util.List;
  36 import java.util.Locale;
  37
  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   public SequenceAnnotationWSClient()
  52   {
  53     // TODO Auto-generated constructor stub
  54   }
  55
  56   public SequenceAnnotationWSClient(final ServiceWithParameters sh,
  57           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
  58   {
  59     super(alignFrame, preset, null);
  60     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   private void initSequenceAnnotationWSClient(final ServiceWithParameters sh,
  67       AlignFrame alignFrame, final 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     AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
  79     if (aaui != null)
  80     {
  81       Class clientClass = aaui.getClient();
  82
  83       // Build an AACon style client - take alignment, return annotation for
  84       // columns
  85
  86       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
  87           .getCalcManager()
  88           .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
  89
  90       SeqAnnotationServiceCalcWorker tmpworker = null;
  91       if (clnts != null)
  92       {
  93         for (AlignCalcWorkerI _worker : clnts)
  94         {
  95           tmpworker = (SeqAnnotationServiceCalcWorker) _worker;
  96           if (tmpworker.hasService()
  97               && tmpworker.getService().getClass().equals(clientClass))
  98           {
  99             break;
 100           }
 101           tmpworker = null;
 102         }
 103       }
 104       final var worker = tmpworker;
 105       if (worker == null)
 106       {
 107         processParams(sh, editParams).thenAccept((startJob) -> {
 108           if (startJob)
 109           {
 110             final SeqAnnotationServiceCalcWorker worker_;
 111             try
 112             {
 113               worker_ = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset,
 114                   paramset);
 115             } catch (Exception x)
 116             {
 117               x.printStackTrace();
 118               throw new Error(
 119                   MessageManager.getString("error.implementation_error"),
 120                   x);
 121             }
 122             alignFrame.getViewport().getCalcManager().registerWorker(worker_);
 123                 // also starts the worker
 124             startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
 125           }
 126         });
 127
 128       }
 129       else
 130       {
 131         WsParamSetI preset_;
 132         if (editParams)
 133         {
 134           paramset = worker.getArguments();
 135           preset_ = worker.getPreset();
 136         }
 137         else
 138         {
 139           preset_ = preset;
 140         }
 141         processParams(sh, editParams, true).thenAccept((startJob) -> {
 142           if (startJob)
 143           {
 144             // reinstate worker if it was blacklisted (might have happened due
 145             // to
 146             // invalid parameters)
 147             alignFrame.getViewport().getCalcManager().enableWorker(worker);
 148             worker.updateParameters(this.preset, paramset);
 149             startSeqAnnotationWorker(sh, alignFrame, preset_, editParams);
 150           }
 151         });
 152       }
 153     }
 154     else
 155     {
 156       startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
 157     }
 158   }
 159
 160   private void startSeqAnnotationWorker(ServiceWithParameters sh,
 161       AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
 162   {
 163     if (!sh.isInteractiveUpdate())
 164     {
 165       // build IUPred style client. take sequences, returns annotation per
 166       // sequence.
 167       processParams(sh, editParams).thenAccept((startJob) -> {
 168         if (startJob)
 169         {
 170           alignFrame.getViewport().getCalcManager().startWorker(
 171               new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
 172         }
 173       });
 174     }
 175   }
 176
 177   public SequenceAnnotationWSClient(AutoCalcSetting fave,
 178           AlignFrame alignFrame, boolean b)
 179   {
 180     super(alignFrame, fave.getPreset(), fave.getArgumentSet());
 181     initSequenceAnnotationWSClient(fave.getService(), alignFrame,
 182             fave.getPreset(), b);
 183   }
 184
 185   /*
 186    * (non-Javadoc)
 187    *
 188    * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
 189    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
 190    */
 191   @Override
 192   public void attachWSMenuEntry(JMenu wsmenu,
 193           final ServiceWithParameters service,
 194           final AlignFrame alignFrame)
 195   {
 196     if (Jws2ClientFactory.registerAAConWSInstance(wsmenu,
 197             service, alignFrame))
 198     {
 199       // Alignment dependent analysis calculation WS gui
 200       return;
 201     }
 202     boolean hasparams = service.hasParameters();
 203     String calcName = service.getName();
 204     if (calcName.endsWith("WS"))
 205     {
 206       // Remove "WS" suffix
 207       calcName = calcName.substring(0, calcName.length() - 2);
 208     }
 209
 210     JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
 211             "label.calcname_with_default_settings", new String[]
 212             { calcName }));
 213     annotservice.addActionListener(new ActionListener()
 214     {
 215
 216       @Override
 217       public void actionPerformed(ActionEvent e)
 218       {
 219         new SequenceAnnotationWSClient(service, alignFrame,
 220                 null, false);
 221       }
 222     });
 223     wsmenu.add(annotservice);
 224     if (hasparams)
 225     {
 226       // only add these menu options if the service has user-modifiable
 227       // arguments
 228       annotservice = new JMenuItem(
 229               MessageManager.getString("label.edit_settings_and_run"));
 230       annotservice.setToolTipText(MessageManager.getString(
 231               "label.view_and_change_parameters_before_running_calculation"));
 232
 233       annotservice.addActionListener(new ActionListener()
 234       {
 235         @Override
 236         public void actionPerformed(ActionEvent e)
 237         {
 238           new SequenceAnnotationWSClient(service, alignFrame,
 239                   null, true);
 240         }
 241       });
 242       wsmenu.add(annotservice);
 243       List<WsParamSetI> presets = service.getParamStore().getPresets();
 244       if (presets != null && presets.size() > 0)
 245       {
 246         JMenu presetlist = new JMenu(MessageManager
 247                 .formatMessage("label.run_with_preset", new String[]
 248                 { calcName }));
 249
 250         for (final WsParamSetI preset : presets)
 251         {
 252           final JMenuItem methodR = new JMenuItem(preset.getName());
 253           methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
 254                   + (preset.isModifiable()
 255                           ? MessageManager.getString("label.user_preset")
 256                           : MessageManager
 257                                   .getString("label.service_preset"))
 258                   + "</strong><br/>" + preset.getDescription()));
 259           methodR.addActionListener(new ActionListener()
 260           {
 261             @Override
 262             public void actionPerformed(ActionEvent e)
 263             {
 264               new SequenceAnnotationWSClient(service,
 265                       alignFrame, preset,
 266                       false);
 267             }
 268
 269           });
 270           presetlist.add(methodR);
 271         }
 272         wsmenu.add(presetlist);
 273       }
 274
 275     }
 276     else
 277     {
 278       annotservice = new JMenuItem(
 279               MessageManager.getString("label.view_documentation"));
 280       if (service != null && service.hasDocumentationUrl())
 281       {
 282         annotservice.addActionListener(new ActionListener()
 283         {
 284
 285           @Override
 286           public void actionPerformed(ActionEvent arg0)
 287           {
 288             Desktop.getInstance().showUrl(service.getDocumentationUrl());
 289           }
 290         });
 291         annotservice.setToolTipText(
 292                 JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
 293                         "label.view_service_doc_url", new String[]
 294                         { service.getDocumentationUrl(),
 295                             service.getDocumentationUrl() })));
 296         wsmenu.add(annotservice);
 297       }
 298     }
 299   }
 300 }