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
  37 import javax.swing.JMenu;
  38 import javax.swing.JMenuItem;
  39
  40 /**
  41  * @author jprocter
  42  *
  43  */
  44 public class SequenceAnnotationWSClient extends Jws2Client
  45 {
  46   /**
  47    * initialise a client so its attachWSMenuEntry method can be called.
  48    */
  49   public SequenceAnnotationWSClient()
  50   {
  51     // TODO Auto-generated constructor stub
  52   }
  53
  54   public SequenceAnnotationWSClient(final ServiceWithParameters sh,
  55           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
  56   {
  57     super(alignFrame, preset, null);
  58     initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
  59   }
  60
  61   // dan think. Do I need to change this method to run RNAalifold through the
  62   // GUI
  63
  64   private void initSequenceAnnotationWSClient(final ServiceWithParameters sh,
  65       AlignFrame alignFrame, final WsParamSetI preset, boolean editParams)
  66   {
  67     // dan changed! dan test. comment out if conditional
  68     // if (alignFrame.getViewport().getAlignment().isNucleotide())
  69     // {
  70     // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
  71     // + " can only be used\nfor amino acid alignments.",
  72     // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE);
  73     // return;
  74     //
  75     // }
  76     AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
  77     if (aaui != null)
  78     {
  79       Class clientClass = aaui.getClient();
  80
  81       // Build an AACon style client - take alignment, return annotation for
  82       // columns
  83
  84       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
  85           .getCalcManager()
  86           .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
  87
  88       SeqAnnotationServiceCalcWorker tmpworker = null;
  89       if (clnts != null)
  90       {
  91         for (AlignCalcWorkerI _worker : clnts)
  92         {
  93           tmpworker = (SeqAnnotationServiceCalcWorker) _worker;
  94           if (tmpworker.hasService()
  95               && tmpworker.getService().getClass().equals(clientClass))
  96           {
  97             break;
  98           }
  99           tmpworker = null;
 100         }
 101       }
 102       final var worker = tmpworker;
 103       if (worker == null)
 104       {
 105         processParams(sh, editParams).thenAccept((startJob) -> {
 106           if (startJob)
 107           {
 108             final SeqAnnotationServiceCalcWorker worker_;
 109             try
 110             {
 111               worker_ = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset,
 112                   paramset);
 113             } catch (Exception x)
 114             {
 115               x.printStackTrace();
 116               throw new Error(
 117                   MessageManager.getString("error.implementation_error"),
 118                   x);
 119             }
 120             alignFrame.getViewport().getCalcManager().registerWorker(worker_);
 121                 // also starts the worker
 122             startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
 123           }
 124         });
 125       }
 126       else
 127       {
 128         WsParamSetI preset_;
 129         if (editParams)
 130         {
 131           paramset = worker.getArguments();
 132           preset_ = worker.getPreset();
 133         }
 134         else
 135         {
 136           preset_ = preset;
 137         }
 138         processParams(sh, editParams, true).thenAccept((startJob) -> {
 139           if (startJob)
 140           {
 141             // reinstate worker if it was blacklisted (might have happened due
 142             // to
 143             // invalid parameters)
 144             alignFrame.getViewport().getCalcManager().enableWorker(worker);
 145             worker.updateParameters(this.preset, paramset);
 146             startSeqAnnotationWorker(sh, alignFrame, preset_, editParams);
 147           }
 148         });
 149
 150         if (!processParams(sh, editParams, true).toCompletableFuture().join())
 151         {
 152           return;
 153         }
 154       }
 155     }
 156     else
 157     {
 158       startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
 159     }
 160   }
 161
 162   private void startSeqAnnotationWorker(ServiceWithParameters sh,
 163       AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
 164   {
 165     if (!sh.isInteractiveUpdate())
 166     {
 167       // build IUPred style client. take sequences, returns annotation per
 168       // sequence.
 169       processParams(sh, editParams).thenAccept((startJob) -> {
 170         if (startJob)
 171         {
 172           alignFrame.getViewport().getCalcManager().startWorker(
 173               new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
 174         }
 175       });
 176     }
 177   }
 178
 179   public SequenceAnnotationWSClient(AutoCalcSetting fave,
 180           AlignFrame alignFrame, boolean b)
 181   {
 182     super(alignFrame, fave.getPreset(), fave.getArgumentSet());
 183     initSequenceAnnotationWSClient(fave.getService(), alignFrame,
 184             fave.getPreset(), b);
 185   }
 186
 187   /*
 188    * (non-Javadoc)
 189    *
 190    * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
 191    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
 192    */
 193   @Override
 194   public void attachWSMenuEntry(JMenu wsmenu,
 195           final ServiceWithParameters service,
 196           final AlignFrame alignFrame)
 197   {
 198     if (Jws2ClientFactory.registerAAConWSInstance(wsmenu,
 199             service, alignFrame))
 200     {
 201       // Alignment dependent analysis calculation WS gui
 202       return;
 203     }
 204     boolean hasparams = service.hasParameters();
 205     String calcName = service.getName();
 206     if (calcName.endsWith("WS"))
 207     {
 208       // Remove "WS" suffix
 209       calcName = calcName.substring(0, calcName.length() - 2);
 210     }
 211
 212     JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
 213             "label.calcname_with_default_settings", new String[]
 214             { calcName }));
 215     annotservice.addActionListener(new ActionListener()
 216     {
 217
 218       @Override
 219       public void actionPerformed(ActionEvent e)
 220       {
 221         new SequenceAnnotationWSClient(service, alignFrame,
 222                 null, false);
 223       }
 224     });
 225     wsmenu.add(annotservice);
 226     if (hasparams)
 227     {
 228       // only add these menu options if the service has user-modifiable
 229       // arguments
 230       annotservice = new JMenuItem(
 231               MessageManager.getString("label.edit_settings_and_run"));
 232       annotservice.setToolTipText(MessageManager.getString(
 233               "label.view_and_change_parameters_before_running_calculation"));
 234
 235       annotservice.addActionListener(new ActionListener()
 236       {
 237         @Override
 238         public void actionPerformed(ActionEvent e)
 239         {
 240           new SequenceAnnotationWSClient(service, alignFrame,
 241                   null, true);
 242         }
 243       });
 244       wsmenu.add(annotservice);
 245       List<WsParamSetI> presets = service.getParamStore().getPresets();
 246       if (presets != null && presets.size() > 0)
 247       {
 248         JMenu presetlist = new JMenu(MessageManager
 249                 .formatMessage("label.run_with_preset", new String[]
 250                 { calcName }));
 251
 252         for (final WsParamSetI preset : presets)
 253         {
 254           final JMenuItem methodR = new JMenuItem(preset.getName());
 255           methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
 256                   + (preset.isModifiable()
 257                           ? MessageManager.getString("label.user_preset")
 258                           : MessageManager
 259                                   .getString("label.service_preset"))
 260                   + "</strong><br/>" + preset.getDescription()));
 261           methodR.addActionListener(new ActionListener()
 262           {
 263             @Override
 264             public void actionPerformed(ActionEvent e)
 265             {
 266               new SequenceAnnotationWSClient(service,
 267                       alignFrame, preset,
 268                       false);
 269             }
 270
 271           });
 272           presetlist.add(methodR);
 273         }
 274         wsmenu.add(presetlist);
 275       }
 276
 277     }
 278     else
 279     {
 280       annotservice = new JMenuItem(
 281               MessageManager.getString("label.view_documentation"));
 282       if (service != null && service.hasDocumentationUrl())
 283       {
 284         annotservice.addActionListener(new ActionListener()
 285         {
 286
 287           @Override
 288           public void actionPerformed(ActionEvent arg0)
 289           {
 290             Desktop.getInstance().showUrl(service.getDocumentationUrl());
 291           }
 292         });
 293         annotservice.setToolTipText(
 294                 JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
 295                         "label.view_service_doc_url", new String[]
 296                         { service.getDocumentationUrl(),
 297                             service.getDocumentationUrl() })));
 298         wsmenu.add(annotservice);
 299       }
 300     }
 301   }
 302 }