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     if (sh.action.toLowerCase(Locale.ROOT).contains("disorder"))
 155     {
 156       // build IUPred style client. take sequences, returns annotation per
 157       // sequence.
 158       processParams(sh, editParams).thenAccept((startJob) -> {
 159         if (startJob)
 160         {
 161           alignFrame.getViewport().getCalcManager().startWorker(
 162               new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
 163         }
 164       });
 165     }
 166   }
 167
 168   public SequenceAnnotationWSClient(AutoCalcSetting fave,
 169           AlignFrame alignFrame, boolean b)
 170   {
 171     super(alignFrame, fave.getPreset(), fave.getArgumentSet());
 172     initSequenceAnnotationWSClient(fave.getService(), alignFrame,
 173             fave.getPreset(), b);
 174   }
 175
 176   /*
 177    * (non-Javadoc)
 178    *
 179    * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
 180    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
 181    */
 182   @Override
 183   public void attachWSMenuEntry(JMenu wsmenu,
 184           final ServiceWithParameters service,
 185           final AlignFrame alignFrame)
 186   {
 187     if (Jws2ClientFactory.registerAAConWSInstance(wsmenu,
 188             service, alignFrame))
 189     {
 190       // Alignment dependent analysis calculation WS gui
 191       return;
 192     }
 193     boolean hasparams = service.hasParameters();
 194     String calcName = service.getName();
 195     if (calcName.endsWith("WS"))
 196     {
 197       // Remove "WS" suffix
 198       calcName = calcName.substring(0, calcName.length() - 2);
 199     }
 200
 201     JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
 202             "label.calcname_with_default_settings", new String[]
 203             { calcName }));
 204     annotservice.addActionListener(new ActionListener()
 205     {
 206
 207       @Override
 208       public void actionPerformed(ActionEvent e)
 209       {
 210         new SequenceAnnotationWSClient(service, alignFrame,
 211                 null, false);
 212       }
 213     });
 214     wsmenu.add(annotservice);
 215     if (hasparams)
 216     {
 217       // only add these menu options if the service has user-modifiable
 218       // arguments
 219       annotservice = new JMenuItem(
 220               MessageManager.getString("label.edit_settings_and_run"));
 221       annotservice.setToolTipText(MessageManager.getString(
 222               "label.view_and_change_parameters_before_running_calculation"));
 223
 224       annotservice.addActionListener(new ActionListener()
 225       {
 226         @Override
 227         public void actionPerformed(ActionEvent e)
 228         {
 229           new SequenceAnnotationWSClient(service, alignFrame,
 230                   null, true);
 231         }
 232       });
 233       wsmenu.add(annotservice);
 234       List<WsParamSetI> presets = service.getParamStore().getPresets();
 235       if (presets != null && presets.size() > 0)
 236       {
 237         JMenu presetlist = new JMenu(MessageManager
 238                 .formatMessage("label.run_with_preset", new String[]
 239                 { calcName }));
 240
 241         for (final WsParamSetI preset : presets)
 242         {
 243           final JMenuItem methodR = new JMenuItem(preset.getName());
 244           methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
 245                   + (preset.isModifiable()
 246                           ? MessageManager.getString("label.user_preset")
 247                           : MessageManager
 248                                   .getString("label.service_preset"))
 249                   + "</strong><br/>" + preset.getDescription()));
 250           methodR.addActionListener(new ActionListener()
 251           {
 252             @Override
 253             public void actionPerformed(ActionEvent e)
 254             {
 255               new SequenceAnnotationWSClient(service,
 256                       alignFrame, preset,
 257                       false);
 258             }
 259
 260           });
 261           presetlist.add(methodR);
 262         }
 263         wsmenu.add(presetlist);
 264       }
 265
 266     }
 267     else
 268     {
 269       annotservice = new JMenuItem(
 270               MessageManager.getString("label.view_documentation"));
 271       if (service != null && service.hasDocumentationUrl())
 272       {
 273         annotservice.addActionListener(new ActionListener()
 274         {
 275
 276           @Override
 277           public void actionPerformed(ActionEvent arg0)
 278           {
 279             Desktop.getInstance().showUrl(service.getDocumentationUrl());
 280           }
 281         });
 282         annotservice.setToolTipText(
 283                 JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
 284                         "label.view_service_doc_url", new String[]
 285                         { service.getDocumentationUrl(),
 286                             service.getDocumentationUrl() })));
 287         wsmenu.add(annotservice);
 288       }
 289     }
 290   }
 291 }