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