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.jws2.dm.AAConSettings;
  30 import jalview.ws.jws2.jabaws2.Jws2Instance;
  31 import jalview.ws.params.WsParamSetI;
  32 import jalview.ws.uimodel.AlignAnalysisUIText;
  33
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.util.List;
  37
  38 import javax.swing.JMenu;
  39 import javax.swing.JMenuItem;
  40
  41 /**
  42  * @author jprocter
  43  *
  44  */
  45 public class SequenceAnnotationWSClient extends Jws2Client
  46 {
  47   /**
  48    * initialise a client so its attachWSMenuEntry method can be called.
  49    */
  50   public SequenceAnnotationWSClient()
  51   {
  52     // TODO Auto-generated constructor stub
  53   }
  54
  55   public SequenceAnnotationWSClient(final Jws2Instance sh,
  56           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
  57   {
  58     super(alignFrame, preset, null);
  59     initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
  60   }
  61
  62   // dan think. Do I need to change this method to run RNAalifold through the
  63   // GUI
  64
  65   public void initSequenceAnnotationWSClient(final ServiceWithParameters sh,
  66           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
  67   {
  68     // dan changed! dan test. comment out if conditional
  69     // if (alignFrame.getViewport().getAlignment().isNucleotide())
  70     // {
  71     // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
  72     // + " can only be used\nfor amino acid alignments.",
  73     // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE);
  74     // return;
  75     //
  76     // }
  77     AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
  78     if (aaui != null)
  79     {
  80       Class clientClass = aaui.getClient();
  81
  82       // Build an AACon style client - take alignment, return annotation for
  83       // columns
  84
  85       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
  86               .getCalcManager()
  87               .getRegisteredWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
  88
  89       SeqAnnotationServiceCalcWorker worker = null;
  90       if (clnts != null)
  91       {
  92         for (AlignCalcWorkerI _worker : clnts)
  93         {
  94           worker = (SeqAnnotationServiceCalcWorker) _worker;
  95           if (worker.hasService()
  96                   && worker.getService().getClass().equals(clientClass))
  97           {
  98             break;
  99           }
 100           worker = null;
 101         }
 102       }
 103       if (worker == null)
 104       {
 105         if (!processParams(sh, editParams))
 106         {
 107           return;
 108         }
 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         alignFrame.getViewport().getCalcManager().startWorker(worker);
 122
 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.getAction().toLowerCase().contains("disorder"))
 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(AAConSettings 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, service,
 176             alignFrame))
 177     {
 178       // Alignment dependent analysis calculation WS gui
 179       return;
 180     }
 181     boolean hasparams = service.hasParameters();
 182     // Assume name ends in WS
 183     String calcName = service.getName().substring(0,
 184             service.getName().length() - 2);
 185
 186     JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
 187             "label.calcname_with_default_settings", new String[]
 188             { calcName }));
 189     annotservice.addActionListener(new ActionListener()
 190     {
 191
 192       @Override
 193       public void actionPerformed(ActionEvent e)
 194       {
 195         new SequenceAnnotationWSClient((Jws2Instance) service, alignFrame,
 196                 null, false);
 197       }
 198     });
 199     wsmenu.add(annotservice);
 200     if (hasparams)
 201     {
 202       // only add these menu options if the service has user-modifiable
 203       // arguments
 204       annotservice = new JMenuItem(
 205               MessageManager.getString("label.edit_settings_and_run"));
 206       annotservice.setToolTipText(MessageManager.getString(
 207               "label.view_and_change_parameters_before_running_calculation"));
 208
 209       annotservice.addActionListener(new ActionListener()
 210       {
 211         @Override
 212         public void actionPerformed(ActionEvent e)
 213         {
 214           new SequenceAnnotationWSClient((Jws2Instance) service, alignFrame,
 215                   null, true);
 216         }
 217       });
 218       wsmenu.add(annotservice);
 219       List<WsParamSetI> presets = service.getParamStore().getPresets();
 220       if (presets != null && presets.size() > 0)
 221       {
 222         JMenu presetlist = new JMenu(MessageManager
 223                 .formatMessage("label.run_with_preset", new String[]
 224                 { calcName }));
 225
 226         for (final WsParamSetI preset : presets)
 227         {
 228           final JMenuItem methodR = new JMenuItem(preset.getName());
 229           methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
 230                   + (preset.isModifiable()
 231                           ? MessageManager.getString("label.user_preset")
 232                           : MessageManager
 233                                   .getString("label.service_preset"))
 234                   + "</strong><br/>" + preset.getDescription()));
 235           methodR.addActionListener(new ActionListener()
 236           {
 237             @Override
 238             public void actionPerformed(ActionEvent e)
 239             {
 240               new SequenceAnnotationWSClient((Jws2Instance) service,
 241                       alignFrame, preset,
 242                       false);
 243             }
 244
 245           });
 246           presetlist.add(methodR);
 247         }
 248         wsmenu.add(presetlist);
 249       }
 250
 251     }
 252     else
 253     {
 254       annotservice = new JMenuItem(
 255               MessageManager.getString("label.view_documentation"));
 256       if (service != null && service.hasDocumentationUrl())
 257       {
 258         annotservice.addActionListener(new ActionListener()
 259         {
 260
 261           @Override
 262           public void actionPerformed(ActionEvent arg0)
 263           {
 264             Desktop.instance.showUrl(service.getDocumentationUrl());
 265           }
 266         });
 267         annotservice.setToolTipText(
 268                 JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
 269                         "label.view_service_doc_url", new String[]
 270                         { service.getDocumentationUrl(),
 271                             service.getDocumentationUrl() })));
 272         wsmenu.add(annotservice);
 273       }
 274     }
 275   }
 276 }