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.jws2.dm.AAConSettings;
  29 import jalview.ws.jws2.jabaws2.Jws2Instance;
  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 Jws2Instance 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 Jws2Instance 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     // JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
  71     // + " can only be used\nfor amino acid alignments.",
  72     // "Wrong type of sequences!", JOptionPane.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().getRegisteredWorkersOfClass(clientClass);
  86       AbstractJabaCalcWorker worker;
  87       if (clnts == null || clnts.size() == 0)
  88       {
  89         if (!processParams(sh, editParams))
  90         {
  91           return;
  92         }
  93         try
  94         {
  95           worker = (AbstractJabaCalcWorker) (clientClass
  96                   .getConstructor(new Class[] { Jws2Instance.class,
  97                       AlignFrame.class, WsParamSetI.class, List.class })
  98                   .newInstance(new Object[] { sh, alignFrame, this.preset,
  99                       paramset }));
 100         } catch (Exception x)
 101         {
 102           x.printStackTrace();
 103           throw new Error(
 104                   MessageManager.getString("error.implementation_error"), x);
 105         }
 106         alignFrame.getViewport().getCalcManager().registerWorker(worker);
 107         alignFrame.getViewport().getCalcManager().startWorker(worker);
 108
 109       }
 110       else
 111       {
 112         worker = (AbstractJabaCalcWorker) clnts.get(0);
 113         if (editParams)
 114         {
 115           paramset = worker.getArguments();
 116           preset = worker.getPreset();
 117         }
 118
 119         if (!processParams(sh, editParams, true))
 120         {
 121           return;
 122         }
 123         // reinstate worker if it was blacklisted (might have happened due to
 124         // invalid parameters)
 125         alignFrame.getViewport().getCalcManager().workerMayRun(worker);
 126         worker.updateParameters(this.preset, paramset);
 127       }
 128     }
 129     if (sh.action.toLowerCase().contains("disorder"))
 130     {
 131       // build IUPred style client. take sequences, returns annotation per
 132       // sequence.
 133       if (!processParams(sh, editParams))
 134       {
 135         return;
 136       }
 137
 138       alignFrame
 139               .getViewport()
 140               .getCalcManager()
 141               .startWorker(
 142                       new AADisorderClient(sh, alignFrame, preset, paramset));
 143     }
 144   }
 145
 146   public SequenceAnnotationWSClient(AAConSettings fave,
 147           AlignFrame alignFrame, boolean b)
 148   {
 149     super(alignFrame, fave.getPreset(), fave.getJobArgset());
 150     initSequenceAnnotationWSClient(fave.getService(), alignFrame,
 151             fave.getPreset(), b);
 152   }
 153
 154   /*
 155    * (non-Javadoc)
 156    *
 157    * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
 158    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
 159    */
 160   public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
 161           final AlignFrame alignFrame)
 162   {
 163     if (registerAAConWSInstance(wsmenu, service, alignFrame))
 164     {
 165       // Alignment dependent analysis calculation WS gui
 166       return;
 167     }
 168     boolean hasparams = service.hasParameters();
 169     // Assume name ends in WS
 170     String calcName = service.serviceType.substring(0,
 171             service.serviceType.length() - 2);
 172
 173     JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
 174             "label.calcname_with_default_settings",
 175             new String[] { calcName }));
 176     annotservice.addActionListener(new ActionListener()
 177     {
 178
 179       @Override
 180       public void actionPerformed(ActionEvent e)
 181       {
 182         new SequenceAnnotationWSClient(service, alignFrame, null, false);
 183       }
 184     });
 185     wsmenu.add(annotservice);
 186     if (hasparams)
 187     {
 188       // only add these menu options if the service has user-modifiable
 189       // arguments
 190       annotservice = new JMenuItem(
 191               MessageManager.getString("label.edit_settings_and_run"));
 192       annotservice
 193               .setToolTipText(MessageManager
 194                       .getString("label.view_and_change_parameters_before_running_calculation"));
 195
 196       annotservice.addActionListener(new ActionListener()
 197       {
 198         public void actionPerformed(ActionEvent e)
 199         {
 200           new SequenceAnnotationWSClient(service, alignFrame, null, true);
 201         }
 202       });
 203       wsmenu.add(annotservice);
 204       List<WsParamSetI> presets = service.getParamStore().getPresets();
 205       if (presets != null && presets.size() > 0)
 206       {
 207         JMenu presetlist = new JMenu(MessageManager.formatMessage(
 208                 "label.run_with_preset", new String[] { calcName }));
 209
 210         for (final WsParamSetI preset : presets)
 211         {
 212           final JMenuItem methodR = new JMenuItem(preset.getName());
 213           methodR.setToolTipText(JvSwingUtils.wrapTooltip(
 214                   true,
 215                   "<strong>"
 216                           + (preset.isModifiable() ? MessageManager
 217                                   .getString("label.user_preset")
 218                                   : MessageManager
 219                                           .getString("label.service_preset"))
 220                           + "</strong><br/>" + preset.getDescription()));
 221           methodR.addActionListener(new ActionListener()
 222           {
 223             public void actionPerformed(ActionEvent e)
 224             {
 225               new SequenceAnnotationWSClient(service, alignFrame, preset,
 226                       false);
 227             }
 228
 229           });
 230           presetlist.add(methodR);
 231         }
 232         wsmenu.add(presetlist);
 233       }
 234
 235     }
 236     else
 237     {
 238       annotservice = new JMenuItem(
 239               MessageManager.getString("label.view_documentation"));
 240       if (service.docUrl != null)
 241       {
 242         annotservice.addActionListener(new ActionListener()
 243         {
 244
 245           @Override
 246           public void actionPerformed(ActionEvent arg0)
 247           {
 248             Desktop.instance.showUrl(service.docUrl);
 249           }
 250         });
 251         annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true,
 252                 MessageManager.formatMessage("label.view_service_doc_url",
 253                         new String[] { service.docUrl, service.docUrl })));
 254         wsmenu.add(annotservice);
 255       }
 256     }
 257   }
 258 }