src/jalview/ws2/operations/AnnotationOperation.java

   1 package jalview.ws2.operations;
   2
   3 import java.util.Collections;
   4 import java.util.List;
   5 import java.util.concurrent.CompletionStage;
   6
   7 import javax.swing.JMenu;
   8 import javax.swing.JMenuItem;
   9
  10 import jalview.api.AlignmentViewPanel;
  11 import jalview.datamodel.AlignmentAnnotation;
  12 import jalview.gui.AlignFrame;
  13 import jalview.gui.AlignViewport;
  14 import jalview.gui.WsJobParameters;
  15 import jalview.io.FeaturesFile;
  16 import jalview.util.MessageManager;
  17 import jalview.ws.params.ArgumentI;
  18 import jalview.ws.params.WsParamSetI;
  19 import jalview.ws2.MenuEntryProviderI;
  20 import jalview.ws2.ResultSupplier;
  21 import jalview.ws2.PollingTaskExecutor;
  22 import jalview.ws2.WebServiceI;
  23
  24 /**
  25  *
  26  * @author mmwarowny
  27  *
  28  */
  29 public class AnnotationOperation implements Operation
  30 {
  31   final WebServiceI service;
  32
  33   final String typeName;
  34
  35   final ResultSupplier<List<AlignmentAnnotation>> annotationSupplier;
  36
  37   final ResultSupplier<FeaturesFile> featuresSupplier;
  38
  39   boolean alignmentAnalysis = false;
  40
  41   boolean interactive = false;
  42
  43   public AnnotationOperation(WebServiceI service,
  44       ResultSupplier<List<AlignmentAnnotation>> annotSupplier,
  45       ResultSupplier<FeaturesFile> featSupplier, String operationName)
  46   {
  47     this.service = service;
  48     this.annotationSupplier = annotSupplier;
  49     this.featuresSupplier = featSupplier;
  50     this.typeName = operationName;
  51   }
  52
  53   @Override
  54   public String getName()
  55   {
  56     return service.getName();
  57   }
  58
  59   @Override
  60   public String getTypeName()
  61   {
  62     return typeName;
  63   }
  64
  65   @Override
  66   public String getHostName()
  67   {
  68     return service.getHostName();
  69   }
  70
  71   @Override
  72   public int getMinSequences()
  73   {
  74     return 0;
  75   }
  76
  77   @Override
  78   public int getMaxSequences()
  79   {
  80     return Integer.MAX_VALUE;
  81   }
  82
  83   @Override
  84   public boolean canSubmitGaps()
  85   {
  86     return false;
  87   }
  88
  89   @Override
  90   public boolean isProteinOperation()
  91   {
  92     return true;
  93   }
  94
  95   @Override
  96   public boolean isNucleotideOperation()
  97   {
  98     return true;
  99   }
 100
 101   @Override
 102   public boolean isInteractive()
 103   {
 104     return interactive;
 105   }
 106
 107   public void setInteractive(boolean value)
 108   {
 109     this.interactive = value;
 110   }
 111
 112   @Override
 113   public boolean isAlignmentAnalysis()
 114   {
 115     return alignmentAnalysis;
 116   }
 117
 118   public void setAlignmentAnalysis(boolean value)
 119   {
 120     this.alignmentAnalysis = value;
 121   }
 122
 123   @Override
 124   public boolean getFilterNonStandardSymbols()
 125   {
 126     return false;
 127   }
 128
 129   @Override
 130   public boolean getNeedsAlignedSequences()
 131   {
 132     return false;
 133   }
 134
 135   @Override
 136   public MenuEntryProviderI getMenuBuilder()
 137   {
 138     return this::buildMenu;
 139   }
 140
 141   protected void buildMenu(JMenu parent, AlignFrame frame)
 142   {
 143     final var calcName = service.getName();
 144     PollingTaskExecutor wsExecutor = frame.getViewport().getWSExecutor();
 145     final var calcManager = frame.getViewport().getCalcManager();
 146     {
 147       var item = new JMenuItem(MessageManager.formatMessage(
 148           "label.calcname_with_default_settings", calcName));
 149       item.addActionListener((event) -> {
 150         AlignViewport viewport = frame.getCurrentView();
 151         AlignmentViewPanel alignPanel = frame.alignPanel;
 152         var worker = new AnnotationServiceWorker(this, service,
 153             Collections.emptyList(), viewport, alignPanel, frame, frame,
 154             calcManager);
 155         if (isInteractive())
 156           calcManager.registerWorker(worker);
 157         else
 158           calcManager.startWorker(worker);
 159       });
 160       parent.add(item);
 161     }
 162     if (service.hasParameters())
 163     {
 164       var item = new JMenuItem(
 165           MessageManager.getString("label.edit_settings_and_run"));
 166       item.setToolTipText(MessageManager.getString(
 167           "label.view_and_change_parameters_before_running_calculation"));
 168       item.addActionListener((event) -> {
 169         openEditParamsDialog(service, null, null)
 170             .thenAcceptAsync((arguments) -> {
 171               if (arguments != null)
 172               {
 173                 AlignViewport viewport = frame.getCurrentView();
 174                 AlignmentViewPanel alignPanel = frame.alignPanel;
 175                 var worker = new AnnotationServiceWorker(
 176                     AnnotationOperation.this, service, arguments, viewport,
 177                     alignPanel, frame, frame, calcManager);
 178                 if (isInteractive())
 179                   calcManager.registerWorker(worker);
 180                 else
 181                   calcManager.startWorker(worker);
 182               }
 183             });
 184       });
 185       parent.add(item);
 186     }
 187   }
 188
 189   private CompletionStage<List<ArgumentI>> openEditParamsDialog(
 190       WebServiceI service, WsParamSetI preset, List<ArgumentI> arguments)
 191   {
 192     WsJobParameters jobParams;
 193     if (preset == null && arguments != null && arguments.size() > 0)
 194       jobParams = new WsJobParameters(service.getParamStore(), preset,
 195           arguments);
 196     else
 197       jobParams = new WsJobParameters(service.getParamStore(), preset,
 198           null);
 199     if (preset != null)
 200     {
 201       jobParams.setName(MessageManager.getString(
 202           "label.adjusting_parameters_for_calculation"));
 203     }
 204     var stage = jobParams.showRunDialog();
 205     return stage.thenApply((startJob) -> {
 206       if (startJob)
 207       {
 208         if (jobParams.getPreset() == null)
 209           return jobParams.getJobParams();
 210         else
 211           return jobParams.getPreset().getArguments();
 212       }
 213       else
 214       {
 215         return null;
 216       }
 217     });
 218   }
 219
 220 }