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.JCheckBoxMenuItem;
   8 import javax.swing.JMenu;
   9 import javax.swing.JMenuItem;
  10 import javax.swing.event.MenuEvent;
  11 import javax.swing.event.MenuListener;
  12
  13 import jalview.api.AlignCalcManagerI2;
  14 import jalview.api.AlignmentViewPanel;
  15 import jalview.datamodel.AlignmentAnnotation;
  16 import jalview.gui.AlignFrame;
  17 import jalview.gui.AlignViewport;
  18 import jalview.gui.WsJobParameters;
  19 import jalview.io.FeaturesFile;
  20 import jalview.util.Format;
  21 import jalview.util.MessageManager;
  22 import jalview.ws.params.ArgumentI;
  23 import jalview.ws.params.WsParamSetI;
  24 import jalview.ws2.MenuEntryProviderI;
  25 import jalview.ws2.ResultSupplier;
  26 import jalview.ws2.PollingTaskExecutor;
  27 import jalview.ws2.WebServiceI;
  28
  29 /**
  30  *
  31  * @author mmwarowny
  32  *
  33  */
  34 public class AnnotationOperation implements Operation
  35 {
  36   final WebServiceI service;
  37
  38   final String typeName;
  39
  40   final ResultSupplier<List<AlignmentAnnotation>> annotationSupplier;
  41
  42   final ResultSupplier<FeaturesFile> featuresSupplier;
  43
  44   boolean alignmentAnalysis = false;
  45
  46   boolean interactive = false;
  47
  48   /*
  49    * Is it fine to get rid of AlignAnalysisUIText?
  50    */
  51
  52   public AnnotationOperation(WebServiceI service,
  53       ResultSupplier<List<AlignmentAnnotation>> annotSupplier,
  54       ResultSupplier<FeaturesFile> featSupplier, String operationName)
  55   {
  56     this.service = service;
  57     this.annotationSupplier = annotSupplier;
  58     this.featuresSupplier = featSupplier;
  59     this.typeName = operationName;
  60   }
  61
  62   @Override
  63   public String getName()
  64   {
  65     return service.getName();
  66   }
  67
  68   @Override
  69   public String getTypeName()
  70   {
  71     return typeName;
  72   }
  73
  74   @Override
  75   public String getHostName()
  76   {
  77     return service.getHostName();
  78   }
  79
  80   @Override
  81   public int getMinSequences()
  82   {
  83     return 0;
  84   }
  85
  86   @Override
  87   public int getMaxSequences()
  88   {
  89     return Integer.MAX_VALUE;
  90   }
  91
  92   @Override
  93   public boolean canSubmitGaps()
  94   {
  95     return false;
  96   }
  97
  98   @Override
  99   public boolean isProteinOperation()
 100   {
 101     return true;
 102   }
 103
 104   @Override
 105   public boolean isNucleotideOperation()
 106   {
 107     return true;
 108   }
 109
 110   @Override
 111   public boolean isInteractive()
 112   {
 113     return interactive;
 114   }
 115
 116   public void setInteractive(boolean value)
 117   {
 118     this.interactive = value;
 119   }
 120
 121   @Override
 122   public boolean isAlignmentAnalysis()
 123   {
 124     return alignmentAnalysis;
 125   }
 126
 127   public void setAlignmentAnalysis(boolean value)
 128   {
 129     this.alignmentAnalysis = value;
 130   }
 131
 132   @Override
 133   public boolean getFilterNonStandardSymbols()
 134   {
 135     return false;
 136   }
 137
 138   @Override
 139   public boolean getNeedsAlignedSequences()
 140   {
 141     return false;
 142   }
 143
 144   @Override
 145   public MenuEntryProviderI getMenuBuilder()
 146   {
 147     if (isInteractive())
 148       return this::buildInteractiveMenu;
 149     else
 150       return this::buildClassicMenu;
 151   }
 152
 153   protected void buildClassicMenu(JMenu parent, AlignFrame frame)
 154   {
 155     final var calcName = service.getName();
 156     PollingTaskExecutor wsExecutor = frame.getViewport().getWSExecutor();
 157     final var calcManager = frame.getViewport().getCalcManager();
 158     {
 159       var item = new JMenuItem(MessageManager.formatMessage(
 160           "label.calcname_with_default_settings", calcName));
 161       item.addActionListener((event) -> {
 162         var worker = createWorker(Collections.emptyList(), frame, calcManager);
 163         calcManager.startWorker(worker);
 164       });
 165       parent.add(item);
 166     }
 167     if (service.hasParameters())
 168     {
 169       var item = new JMenuItem(
 170           MessageManager.getString("label.edit_settings_and_run"));
 171       item.setToolTipText(MessageManager.getString(
 172           "label.view_and_change_parameters_before_running_calculation"));
 173       item.addActionListener((event) -> {
 174         openEditParamsDialog(service, null, null)
 175             .thenAcceptAsync((arguments) -> {
 176               if (arguments != null)
 177               {
 178                 var worker = createWorker(arguments, frame, calcManager);
 179                 calcManager.startWorker(worker);
 180               }
 181             });
 182       });
 183       parent.add(item);
 184     }
 185   }
 186
 187   protected void buildInteractiveMenu(JMenu parent, AlignFrame frame)
 188   {
 189     final var calcName = service.getName();
 190     final var calcManager = frame.getViewport().getCalcManager();
 191     final JCheckBoxMenuItem runItem;
 192     {
 193       // TODO use MessageManager and set tool tip text
 194       runItem = new JCheckBoxMenuItem(
 195           String.format("%s calculations", calcName));
 196       runItem.addActionListener((event) -> {
 197         calcManager.removeWorkersForName(calcName);
 198         var worker = createWorker(Collections.emptyList(), frame, calcManager);
 199         calcManager.registerWorker(worker);
 200       });
 201       parent.add(runItem);
 202     }
 203     JMenuItem _editItem = null;
 204     if (service.hasParameters())
 205     {
 206       // TODO use MessageManager and set tool tip text
 207       _editItem = new JMenuItem(
 208           String.format("Edit %s settings", calcName));
 209       _editItem.addActionListener((event) -> {
 210         openEditParamsDialog(service, null, null)
 211             .thenAcceptAsync((arguments) -> {
 212               if (arguments != null)
 213               {
 214                 calcManager.removeWorkersForName(calcName);
 215                 var worker = createWorker(arguments, frame, calcManager);
 216                 calcManager.registerWorker(worker);
 217               }
 218             });
 219       });
 220       parent.add(_editItem);
 221     }
 222     final var editItem = _editItem;
 223
 224     parent.addMenuListener(new MenuListener()
 225       {
 226         @Override
 227         public void menuSelected(MenuEvent e)
 228         {
 229           var isNuc = frame.getViewport().getAlignment().isNucleotide();
 230           var menuEnabled = (isNuc && isNucleotideOperation()) ||
 231               (!isNuc && isProteinOperation());
 232           runItem.setEnabled(menuEnabled);
 233           if (editItem != null)
 234             editItem.setEnabled(menuEnabled);
 235           boolean currentlyRunning = calcManager.getWorkersForName(calcName).size() > 0;
 236           runItem.setSelected(currentlyRunning);
 237         }
 238
 239         @Override
 240         public void menuDeselected(MenuEvent e) {}
 241
 242         @Override
 243         public void menuCanceled(MenuEvent e) {}
 244       });
 245   }
 246
 247   private AnnotationServiceWorker createWorker(
 248       List<ArgumentI> arguments, AlignFrame frame, AlignCalcManagerI2 calcManager)
 249   {
 250     /* What is the purpose of AlignViewport and AlignmentViewPanel? */
 251     AlignViewport viewport = frame.getCurrentView();
 252     AlignmentViewPanel alignPanel = frame.alignPanel;
 253     return new AnnotationServiceWorker(this, service,
 254         arguments, viewport, alignPanel, frame, frame,
 255         calcManager);
 256   }
 257
 258   private CompletionStage<List<ArgumentI>> openEditParamsDialog(
 259       WebServiceI service, WsParamSetI preset, List<ArgumentI> arguments)
 260   {
 261     WsJobParameters jobParams;
 262     if (preset == null && arguments != null && arguments.size() > 0)
 263       jobParams = new WsJobParameters(service.getParamStore(), preset,
 264           arguments);
 265     else
 266       jobParams = new WsJobParameters(service.getParamStore(), preset,
 267           null);
 268     if (preset != null)
 269     {
 270       jobParams.setName(MessageManager.getString(
 271           "label.adjusting_parameters_for_calculation"));
 272     }
 273     var stage = jobParams.showRunDialog();
 274     return stage.thenApply((startJob) -> {
 275       if (startJob)
 276       {
 277         if (jobParams.getPreset() == null)
 278           return jobParams.getJobParams();
 279         else
 280           return jobParams.getPreset().getArguments();
 281       }
 282       else
 283       {
 284         return null;
 285       }
 286     });
 287   }
 288
 289 }