src/jalview/ws2/operations/AnnotationOperation.java

   1 package jalview.ws2.operations;
   2
   3 import java.io.IOException;
   4 import java.util.Collections;
   5 import java.util.HashMap;
   6 import java.util.List;
   7 import java.util.concurrent.CancellationException;
   8 import java.util.concurrent.CompletionStage;
   9
  10 import javax.swing.JMenu;
  11 import javax.swing.JMenuItem;
  12
  13 import jalview.api.AlignmentViewPanel;
  14 import jalview.bin.Cache;
  15 import jalview.datamodel.AlignmentAnnotation;
  16 import jalview.gui.AlignFrame;
  17 import jalview.gui.AlignViewport;
  18 import jalview.gui.WsJobParameters;
  19 import jalview.io.AnnotationFile;
  20 import jalview.io.FeaturesFile;
  21 import jalview.util.MathUtils;
  22 import jalview.util.MessageManager;
  23 import jalview.workers.AlignCalcManager2;
  24 import jalview.ws.params.ArgumentI;
  25 import jalview.ws.params.WsParamSetI;
  26 import jalview.ws2.MenuEntryProviderI;
  27 import jalview.ws2.ResultSupplier;
  28 import jalview.ws2.WSJob;
  29 import jalview.ws2.WSJobStatus;
  30 import jalview.ws2.PollingTaskExecutor;
  31 import jalview.ws2.WebServiceI;
  32 import jalview.ws2.WebServiceWorkerI;
  33 import jalview.ws2.utils.WSJobList;
  34
  35 import static java.lang.String.format;
  36
  37 /**
  38  *
  39  * @author mmwarowny
  40  *
  41  */
  42 public class AnnotationOperation implements Operation
  43 {
  44   final WebServiceI service;
  45
  46   final String typeName;
  47
  48   final ResultSupplier<List<AlignmentAnnotation>> annotationSupplier;
  49
  50   final ResultSupplier<FeaturesFile> featuresSupplier;
  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 false;
 114   }
 115
 116   @Override
 117   public boolean isAlignmentAnalysis()
 118   {
 119     return false;
 120   }
 121
 122   @Override
 123   public boolean getFilterNonStandardSymbols()
 124   {
 125     return false;
 126   }
 127
 128   @Override
 129   public boolean getNeedsAlignedSequences()
 130   {
 131     return false;
 132   }
 133
 134   @Override
 135   public MenuEntryProviderI getMenuBuilder()
 136   {
 137     return this::buildMenu;
 138   }
 139
 140   protected void buildMenu(JMenu parent, AlignFrame frame)
 141   {
 142     final var calcName = service.getName();
 143     PollingTaskExecutor wsExecutor = frame.getViewport().getWSExecutor();
 144     final var calcManager = frame.getViewport().getCalcManager();
 145     {
 146       var item = new JMenuItem(MessageManager.formatMessage(
 147           "label.calcname_with_default_settings", calcName));
 148       item.addActionListener((event) -> {
 149         AlignViewport viewport = frame.getCurrentView();
 150         AlignmentViewPanel alignPanel = frame.alignPanel;
 151         var worker = new AnnotationServiceWorker(this, service,
 152             Collections.emptyList(), viewport, alignPanel, frame, frame,
 153             calcManager);
 154         calcManager.startWorker(worker);
 155         // TODO create and submit AnnotataionServiceWorker
 156       });
 157       parent.add(item);
 158     }
 159     if (service.hasParameters())
 160     {
 161       var item = new JMenuItem(
 162           MessageManager.getString("label.edit_settings_and_run"));
 163       item.setToolTipText(MessageManager.getString(
 164           "label.view_and_change_parameters_before_running_calculation"));
 165       item.addActionListener((event) -> {
 166         openEditParamsDialog(service, null, null)
 167             .thenAcceptAsync((arguments) -> {
 168               if (arguments != null)
 169               {
 170                 AlignViewport viewport = frame.getCurrentView();
 171                 AlignmentViewPanel alignPanel = frame.alignPanel;
 172                 var worker = new AnnotationServiceWorker(
 173                     AnnotationOperation.this, service, arguments, viewport,
 174                     alignPanel, frame, frame, calcManager);
 175                 calcManager.startWorker(worker);
 176               }
 177             });
 178       });
 179     }
 180   }
 181
 182   private CompletionStage<List<ArgumentI>> openEditParamsDialog(
 183       WebServiceI service, WsParamSetI preset, List<ArgumentI> arguments)
 184   {
 185     WsJobParameters jobParams;
 186     if (preset == null && arguments != null && arguments.size() > 0)
 187       jobParams = new WsJobParameters(service.getParamStore(), preset,
 188           arguments);
 189     else
 190       jobParams = new WsJobParameters(service.getParamStore(), preset,
 191           null);
 192     if (preset != null)
 193     {
 194       jobParams.setName(MessageManager.getString(
 195           "label.adjusting_parameters_for_calculation"));
 196     }
 197     var stage = jobParams.showRunDialog();
 198     return stage.thenApply((startJob) -> {
 199       if (startJob)
 200       {
 201         if (jobParams.getPreset() == null)
 202           return jobParams.getJobParams();
 203         else
 204           return jobParams.getPreset().getArguments();
 205       }
 206       else
 207       {
 208         return null;
 209       }
 210     });
 211   }
 212
 213 }