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   /*
  44    * Is it fine to get rid of AlignAnalysisUIText?
  45    */
  46
  47   public AnnotationOperation(WebServiceI service,
  48       ResultSupplier<List<AlignmentAnnotation>> annotSupplier,
  49       ResultSupplier<FeaturesFile> featSupplier, String operationName)
  50   {
  51     this.service = service;
  52     this.annotationSupplier = annotSupplier;
  53     this.featuresSupplier = featSupplier;
  54     this.typeName = operationName;
  55   }
  56
  57   @Override
  58   public String getName()
  59   {
  60     return service.getName();
  61   }
  62
  63   @Override
  64   public String getTypeName()
  65   {
  66     return typeName;
  67   }
  68
  69   @Override
  70   public String getHostName()
  71   {
  72     return service.getHostName();
  73   }
  74
  75   @Override
  76   public int getMinSequences()
  77   {
  78     return 0;
  79   }
  80
  81   @Override
  82   public int getMaxSequences()
  83   {
  84     return Integer.MAX_VALUE;
  85   }
  86
  87   @Override
  88   public boolean canSubmitGaps()
  89   {
  90     return false;
  91   }
  92
  93   @Override
  94   public boolean isProteinOperation()
  95   {
  96     return true;
  97   }
  98
  99   @Override
 100   public boolean isNucleotideOperation()
 101   {
 102     return true;
 103   }
 104
 105   @Override
 106   public boolean isInteractive()
 107   {
 108     return interactive;
 109   }
 110
 111   public void setInteractive(boolean value)
 112   {
 113     this.interactive = value;
 114   }
 115
 116   @Override
 117   public boolean isAlignmentAnalysis()
 118   {
 119     return alignmentAnalysis;
 120   }
 121
 122   public void setAlignmentAnalysis(boolean value)
 123   {
 124     this.alignmentAnalysis = value;
 125   }
 126
 127   @Override
 128   public boolean getFilterNonStandardSymbols()
 129   {
 130     return false;
 131   }
 132
 133   @Override
 134   public boolean getNeedsAlignedSequences()
 135   {
 136     return false;
 137   }
 138
 139   @Override
 140   public MenuEntryProviderI getMenuBuilder()
 141   {
 142     return this::buildMenu;
 143   }
 144
 145   protected void buildMenu(JMenu parent, AlignFrame frame)
 146   {
 147     final var calcName = service.getName();
 148     PollingTaskExecutor wsExecutor = frame.getViewport().getWSExecutor();
 149     final var calcManager = frame.getViewport().getCalcManager();
 150     {
 151       var item = new JMenuItem(MessageManager.formatMessage(
 152           "label.calcname_with_default_settings", calcName));
 153       item.addActionListener((event) -> {
 154         /* What is the purpose of AlignViewport and AlignmentViewPanel? */
 155         AlignViewport viewport = frame.getCurrentView();
 156         AlignmentViewPanel alignPanel = frame.alignPanel;
 157         var worker = new AnnotationServiceWorker(this, service,
 158             Collections.emptyList(), viewport, alignPanel, frame, frame,
 159             calcManager);
 160         if (isInteractive())
 161           calcManager.registerWorker(worker);
 162         else
 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                 AlignViewport viewport = frame.getCurrentView();
 179                 AlignmentViewPanel alignPanel = frame.alignPanel;
 180                 var worker = new AnnotationServiceWorker(
 181                     AnnotationOperation.this, service, arguments, viewport,
 182                     alignPanel, frame, frame, calcManager);
 183                 if (isInteractive())
 184                   calcManager.registerWorker(worker);
 185                 else
 186                   calcManager.startWorker(worker);
 187               }
 188             });
 189       });
 190       parent.add(item);
 191     }
 192   }
 193
 194   private CompletionStage<List<ArgumentI>> openEditParamsDialog(
 195       WebServiceI service, WsParamSetI preset, List<ArgumentI> arguments)
 196   {
 197     WsJobParameters jobParams;
 198     if (preset == null && arguments != null && arguments.size() > 0)
 199       jobParams = new WsJobParameters(service.getParamStore(), preset,
 200           arguments);
 201     else
 202       jobParams = new WsJobParameters(service.getParamStore(), preset,
 203           null);
 204     if (preset != null)
 205     {
 206       jobParams.setName(MessageManager.getString(
 207           "label.adjusting_parameters_for_calculation"));
 208     }
 209     var stage = jobParams.showRunDialog();
 210     return stage.thenApply((startJob) -> {
 211       if (startJob)
 212       {
 213         if (jobParams.getPreset() == null)
 214           return jobParams.getJobParams();
 215         else
 216           return jobParams.getPreset().getArguments();
 217       }
 218       else
 219       {
 220         return null;
 221       }
 222     });
 223   }
 224
 225 }