src/jalview/ws2/gui/AlignmentMenuBuilder.java

   1 package jalview.ws2.gui;
   2
   3 import static java.lang.String.format;
   4
   5 import java.awt.event.MouseAdapter;
   6 import java.awt.event.MouseEvent;
   7 import java.util.Collections;
   8 import java.util.List;
   9 import java.util.Objects;
  10 import java.util.concurrent.CompletionStage;
  11 import javax.swing.JMenu;
  12 import javax.swing.JMenuItem;
  13 import javax.swing.ToolTipManager;
  14
  15 import jalview.datamodel.AlignmentView;
  16 import jalview.gui.AlignFrame;
  17 import jalview.gui.AlignViewport;
  18 import jalview.gui.JvSwingUtils;
  19 import jalview.gui.WebserviceInfo;
  20 import jalview.gui.WsJobParameters;
  21 import jalview.util.MessageManager;
  22 import jalview.ws.params.ArgumentI;
  23 import jalview.ws.params.ParamDatastoreI;
  24 import jalview.ws.params.WsParamSetI;
  25 import jalview.ws2.PollingTaskExecutor;
  26 import jalview.ws2.operations.AlignmentOperation;
  27 import jalview.ws2.operations.AlignmentWorker;
  28
  29 public class AlignmentMenuBuilder implements MenuEntryProviderI
  30 {
  31   AlignmentOperation operation;
  32
  33   public AlignmentMenuBuilder(AlignmentOperation operation)
  34   {
  35     this.operation = operation;
  36   }
  37
  38   public void buildMenu(JMenu parent, AlignFrame frame)
  39   {
  40     if (operation.canSubmitGaps())
  41     {
  42       var alignSubmenu = new JMenu(operation.getName());
  43       buildMenu(alignSubmenu, frame, false);
  44       parent.add(alignSubmenu);
  45       var realignSubmenu = new JMenu(MessageManager.formatMessage(
  46           "label.realign_with_params", operation.getName()));
  47       realignSubmenu.setToolTipText(MessageManager
  48           .getString("label.align_sequences_to_existing_alignment"));
  49       buildMenu(realignSubmenu, frame, true);
  50       parent.add(realignSubmenu);
  51     }
  52     else
  53     {
  54       buildMenu(parent, frame, false);
  55     }
  56   }
  57
  58   protected void buildMenu(JMenu parent, AlignFrame frame,
  59       boolean submitGaps)
  60   {
  61     final String action = submitGaps ? "Align" : "Realign";
  62     final var calcName = operation.getName();
  63
  64     {
  65       var item = new JMenuItem(MessageManager.formatMessage(
  66           "label.calcname_with_default_settings", calcName));
  67       item.setToolTipText(MessageManager
  68           .formatMessage("label.action_with_default_settings", action));
  69       item.addActionListener((event) -> {
  70         final AlignmentView msa = frame.gatherSequencesForAlignment();
  71         if (msa != null)
  72         {
  73           startWorker(frame, msa, Collections.emptyList(), submitGaps);
  74         }
  75       });
  76       parent.add(item);
  77     }
  78
  79     if (operation.hasParameters())
  80     {
  81       var item = new JMenuItem(
  82           MessageManager.getString("label.edit_settings_and_run"));
  83       item.setToolTipText(MessageManager.getString(
  84           "label.view_and_change_parameters_before_alignment"));
  85       item.addActionListener((event) -> {
  86         AlignmentView msa = frame.gatherSequencesForAlignment();
  87         if (msa != null)
  88         {
  89           openEditParamsDialog(operation.getParamStore(), null, null)
  90               .thenAcceptAsync((arguments) -> {
  91                 if (arguments != null)
  92                 {
  93                   startWorker(frame, msa, arguments, submitGaps);
  94                 }
  95               });
  96         }
  97       });
  98       parent.add(item);
  99     }
 100
 101     var presets = operation.getParamStore().getPresets();
 102     if (presets != null && presets.size() > 0)
 103     {
 104       final var presetList = new JMenu(MessageManager
 105           .formatMessage("label.run_with_preset_params", calcName));
 106       final var showToolTipFor = ToolTipManager.sharedInstance()
 107           .getDismissDelay();
 108       for (final var preset : presets)
 109       {
 110         var item = new JMenuItem(preset.getName());
 111         final int QUICK_TOOLTIP = 1500;
 112         item.addMouseListener(new MouseAdapter()
 113         {
 114           @Override
 115           public void mouseEntered(MouseEvent e)
 116           {
 117             ToolTipManager.sharedInstance().setDismissDelay(QUICK_TOOLTIP);
 118           }
 119
 120           @Override
 121           public void mouseExited(MouseEvent e)
 122           {
 123             ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
 124           }
 125         });
 126         String tooltip = JvSwingUtils.wrapTooltip(true,
 127             format("<strong>%s</strong><br/>%s",
 128                 MessageManager.getString(
 129                     preset.isModifiable() ? "label.user_preset"
 130                         : "label.service_preset"),
 131                 preset.getDescription()));
 132         item.setToolTipText(tooltip);
 133         item.addActionListener((event) -> {
 134           AlignmentView msa = frame.gatherSequencesForAlignment();
 135           startWorker(frame, msa, preset.getArguments(), submitGaps);
 136         });
 137         presetList.add(item);
 138       }
 139       parent.add(presetList);
 140     }
 141   }
 142
 143   private CompletionStage<List<ArgumentI>> openEditParamsDialog(
 144       ParamDatastoreI paramStore, WsParamSetI preset,
 145       List<ArgumentI> arguments)
 146   {
 147     WsJobParameters jobParams;
 148     if (preset == null && arguments != null && arguments.size() > 0)
 149       jobParams = new WsJobParameters(paramStore, preset, arguments);
 150     else
 151       jobParams = new WsJobParameters(paramStore, preset, null);
 152     if (preset != null)
 153     {
 154       jobParams.setName(MessageManager.getString(
 155           "label.adjusting_parameters_for_calculation"));
 156     }
 157     var stage = jobParams.showRunDialog();
 158     return stage.thenApply((startJob) -> {
 159       if (startJob)
 160       {
 161         if (jobParams.getPreset() == null)
 162         {
 163           return jobParams.getJobParams();
 164         }
 165         else
 166         {
 167           return jobParams.getPreset().getArguments();
 168         }
 169       }
 170       else
 171       {
 172         return null;
 173       }
 174     });
 175   }
 176
 177   private void startWorker(AlignFrame frame, AlignmentView msa,
 178       List<ArgumentI> arguments, boolean submitGaps)
 179   {
 180     AlignViewport viewport = frame.getViewport();
 181     PollingTaskExecutor executor = frame.getViewport().getWSExecutor();
 182     if (msa != null)
 183     {
 184
 185       String panelInfo = String.format("%s using service hosted at %s%n%s",
 186           operation.getName(), operation.getHostName(),
 187           Objects.requireNonNullElse(operation.getDescription(), ""));
 188       var wsInfo = new WebserviceInfo(operation.getName(), panelInfo, false);
 189
 190       final String alnTitle = frame.getTitle();
 191       AlignmentWorker worker = new AlignmentWorker(operation, msa,
 192           arguments, submitGaps, true, viewport);
 193       String outputHeader = String.format("%s of %s%nJob details%n",
 194           submitGaps ? "Re-alignment" : "Alignment", alnTitle);
 195
 196       var awl = new AlignmentProgressUpdater(worker, wsInfo, frame,
 197           outputHeader);
 198       worker.setResultConsumer(awl);
 199       worker.addListener(awl);
 200
 201       executor.submit(worker);
 202     }
 203
 204   }
 205
 206 }