content: /*
   * The MIT License (MIT)
   *
   * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine
   *
   * Permission is hereby granted, free of charge, to any person obtaining a copy
   * of this software and associated documentation files (the "Software"), to deal
   * in the Software without restriction, including without limitation the rights
   * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   * copies of the Software, and to permit persons to whom the Software is
   * furnished to do so, subject to the following conditions:
   *
   * The above copyright notice and this permission notice shall be included in
   * all copies or substantial portions of the Software.
   *
   *  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   *  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   *  FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE
   *  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   *  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   *  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   *  THE SOFTWARE.
   */
  
  package juicebox.assembly;
  
  import juicebox.HiC;
  import juicebox.HiCGlobals;
  import juicebox.gui.SuperAdapter;
  import juicebox.track.feature.Feature2D;
  
  import java.util.List;
  
  /**
   * Created by nathanielmusial on 7/10/17.
   */
  public class AssemblyOperationExecutor {
  
      public static void splitContig(Feature2D originalContig, Feature2D debrisContig, SuperAdapter superAdapter, HiC hic, boolean moveTo) {
          AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler();
          assemblyScaffoldHandler.editScaffold(originalContig, debrisContig);
          performAssemblyAction(superAdapter, assemblyScaffoldHandler, true);
      }
  
      public static void invertSelection(SuperAdapter superAdapter, List<Feature2D> selectedFeatures) {
          if (selectedFeatures != null && !selectedFeatures.isEmpty()) {
              AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler();
              assemblyScaffoldHandler.invertSelection(selectedFeatures);
              performAssemblyAction(superAdapter, assemblyScaffoldHandler, true);
          }
      }
  
      public static void moveSelection(SuperAdapter superAdapter, List<Feature2D> selectedFeatures, Feature2D featureOrigin) {
          if (selectedFeatures != null && !selectedFeatures.isEmpty()) {
              AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler();
              assemblyScaffoldHandler.moveSelection(selectedFeatures, featureOrigin);
              performAssemblyAction(superAdapter, assemblyScaffoldHandler, true);
          }
      }
  
      public static void moveAndDisperseSelection(SuperAdapter superAdapter, List<Feature2D> selectedFeatures, Feature2D featureOrigin) {
          if (selectedFeatures != null && !selectedFeatures.isEmpty()) {
              AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler();
              assemblyScaffoldHandler.moveSelection(selectedFeatures, featureOrigin);
              assemblyScaffoldHandler.multiSplit(selectedFeatures);
              performAssemblyAction(superAdapter, assemblyScaffoldHandler, true);
          }
      }
  
      public static void toggleGroup(SuperAdapter superAdapter, Feature2D upstreamFeature2D, Feature2D downstreamFeature2D) {
          if (upstreamFeature2D != null && downstreamFeature2D != null) {
              AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler();
              assemblyScaffoldHandler.toggleGroup(upstreamFeature2D, downstreamFeature2D);
              performAssemblyAction(superAdapter, assemblyScaffoldHandler, HiCGlobals.phasing);
          }
      }
  
      public static void multiMerge(SuperAdapter superAdapter, List<Feature2D> selectedFeatures) {
          if (selectedFeatures != null && !selectedFeatures.isEmpty()) {
              AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler();
              assemblyScaffoldHandler.multiMerge(selectedFeatures.get(0), selectedFeatures.get(selectedFeatures.size() - 1));
              performAssemblyAction(superAdapter, assemblyScaffoldHandler, false);
          }
      }
  
      public static void multiSplit(SuperAdapter superAdapter, List<Feature2D> selectedFeatures) {
          if (selectedFeatures != null && !selectedFeatures.isEmpty()) {
              AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler();
              assemblyScaffoldHandler.multiSplit(selectedFeatures);
              performAssemblyAction(superAdapter, assemblyScaffoldHandler, false);
          }
      }
  
      public static void phaseMerge(SuperAdapter superAdapter, List<Integer> selectedFeatures) {
          if (selectedFeatures != null && !selectedFeatures.isEmpty()) {
              AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler();
              assemblyScaffoldHandler.phaseMerge(selectedFeatures);
              performAssemblyAction(superAdapter, assemblyScaffoldHandler, true);
          }
      }
  
      private static void performAssemblyAction(final SuperAdapter superAdapter, final AssemblyScaffoldHandler assemblyScaffoldHandler, final Boolean refreshMap) {
  
          superAdapter.getAssemblyStateTracker().assemblyActionPerformed(assemblyScaffoldHandler, refreshMap);
          if (refreshMap) superAdapter.safeClearAllMZDCache();
  
      }
  }
  