content: /*
   * The MIT License (MIT)
   *
   * Copyright (c) 2011-2020 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 NONINFRINGEMENT. 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.DirectoryManager;
  import juicebox.HiCGlobals;
  import juicebox.gui.SuperAdapter;
  
  import java.util.Stack;
  
  /**
   * Created by nathanielmusial on 7/5/17.
   */
  public class AssemblyStateTracker {
      private final Stack<AssemblyScaffoldHandler> undoStack;
      private final Stack<AssemblyScaffoldHandler> redoStack;
      private final AssemblyScaffoldHandler initialAssemblyScaffoldHandler;
      private final SuperAdapter superAdapter;
      private final String autoSaveFileName;
      private int counter = 0;
  
      public AssemblyStateTracker(AssemblyScaffoldHandler assemblyScaffoldHandler, SuperAdapter superAdapter) {
  
          undoStack = new Stack<>();
          undoStack.push(assemblyScaffoldHandler);
          redoStack = new Stack<>();
          this.initialAssemblyScaffoldHandler = assemblyScaffoldHandler;
          this.superAdapter = superAdapter;
          this.autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" + (SuperAdapter.getDatasetTitle().split(".+?/(?=[^/]+$)")[1]).split("\\.(?=[^\\.]+$)")[0] + ".review.autosave";
      }
  
      public AssemblyScaffoldHandler getAssemblyHandler() {
          return undoStack.peek();
      }
  
      public AssemblyScaffoldHandler getNewAssemblyHandler() {
          return new AssemblyScaffoldHandler(undoStack.peek());
      }
  
      public void resetState() {
          undoStack.clear();
          assemblyActionPerformed(initialAssemblyScaffoldHandler, true);
          superAdapter.safeClearAllMZDCache();
      }
  
      public AssemblyScaffoldHandler getInitialAssemblyScaffoldHandler() {
          return initialAssemblyScaffoldHandler;
      }
  
      public void assemblyActionPerformed(AssemblyScaffoldHandler assemblyScaffoldHandler, boolean refreshMap) {
          counter++;
          redoStack.clear();
          undoStack.push(assemblyScaffoldHandler);
          if (counter % 20 == 0) {
              if (HiCGlobals.phasing) {
                  PsfFileExporter psfFileExporter = new PsfFileExporter(assemblyScaffoldHandler, autoSaveFileName);
                  psfFileExporter.exportPsfFile();
              } else {
                  AssemblyFileExporter assemblyFileExporter = new AssemblyFileExporter(assemblyScaffoldHandler, autoSaveFileName);
                  assemblyFileExporter.exportAssemblyFile();
              }
          }
          while (undoStack.size() > 50) { //keeps stack at size of 50 or less
              undoStack.remove(0);
          }
          assemblyScaffoldHandler.updateAssembly(refreshMap);
          regenerateLayers(refreshMap);
      }
  
  
      private void regenerateLayers(boolean refreshMap) {
          AssemblyScaffoldHandler assemblyScaffoldHandler = undoStack.peek();
          if (refreshMap) {
              superAdapter.getMainLayer().getFeatureHandler().setLoopList(assemblyScaffoldHandler.getScaffoldFeature2DHandler().getAllVisibleLoops());
          }
          superAdapter.getGroupLayer().getFeatureHandler().setLoopList(assemblyScaffoldHandler.getSuperscaffoldFeature2DHandler().getAllVisibleLoops());
      }
  
      public boolean checkUndo() {
          return undoStack.size() > 1;
      }
  
      public void undo() {
          if (checkUndo()) {
              redoStack.push(undoStack.pop());
  
              undoStack.peek().updateAssembly(true);
              regenerateLayers(true);
              superAdapter.safeClearAllMZDCache();
          }
      }
  
      public boolean checkRedo() {
          return !redoStack.empty();
      }
  
      public void redo() {
          if (checkRedo()) {
              undoStack.push(redoStack.pop());
  
              undoStack.peek().updateAssembly(true);
              regenerateLayers(true);
              superAdapter.safeClearAllMZDCache();
          }
      }
  }