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.track.feature;
  
  import juicebox.mapcolorui.Feature2DHandler;
  
  import java.io.File;
  import java.io.PrintWriter;
  import java.util.ArrayList;
  import java.util.List;
  
  /**
   * Created by muhammadsaadshamim on 11/2/16.
   */
  class CustomAnnotationRTree2DHandler extends Feature2DHandler {
  
      public CustomAnnotationRTree2DHandler(Feature2DList inputList) {
          clearLists();
          setLoopList(inputList);
      }
  
      public void add(int chr1Idx, int chr2Idx, Feature2D feature) {
          loopList.add(chr1Idx, chr2Idx, feature);
          // TODO can be optimized further i.e. no need to remake entire rtree, just add necessary nodes
          remakeRTree();
      }
  
      public int getNumberOfFeatures() {
          return loopList.getNumTotalFeatures();
      }
  
      public void addAttributeFieldToAll(String key, String aNull) {
          loopList.addDefaultAttribute(key, aNull);
      }
  
      /**
       * Export feature list to given file path
       *
       * @param outputFile
       */
      public void autoSaveNew(PrintWriter outputFile, Feature2D feature) {
          loopList.autoSaveNew(outputFile, feature);
      }
  
      /**
       * Export feature list to given file path
       *
       * @param outputFile
       */
      public void autoSaveAll(PrintWriter outputFile) {
          loopList.autoSaveAll(outputFile);
      }
  
      public boolean checkAndRemoveFeature(int idx1, int idx2, Feature2D feature2D) {
          boolean somethingWasDeleted = loopList.checkAndRemoveFeature(idx1, idx2, feature2D);
          if (somethingWasDeleted)
              remakeRTree();
          // TODO can be optimized further i.e. no need to remake entire rtree, just delete necessary nodes
  
          return somethingWasDeleted;
      }
  
      public Feature2DList getOverlap(Feature2DList inputList) {
          Feature2DList overlapFeature2DList = new Feature2DList();
          overlapFeature2DList.add(loopList.getOverlap(inputList));
          return overlapFeature2DList;
      }
  
      public Feature2D extractSingleFeature() {
          //noinspection LoopStatementThatDoesntLoop
          return loopList.extractSingleFeature();
      }
  
      public List<Feature2D> get(int chrIdx1, int chrIdx2) {
  
          return new ArrayList<>(loopList.get(chrIdx1, chrIdx2));
      }
  
      public boolean exportFeatureList(File file, boolean b, Feature2DList.ListFormat na) {
          Feature2DList mergedList = new Feature2DList();
          mergedList.add(loopList);
          return mergedList.exportFeatureList(file, b, na);
      }
  }
  