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;
  
  import juicebox.HiC;
  import org.broad.igv.feature.LocusScore;
  import org.broad.igv.renderer.DataRange;
  import org.broad.igv.track.DataTrack;
  import org.broad.igv.track.WindowFunction;
  
  import java.awt.*;
  import java.util.Collection;
  import java.util.List;
  
  /**
   * @author jrobinso
   *         Date: 11/8/12
   *         Time: 10:16 AM
   */
  public class HiCIGVDataAdapter extends HiCDataAdapter {
  
      private final DataTrack igvTrack;
  
  
      public HiCIGVDataAdapter(HiC hic, DataTrack igvTrack) {
          super(hic);
          this.igvTrack = igvTrack;
      }
  
      public double getMax() {
          return igvTrack.getDataRange().getMaximum();
      }
  
      public String getName() {
          return igvTrack.getName();
      }
  
      @Override
      public void setName(String text) {
          igvTrack.setName(text);
      }
  
      public Color getPosColor() {
          return igvTrack.getColor();
      }
  
      @Override
      public void setColor(Color selectedColor) {
          igvTrack.setColor(selectedColor);
      }
  
      public boolean isLogScale() {
          return igvTrack.getDataRange().isLog();
      }
  
      public Color getNegColor() {
          return igvTrack.getAltColor();
      }
  
      @Override
      public void setNegColor(Color selectedColor) {
          igvTrack.setAltColor(selectedColor);
      }
  
      public DataRange getDataRange() {
          return igvTrack.getDataRange();
      }
  
      @Override
      public void setDataRange(DataRange dataRange) {
          igvTrack.setDataRange(dataRange);
      }
  
      @Override
      public Collection<WindowFunction> getAvailableWindowFunctions() {
          return igvTrack.getAvailableWindowFunctions();
      }
  
      protected List<LocusScore> getLocusScores(String chr, long gStart, long gEnd, int zoom, WindowFunction windowFunction) {
          igvTrack.setWindowFunction(windowFunction);
          org.broad.igv.track.LoadedDataInterval<List<LocusScore>> scores = igvTrack.getSummaryScores(chr, (int) gStart, (int) gEnd, zoom);
          // Problems with human not having the "chr".  Return scores if not 0, otherwise try adding "chr"
          if (scores.getFeatures().size() > 0) return scores.getFeatures();
          else return igvTrack.getSummaryScores("chr" + chr, (int) gStart, (int) gEnd, zoom).getFeatures();
      }
  }
  