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.encode;
  
  import java.io.File;
  import java.util.Collection;
  import java.util.Map;
  
  /**
   * @author jrobinso
   *         Date: 10/31/13
   *         Time: 10:11 PM
   */
  public class EncodeFileRecord {
  
      private final String path;
      private final Map<String, String> attributes;
      private boolean selected = false;
      private String trackName;
  
      public EncodeFileRecord(String path, Map<String, String> attributes) {
          this.path = path;
          this.attributes = attributes;
      }
  
      public String getPath() {
          return path;
      }
  
      public String getFileType() {
          //String off trailing gz, if present
          String filetype = path;
          if (filetype.endsWith(".gz")) {
              filetype = filetype.substring(0, filetype.length() - 3);
          }
          int idx = filetype.lastIndexOf(".");
          return filetype.substring(idx + 1);
      }
  
      public String getAttributeValue(String name) {
          String value = attributes.get(name);
          if (name.equals("type") && value == null) value = getFileType();
          return value;
      }
  
      public Collection<String> getAttributeNames() {
          return attributes.keySet();
      }
  
      public boolean containsText(String filter) {
          for (String value : attributes.values()) {
              if (value.contains(filter)) return true;
          }
          return false;
      }
  
      boolean isSelected() {
          return selected;
      }
  
      public void setSelected(boolean selected) {
          this.selected = selected;
      }
  
      /**
       * Return a friendly name for the track.  Unfortunately it is neccessary to hardcode certain attributes.
       *
       * @return
       */
      public String getTrackName() {
  
          if (trackName == null) {
              StringBuilder sb = new StringBuilder();
              if (attributes.containsKey("cell")) sb.append(attributes.get("cell")).append(" ");
              if (attributes.containsKey("antibody")) sb.append(attributes.get("antibody")).append(" ");
              if (attributes.containsKey("dataType")) sb.append(attributes.get("dataType")).append(" ");
              if (attributes.containsKey("view")) sb.append(attributes.get("view")).append(" ");
              if (attributes.containsKey("replicate")) sb.append("rep ").append(attributes.get("replicate"));
  
              trackName = sb.toString().trim();
              if (sb.length() == 0) trackName = (new File(path)).getName();
          }
  
          return trackName;
  
      }
  
      /**
       * Test if record has a eough of meta-data to be interpretable
       *
       * @return
       */
      public boolean hasMetaData() {
  
          return (attributes.containsKey("cell")) || (attributes.containsKey("antibody") || attributes.containsKey("Biosample"));
  
      }
  }
  