com.hfg.bio.taxonomy.NCBITaxonNodeRank Maven / Gradle / Ivy

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com.hfg xml, html, svg, and bioinformatics utility library
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package com.hfg.bio.taxonomy;

import java.io.Serializable;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;


//------------------------------------------------------------------------------
/**
 * NCBI taxonomy levels.
 * 
 * Based on values in the nodes.dmp file in ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
 * 
 *
 * @author J. Alex Taylor, hairyfatguy.com
 */
//------------------------------------------------------------------------------
// com.hfg XML/HTML Coding Library
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
//
// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
// [email protected]
//------------------------------------------------------------------------------

public class NCBITaxonNodeRank implements Comparable, Serializable
{

   //**************************************************************************
   // PRIVATE FIELDS
   //**************************************************************************

   private String mName;
   private int    mRank;

   private static Map sUniqueMap = new HashMap<>(30);

   //**************************************************************************
   // PUBLIC FIELDS
   //**************************************************************************

   public static NCBITaxonNodeRank SUPERKINGDOM  = new NCBITaxonNodeRank(30, "superkingdom");
   public static NCBITaxonNodeRank KINGDOM       = new NCBITaxonNodeRank(29, "kingdom");
   public static NCBITaxonNodeRank SUBKINGDOM    = new NCBITaxonNodeRank(28, "subkingdom");
   public static NCBITaxonNodeRank SUPERPHYLUM   = new NCBITaxonNodeRank(27, "superphylum");
   public static NCBITaxonNodeRank PHYLUM        = new NCBITaxonNodeRank(26, "phylum");
   public static NCBITaxonNodeRank SUBPHYLUM     = new NCBITaxonNodeRank(25, "subphylum");
   public static NCBITaxonNodeRank SUPERCLASS    = new NCBITaxonNodeRank(24, "superclass");
   public static NCBITaxonNodeRank CLASS         = new NCBITaxonNodeRank(23, "class");
   public static NCBITaxonNodeRank SUBCLASS      = new NCBITaxonNodeRank(22, "subclass");
   public static NCBITaxonNodeRank INFRACLASS    = new NCBITaxonNodeRank(21, "infraclass");
   public static NCBITaxonNodeRank COHORT        = new NCBITaxonNodeRank(20, "cohort");
   public static NCBITaxonNodeRank SUPERORDER    = new NCBITaxonNodeRank(19, "superorder");
   public static NCBITaxonNodeRank ORDER         = new NCBITaxonNodeRank(18, "order");
   public static NCBITaxonNodeRank SUBORDER      = new NCBITaxonNodeRank(17, "suborder");
   public static NCBITaxonNodeRank PARVORDER     = new NCBITaxonNodeRank(16, "parvorder");
   public static NCBITaxonNodeRank INFRAORDER    = new NCBITaxonNodeRank(15, "infraorder");
   public static NCBITaxonNodeRank SUPERFAMILY   = new NCBITaxonNodeRank(14, "superfamily");
   public static NCBITaxonNodeRank FAMILY        = new NCBITaxonNodeRank(13, "family");
   public static NCBITaxonNodeRank SUBFAMILY     = new NCBITaxonNodeRank(12, "subfamily");
   public static NCBITaxonNodeRank TRIBE         = new NCBITaxonNodeRank(11, "tribe");
   public static NCBITaxonNodeRank SUBTRIBE      = new NCBITaxonNodeRank(10, "subtribe");
   public static NCBITaxonNodeRank GENUS         = new NCBITaxonNodeRank( 9, "genus");
   public static NCBITaxonNodeRank SUBGENUS      = new NCBITaxonNodeRank( 8, "subgenus");
   public static NCBITaxonNodeRank SPECIES_GROUP = new NCBITaxonNodeRank( 7, "species group");
   public static NCBITaxonNodeRank SPECIES_SUBGROUP = new NCBITaxonNodeRank(6, "species subgroup");
   public static NCBITaxonNodeRank SPECIES       = new NCBITaxonNodeRank( 5, "species");
   public static NCBITaxonNodeRank SUBSPECIES    = new NCBITaxonNodeRank( 4, "subspecies");
   public static NCBITaxonNodeRank VARIETAS      = new NCBITaxonNodeRank( 3, "varietas");
   public static NCBITaxonNodeRank FORMA         = new NCBITaxonNodeRank( 2, "forma");
   public static NCBITaxonNodeRank NO_RANK       = new NCBITaxonNodeRank( 0, "no rank");


   //**************************************************************************
   // CONSTRUCTORS
   //**************************************************************************

   //--------------------------------------------------------------------------
   private NCBITaxonNodeRank(int inRank, String inName)
   {
      mRank = inRank;
      mName = inName;

      if (sUniqueMap.containsKey(mName))
      {
         throw new RuntimeException("A object already exists with the name '" + mName + "'!");
      }

      sUniqueMap.put(mName, this);
   }

   //**************************************************************************
   // PUBLIC METHODS
   //**************************************************************************

   //--------------------------------------------------------------------------
   public static Collection values()
   {
      return sUniqueMap.values();
   }

   //--------------------------------------------------------------------------
   public static NCBITaxonNodeRank valueOf(String inValue)
   {
      return sUniqueMap.get(inValue);
   }

   //--------------------------------------------------------------------------
   public int compareTo(NCBITaxonNodeRank inObj)
   {
      return inObj != null ? mRank - inObj.mRank : 1;
   }

   //--------------------------------------------------------------------------
   public String name()
   {
      return mName;
   }

   //--------------------------------------------------------------------------
   /**
    The same as name().
    */
   @Override
   public String toString()
   {
      return name();
   }

   //**************************************************************************
   // PRIVATE METHODS
   //**************************************************************************

   //--------------------------------------------------------------------------
   /**
    * This method is called after de-serialization, allowing the object
    * to nominate a replacement object to be used in the output
    * graph instead of this object. We don't want multiple objects of each type
    * to exist in a target VM, so instances replace themselves with
    * local objects.
    */
   private Object readResolve()
   {
      return sUniqueMap.get(mName);
   }
}