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com.hfg xml, html, svg, and bioinformatics utility library
There is a newer version: 20240423
package com.hfg.bio.seq;


import java.util.regex.Pattern;

import com.hfg.bio.HfgBioXML;
import com.hfg.bio.Strand;
import com.hfg.bio.seq.format.feature.genbank.GenBankFeatureLocation;
import com.hfg.bio.taxonomy.ncbi.NCBITaxon;
import com.hfg.util.CompareUtil;
import com.hfg.util.StringUtil;
import com.hfg.xml.XMLTag;

//------------------------------------------------------------------------------
/**
 Genomic location.
 
 @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 GenomicLocation extends GenBankFeatureLocation
{
   private String mAssembly;
   private String mBuild;
   private NCBITaxon mTaxon;
   private String mChromosome;
   private Integer mChromosomeNum;
   private String mContig;
   private Strand mStrand;

   private static final Pattern NUM_PATTERN = Pattern.compile("\\d+");

   //###########################################################################
   // CONSTRUCTORS
   //###########################################################################

   //--------------------------------------------------------------------------
   public GenomicLocation()
   {
      super(null);
   }

   //--------------------------------------------------------------------------
   public GenomicLocation(String inLocationString)
   {
      super(inLocationString);
   }

   //---------------------------------------------------------------------------
   public GenomicLocation(XMLTag inXMLTag)
   {
      this();

      inXMLTag.verifyTagName(HfgBioXML.GENOMIC_LOC_TAG);

      setAssembly(inXMLTag.getAttributeValue(HfgBioXML.ASSEMBLY_ATT));
      setBuild(inXMLTag.getAttributeValue(HfgBioXML.BUILD_ATT));

      if (inXMLTag.hasAttribute(HfgBioXML.CHROMOSOME_ATT))
      {
         setChromosome(inXMLTag.getAttributeValue(HfgBioXML.CHROMOSOME_ATT));
      }

      if (inXMLTag.hasAttribute(HfgBioXML.CONTIG_ATT))
      {
         setContig(inXMLTag.getAttributeValue(HfgBioXML.CONTIG_ATT));
      }

      if (inXMLTag.hasAttribute(HfgBioXML.CONTIG_LENGTH_ATT))
      {
         setSeqLength(Integer.parseInt(inXMLTag.getAttributeValue(HfgBioXML.CONTIG_LENGTH_ATT)));
      }

      if (inXMLTag.hasAttribute(HfgBioXML.TAXON_ATT))
      {
         setTaxon(NCBITaxon.getByTaxonId(Integer.parseInt(inXMLTag.getAttributeValue(HfgBioXML.TAXON_ATT))));
      }

      if (inXMLTag.hasAttribute(HfgBioXML.STRAND_ATT))
      {
         setStrand(Strand.valueOf(inXMLTag.getAttributeValue(HfgBioXML.STRAND_ATT)));
      }

      append(inXMLTag.getUnescapedContent());
   }

   //###########################################################################
   // PUBLIC METHODS
   //###########################################################################

   //--------------------------------------------------------------------------
   @Override
   public GenomicLocation clone()
   {
      GenomicLocation copy = (GenomicLocation) super.clone();

      return copy;
   }

   //--------------------------------------------------------------------------
   public XMLTag toXMLTag()
   {
      XMLTag tag = new XMLTag(HfgBioXML.GENOMIC_LOC_TAG);

      if (StringUtil.isSet(getAssembly()))
      {
         tag.setAttribute(HfgBioXML.ASSEMBLY_ATT, getAssembly());
      }

      if (StringUtil.isSet(getBuild()))
      {
         tag.setAttribute(HfgBioXML.BUILD_ATT, getBuild());
      }

      if (getTaxon() != null)
      {
         tag.setAttribute(HfgBioXML.TAXON_ATT, getTaxon().getTaxonId());
      }

      if (getChromosome() != null)
      {
         tag.setAttribute(HfgBioXML.CHROMOSOME_ATT, getChromosome());
      }

      if (getContig() != null)
      {
         tag.setAttribute(HfgBioXML.CONTIG_ATT, getContig());
      }

      if (getSeqLength() != null)
      {
         tag.setAttribute(HfgBioXML.CONTIG_LENGTH_ATT, getSeqLength());
      }

      if (getStrand() != null)
      {
         tag.setAttribute(HfgBioXML.STRAND_ATT, getStrand());
      }

      tag.setContent(toString());

      return tag;
   }


   //--------------------------------------------------------------------------
   public GenomicLocation setAssembly(String inValue)
   {
      mAssembly = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public String getAssembly()
   {
      return mAssembly;
   }


   //--------------------------------------------------------------------------
   public GenomicLocation setBuild(String inValue)
   {
      mBuild = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public String getBuild()
   {
      return mBuild;
   }


   //--------------------------------------------------------------------------
   public GenomicLocation setChromosome(String inValue)
   {
      mChromosome = inValue;

      if (inValue != null
          && NUM_PATTERN.matcher(inValue).matches())
      {
         mChromosomeNum = Integer.parseInt(inValue);
      }

      return this;
   }

   //--------------------------------------------------------------------------
   public String getChromosome()
   {
      return mChromosome;
   }


   //--------------------------------------------------------------------------
   public GenomicLocation setContig(String inValue)
   {
      mContig = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public String getContig()
   {
      return mContig;
   }

   //--------------------------------------------------------------------------
   @Override
   public GenomicLocation setSeqLength(Integer inValue)
   {
      return (GenomicLocation) super.setSeqLength(inValue);
   }


   //--------------------------------------------------------------------------
   public GenomicLocation setTaxon(NCBITaxon inValue)
   {
      mTaxon = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public NCBITaxon getTaxon()
   {
      return mTaxon;
   }


   //--------------------------------------------------------------------------
   public GenomicLocation setStrand(Strand inValue)
   {
      mStrand = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Strand getStrand()
   {
      return mStrand;
   }


   //--------------------------------------------------------------------------
   public int compareTo(GenomicLocation inObj2)
   {
      int result = -1;
      if (inObj2 != null)
      {
         if (mChromosomeNum != null
             && inObj2.mChromosomeNum != null)
         {
            result = CompareUtil.compare(mChromosomeNum, inObj2.mChromosomeNum);
         }
         else
         {
            result = CompareUtil.compare(getChromosome(), inObj2.getChromosome());
            // Handle situation where one chromosome is called 'Unknown' and the other is called 'Un'
            if (result != 0
                && getChromosome() != null
                && inObj2.getChromosome() != null
                && ((getChromosome().equalsIgnoreCase("Unknown") || getChromosome().equalsIgnoreCase("Un"))
                    && (inObj2.getChromosome().equalsIgnoreCase("Unknown") || inObj2.getChromosome().equalsIgnoreCase("Un"))))
            {
               result = 0;
            }
         }


         if (0 == result)
         {
            result = CompareUtil.compare(getContig(), inObj2.getContig());
         }

         if (0 == result)
         {
            result = super.compareTo(inObj2);
         }
      }

      return result;
   }
}