com.hfg.bio.seq.format.feature.SeqFeatureImpl Maven / Gradle / Ivy

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com.hfg xml, html, svg, and bioinformatics utility library
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package com.hfg.bio.seq.format.feature;

import java.util.ArrayList;
import java.util.List;

import com.hfg.util.CompareUtil;
import com.hfg.util.collection.CollectionUtil;

//------------------------------------------------------------------------------
/**
 Basic implementation of SeqFeature interface.
 
  @author J. Alex Taylor, hairyfatguy.com
 
 */
//------------------------------------------------------------------------------
// com.hfg 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 abstract class SeqFeatureImpl implements SeqFeature, Comparable
{
   private FeatureKey             mName;
   private SeqFeatureLocation     mLocation;
   private List mQualifiers;

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

   //---------------------------------------------------------------------------
   public SeqFeatureImpl(FeatureKey inName, SeqFeatureLocation inLocation)
   {
      mName = inName;
      mLocation = inLocation;
   }

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

   //---------------------------------------------------------------------------
   @Override
   public String toString()
   {
      return name().name();
   }

   //---------------------------------------------------------------------------
   @Override
   public boolean equals(Object inObj2)
   {
      return (0 == compareTo(inObj2));
   }

   //---------------------------------------------------------------------------
   @Override
   public int hashCode()
   {
      return (getLocation() != null ? getLocation().hashCode() : 0);
   }

   //---------------------------------------------------------------------------
   @Override
   public int compareTo(Object inObj2)
   {
      int result = -1;

      if (inObj2 instanceof SeqFeature)
      {
         result = CompareUtil.compare(getLocation(), ((SeqFeature) inObj2).getLocation());
      }

      return result;
   }

   //---------------------------------------------------------------------------
   @Override
   public FeatureKey name()
   {
      return mName;
   }

   //---------------------------------------------------------------------------
   public SeqFeatureLocation getLocation()
   {
      return mLocation;
   }

   //---------------------------------------------------------------------------
   public SeqFeature addQualifier(FeatureQualifier inValue)
   {
      if (null == mQualifiers)
      {
         mQualifiers = new ArrayList(25);
      }

      mQualifiers.add(inValue);

      return this;
   }

   //---------------------------------------------------------------------------
   public List getQualifiers()
   {
      return mQualifiers;
   }

   //---------------------------------------------------------------------------
   public List getQualifiers(String inQualifierName)
   {
      List qualifiers = null;

      if (CollectionUtil.hasValues(mQualifiers))
      {
         for (FeatureQualifier qualifier : mQualifiers)
         {
            if (qualifier.name().equals(inQualifierName))
            {
               if (null == qualifiers)
               {
                  qualifiers = new ArrayList(25);
               }

               qualifiers.add(qualifier);
            }
         }
      }

      return qualifiers;
   }

}