package com.hfg.bio.seq;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.Set;

import com.hfg.bio.DbXref;
import com.hfg.bio.seq.format.SeqCitation;
import com.hfg.bio.seq.format.feature.FeatureKey;
import com.hfg.bio.seq.format.feature.SeqFeature;
import com.hfg.bio.seq.format.feature.qualifier.MolType;
import com.hfg.bio.taxonomy.ncbi.NCBITaxon;
import com.hfg.bio.taxonomy.SeqRepositoryDivision;
import com.hfg.util.collection.OrderedSet;
import com.hfg.xml.XMLNode;

//------------------------------------------------------------------------------
/**
 Exetended biological protein, DNA, or RNA sequence with support for features,
 citations, db xrefs, etc.
 <div>
  @author J. Alex Taylor, hairyfatguy.com
 </div>
 */
//------------------------------------------------------------------------------
// 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
// jataylor@hairyfatguy.com
//------------------------------------------------------------------------------

public abstract class BioSequencePlusImpl extends BioSequenceImpl implements BioSequencePlus
{

   private SeqRepositoryDivision mSeqRepositoryDivision;
   private MolType               mMolType;
   private SeqTopology           mSeqTopology;
   private List<SeqFeature>      mFeatures;
   private List<SeqCitation>     mCitations;
   private List<DbXref>          mDbXRefs;
   private Set<String>           mKeywords;
   private Date                  mRevisionDate;
   private Clone                 mClone;
   private NCBITaxon             mNCBITaxon;
   private List<Throwable>       mParseExceptions;

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

   //--------------------------------------------------------------------------
   public BioSequencePlusImpl()
   {

   }

   //--------------------------------------------------------------------------
   public BioSequencePlusImpl(XMLNode inXML)
   {
      super(inXML);

      // TODO: Add support for features, citations, etc.
   }

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

   //--------------------------------------------------------------------------
   public XMLNode toXMLNode()
   {
      XMLNode node = super.toXMLNode();

      // TODO: Add support for features, citations, etc.

      return node;
   }

   //--------------------------------------------------------------------------
   @Override
   public BioSequencePlusImpl clone()
   {
      BioSequencePlusImpl theClone = (BioSequencePlusImpl) super.clone();


      if (mFeatures != null)
      {
         // For right now this is a shallow clone of the features
         theClone.mFeatures = new ArrayList<>(mFeatures);
      }

      if (mCitations != null)
      {
         // For right now this is a shallow clone of the citations
         theClone.mCitations = new ArrayList<>(mCitations);
      }

      if (mDbXRefs != null)
      {
         // For right now this is a shallow clone of the dbxrefs
         theClone.mDbXRefs = new ArrayList<>(mDbXRefs);
      }

      return theClone;
   }


   //--------------------------------------------------------------------------
   public BioSequenceImpl addFeature(SeqFeature inValue)
   {
      if (null == mFeatures)
      {
         mFeatures = new ArrayList<>(25);
      }

      mFeatures.add(inValue);

      return this;
   }

   //--------------------------------------------------------------------------
   public List<SeqFeature> getFeatures()
   {
      return mFeatures;
   }

   //--------------------------------------------------------------------------
   public List<SeqFeature> getFeatures(FeatureKey inFeatureKey)
   {
      List<SeqFeature> requestedFeatures = new ArrayList<SeqFeature>();
      if (mFeatures != null)
      {
         for (SeqFeature feature : mFeatures)
         {
            if (feature.name().equals(inFeatureKey))
            {
               requestedFeatures.add(feature);
            }
         }
      }

      return requestedFeatures;
   }

   //--------------------------------------------------------------------------
   public void clearFeatures()
   {
      if (mFeatures != null)
      {
         mFeatures.clear();
      }
   }


   //--------------------------------------------------------------------------
   public BioSequenceImpl setReferences(List<SeqCitation> inValues)
   {
      mCitations = inValues != null ? new ArrayList<>(inValues) : null;

      return this;
   }

   //--------------------------------------------------------------------------
   public BioSequenceImpl addReference(SeqCitation inValue)
   {
      if (null == mCitations)
      {
         mCitations = new ArrayList<>(5);
      }

      mCitations.add(inValue);

      return this;
   }

   //--------------------------------------------------------------------------
   public List<SeqCitation> getReferences()
   {
      return mCitations;
   }

   //--------------------------------------------------------------------------
   public void clearReferences()
   {
      if (mCitations != null)
      {
         mCitations.clear();
      }
   }


   //--------------------------------------------------------------------------
   public BioSequenceImpl addDbXref(DbXref inValue)
   {
      if (null == mDbXRefs)
      {
         mDbXRefs = new ArrayList<>(5);
      }

      mDbXRefs.add(inValue);

      return this;
   }

   //--------------------------------------------------------------------------
   public List<DbXref> getDbXrefs()
   {
      return mDbXRefs;
   }

   //--------------------------------------------------------------------------
   public void clearDbXrefs()
   {
      if (mDbXRefs != null)
      {
         mDbXRefs.clear();
      }
   }


   //--------------------------------------------------------------------------
   public BioSequenceImpl addKeyword(String inValue)
   {
      if (null == mKeywords)
      {
         mKeywords = new OrderedSet<>(10);
      }

      mKeywords.add(inValue);

      return this;
   }

   //--------------------------------------------------------------------------
   public BioSequenceImpl addKeywords(Collection<String> inValues)
   {
      if (inValues != null)
      {
         if (null == mKeywords)
         {
            mKeywords = new OrderedSet<>(10);
         }

         mKeywords.addAll(inValues);
      }

      return this;
   }

   //--------------------------------------------------------------------------
   public BioSequenceImpl addKeywords(String[] inValues)
   {
      if (inValues != null)
      {
         if (null == mKeywords)
         {
            mKeywords = new OrderedSet<>(10);
         }

         mKeywords.addAll(Arrays.asList(inValues));
      }

      return this;
   }

   //--------------------------------------------------------------------------
   public Set<String> getKeywords()
   {
      return mKeywords;
   }

   //--------------------------------------------------------------------------
   public void clearKeywords()
   {
      if (mKeywords != null)
      {
         mKeywords.clear();
      }
   }


   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setSeqRepositoryDivision(SeqRepositoryDivision inValue)
   {
      mSeqRepositoryDivision = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public SeqRepositoryDivision getSeqRepositoryDivision()
   {
      return mSeqRepositoryDivision;
   }


   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setMolType(MolType inValue)
   {
      mMolType = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public MolType getMolType()
   {
      return mMolType;
   }


   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setSeqTopology(SeqTopology inValue)
   {
      mSeqTopology = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public SeqTopology getSeqTopology()
   {
      return mSeqTopology;
   }


   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setRevisionDate(Date inValue)
   {
      mRevisionDate = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Date getRevisionDate()
   {
      return mRevisionDate;
   }


   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setClone(Clone inValue)
   {
      mClone = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Clone getClone()
   {
      return mClone;
   }


   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setNCBITaxon(NCBITaxon inValue)
   {
      mNCBITaxon = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public NCBITaxon getNCBITaxon()
   {
      return mNCBITaxon;
   }



   //--------------------------------------------------------------------------
   public void addParseException(Throwable inException)
   {
      if (null == mParseExceptions)
      {
         mParseExceptions = new ArrayList<>(4);
      }

      mParseExceptions.add(inException);
   }

   //--------------------------------------------------------------------------
   public void clearParseExceptions()
   {
      mParseExceptions = null;
   }

   //--------------------------------------------------------------------------
   public List<Throwable> getParseExceptions()
   {
      return mParseExceptions;
   }

}