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

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.CollectionUtil;

//------------------------------------------------------------------------------
/**
 Interface for an exetended biological protein, DNA, or RNA sequence with support for features,
 citations, db xrefs, etc.
 
  @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 interface BioSequencePlus extends BioSequence
{
   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setSeqRepositoryDivision(SeqRepositoryDivision inValue);

   //--------------------------------------------------------------------------
   public SeqRepositoryDivision getSeqRepositoryDivision();


   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setMolType(MolType inValue);

   //--------------------------------------------------------------------------
   public MolType getMolType();


   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setSeqTopology(SeqTopology inValue);

   //--------------------------------------------------------------------------
   public SeqTopology getSeqTopology();


   //--------------------------------------------------------------------------
   public BioSequence addFeature(SeqFeature inValue);

   //--------------------------------------------------------------------------
   public List getFeatures();

   //--------------------------------------------------------------------------
   public List getFeatures(FeatureKey inFeatureKey);

   //--------------------------------------------------------------------------
   public void clearFeatures();


   //--------------------------------------------------------------------------
   public BioSequence addReference(SeqCitation inValue);

   //--------------------------------------------------------------------------
   public List getReferences();

   //--------------------------------------------------------------------------
   public void clearReferences();


   //--------------------------------------------------------------------------
   public BioSequence addDbXref(DbXref inValue);

   //--------------------------------------------------------------------------
   public List getDbXrefs();

   //--------------------------------------------------------------------------
   public void clearDbXrefs();


   //--------------------------------------------------------------------------
   public BioSequence addKeyword(String inValue);

   //--------------------------------------------------------------------------
   public BioSequence addKeywords(Collection inValues);

   //--------------------------------------------------------------------------
   public BioSequence addKeywords(String[] inValues);

   //--------------------------------------------------------------------------
   public Set getKeywords();

   //--------------------------------------------------------------------------
   public void clearKeywords();


   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setRevisionDate(Date inValue);

   //--------------------------------------------------------------------------
   public Date getRevisionDate();


   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setClone(Clone inValue);

   //--------------------------------------------------------------------------
   public Clone getClone();


   //--------------------------------------------------------------------------
   public BioSequencePlusImpl setNCBITaxon(NCBITaxon inValue);

   //--------------------------------------------------------------------------
   public NCBITaxon getNCBITaxon();


   //--------------------------------------------------------------------------
   public default boolean hadParseExceptions()
   {
      return CollectionUtil.hasValues(getParseExceptions());
   }

   //--------------------------------------------------------------------------
   public void addParseException(Throwable inException);

   //--------------------------------------------------------------------------
   public List getParseExceptions();

   //--------------------------------------------------------------------------
   public void clearParseExceptions();

}