001package com.hfg.bio.seq.alignment.assembler;
002
003
004//------------------------------------------------------------------------------
005
006import java.util.Collection;
007
008import com.hfg.bio.seq.NucleicAcid;
009import com.hfg.bio.seq.format.abi.ABIF;
010
011/**
012 * Tool for assembling reads into contigs.
013 *
014 * @author J. Alex Taylor, hairyfatguy.com
015 */
016//------------------------------------------------------------------------------
017// com.hfg XML/HTML Coding Library
018//
019// This library is free software; you can redistribute it and/or
020// modify it under the terms of the GNU Lesser General Public
021// License as published by the Free Software Foundation; either
022// version 2.1 of the License, or (at your option) any later version.
023//
024// This library is distributed in the hope that it will be useful,
025// but WITHOUT ANY WARRANTY; without even the implied warranty of
026// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
027// Lesser General Public License for more details.
028//
029// You should have received a copy of the GNU Lesser General Public
030// License along with this library; if not, write to the Free Software
031// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
032//
033// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
034// jataylor@hairyfatguy.com
035//------------------------------------------------------------------------------
036
037public class ContigAssembler
038{
039
040   //###########################################################################
041   // CONSTRUCTORS
042   //###########################################################################
043
044   //--------------------------------------------------------------------------
045   public ContigAssembler()
046   {
047   }
048
049   //###########################################################################
050   // PUBLIC METHODS
051   //###########################################################################
052
053   //--------------------------------------------------------------------------
054   public ContigAssemblerResults assemble(Collection<NucleicAcid> inReads)
055   {
056      ContigAssemblerResults results = new ContigAssemblerResults();
057
058      
059
060      return results;
061   }
062
063}