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package com.hfg.bio.seq.format;

import com.hfg.bio.seq.BioSequenceFactory;
import com.hfg.bio.seq.NucleicAcid;
import com.hfg.util.BooleanUtil;
import com.hfg.util.StringUtil;

//------------------------------------------------------------------------------
/**
 FASTQ sequence format from Illumina. Fields are parsed from the header line into
 attributes on the sequence object.
 
 See Illumina's file format description.
 

 
 @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 class IlluminaFASTQ extends FASTQ
{
   //###########################################################################
   // CONSTRUCTORS
   //###########################################################################

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

   //---------------------------------------------------------------------------
   public IlluminaFASTQ(BioSequenceFactory inSeqFactory)
   {
      super(inSeqFactory);
   }

   //###########################################################################
   // PROTECTED METHODS
   //###########################################################################

   //---------------------------------------------------------------------------
   // See: https://support.illumina.com/help/BaseSpace_OLH_009008/Content/Source/Informatics/BS/FileFormat_FASTQ-files_swBS.htm
   // Header line format:
   // @::::::: :::
   //
   // Ex: @HWI-M01141:63:A4NDL:1:1101:16668:1377 1:N:0:TATAGCGAGACACCGT
   //     instrument = HWI-M01141
   //     run number = 63
   //     flowcell ID = A4NDL
   //     lane = 1
   //     tile = 1101
   //     x-pos = 16668
   //     y-pos = 1377
   //     UMI (optional) =
   //     read = 1
   //     is filtered = N
   //     control number = 0
   //     index = TATAGCGAGACACCGT
   protected void parseHeaderLine(String inLine, T inSeq)
   {
      // Let the super class break the header line into id and description
      super.parseHeaderLine(inLine, inSeq);

      // Extract Illumina fields from the id
      String[] fields = inSeq.getID().split(":");
      if (fields.length < 7
          || fields.length > 8)
      {
         throw new SeqFormatException("Unexpected number of fields in the header id " + StringUtil.singleQuote(inSeq.getID()) + "!");
      }

      inSeq.setAttribute("instrument", fields[0]);
      inSeq.setAttribute("run number", Integer.parseInt(fields[1]));
      inSeq.setAttribute("flowcell ID", fields[2]);
      inSeq.setAttribute("lane", Integer.parseInt(fields[3]));
      inSeq.setAttribute("tile", Integer.parseInt(fields[4]));
      inSeq.setAttribute("x-pos", Integer.parseInt(fields[5]));
      inSeq.setAttribute("y-pos", Integer.parseInt(fields[6]));
      if (8 == fields.length)
      {
         inSeq.setAttribute("UMI", fields[7]);
      }

      // Extract Illumina fields from the description
      fields = inSeq.getDescription().split(":");
      if (fields.length != 4)
      {
         throw new SeqFormatException("Unexpected number of fields in the header description " + StringUtil.singleQuote(inSeq.getDescription()) + "!");
      }

      inSeq.setAttribute("read", Integer.parseInt(fields[0]));
      inSeq.setAttribute("is filtered", BooleanUtil.valueOf(fields[1]));
      inSeq.setAttribute("control number", Integer.parseInt(fields[2]));
      inSeq.setAttribute("index", fields[3]);

   }

}