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

import com.hfg.bio.seq.BioSequence;
import com.hfg.bio.seq.BioSequenceFactory;
import com.hfg.util.StringUtil;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.StringReader;
import java.util.List;


//------------------------------------------------------------------------------
/**
 Base class for readable sequence formats.
 
   @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 ReadableSeqFormatBase implements ReadableSeqFormat
{
   private BioSequenceFactory mSeqFactory;

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

   //---------------------------------------------------------------------------
   public ReadableSeqFormatBase(BioSequenceFactory inSeqFactory)
   {
      mSeqFactory = inSeqFactory;
   }

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

   //---------------------------------------------------------------------------
   public BioSequenceFactory getBioSequenceFactory()
   {
      return mSeqFactory;
   }


   //---------------------------------------------------------------------------
   public List read(File inFile)
         throws SeqIOException
   {
      try
      {
         BufferedSeqReader reader = new BufferedSeqReader(new BufferedReader(new FileReader(inFile)), this);

         return reader.readAll();
      }
      catch (SeqIOException e)
      {
         throw e;
      }
      catch (Exception e)
      {
         throw new SeqIOException("Problem reading sequences from " + StringUtil.singleQuote(inFile.getPath()) + "!", e);
      }
   }

   //---------------------------------------------------------------------------
   public List read(BufferedReader inReader)
         throws SeqIOException
   {
      try
      {
         BufferedSeqReader reader = new BufferedSeqReader(inReader, this);

         return reader.readAll();
      }
      catch (SeqIOException e)
      {
         throw e;
      }
      catch (Exception e)
      {
         throw new SeqIOException("Problem reading sequences!", e);
      }
   }

   //---------------------------------------------------------------------------
   public T readRecord(CharSequence inString)
         throws SeqIOException
   {
      T seq = null;

      BufferedReader reader = null;
      try
      {
         reader = new BufferedReader(new StringReader(inString.toString()));
         seq = readRecord(reader);
      }
      finally
      {
         if (reader != null)
         {
            try
            {
               reader.close();
            }
            catch (IOException e)
            {
               throw new SeqIOException(e);
            }
         }
      }

      return seq;
   }

}