/* RawStreamSequence.java
 *
 * created: Mon Jun 14 1999
 *
 * This file is part of Artemis
 *
 * Copyright(C) 1999  Genome Research Limited
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or(at your option) any later version.
 *
 * This program 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 General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/RawStreamSequence.java,v 1.10 2008-12-09 11:48:14 tjc Exp $
 */

package uk.ac.sanger.artemis.io;

import uk.ac.sanger.artemis.sequence.BasePattern;
import uk.ac.sanger.artemis.util.LinePushBackReader;

import java.io.IOException;
import java.io.Writer;
import java.util.Vector;

/**
 *  This is a subclass of StreamSequence containing raw sequence.
 *
 *  @author Kim Rutherford
 *  @version $Id: RawStreamSequence.java,v 1.10 2008-12-09 11:48:14 tjc Exp $
 **/

public class RawStreamSequence extends StreamSequence 
{

  /**
   *  The _character_ positions of the header lines relative to the sequence.
   *  This is in the same order as fasta_header_strings.
   **/
  private Vector<Integer> fasta_header_positions = null;

  /**
   *  This Vector holds the fasta headers (if any) that where seen while
   *  reading the sequence.  This is in the same order as
   *  fasta_header_positions.
   **/
  private Vector<String> fasta_header_strings = null;

  /**
   *  Create a new RawStreamSequence object from a stream containing raw
   *  bases.
   *  @param in_stream The stream to read from.  When the constructor returns
   *    the stream will at the next line after the sequence.
   **/
  public RawStreamSequence(final LinePushBackReader in_stream)
      throws IOException 
  {
    readSequence(in_stream);
  }

  /**
   *  Make a new RawStreamSequence containing the same sequence as the given
   *  Sequence.
   **/
  public RawStreamSequence(final Sequence sequence) 
  {
    this(new String(sequence.getCharSubSequence(1, sequence.length())));

    if(sequence instanceof RawStreamSequence) 
    {
      final RawStreamSequence raw_stream_sequence =
                                      (RawStreamSequence) sequence;
      this.fasta_header_positions =
        (Vector)raw_stream_sequence.fasta_header_positions.clone();
      this.fasta_header_strings =
        (Vector)raw_stream_sequence.fasta_header_strings.clone();
    }
  }

  /**
   *  Make a new RawStreamSequence containing the same sequence as the given
   *  String
   **/
  public RawStreamSequence(final String sequence_string) 
  {
    setFromChar(sequence_string.toCharArray());
  }

  /**
   *  Return a new StreamSequence object that is a copy of this one.
   **/
  public StreamSequence copy() 
  {
    return new RawStreamSequence(this);
  }

  /**
   *  Return the sequence type (RAW_FORMAT for this class).
   **/
  public int getFormatType() 
  {
    return StreamSequenceFactory.RAW_FORMAT;
  }

  /**
   *  Read the header for this sequence(if any).
   **/
  protected void readHeader(final LinePushBackReader in_stream)
      throws IOException 
  {
    // no header for raw sequence
  }

  /**
   *  This method will read raw sequence from the stream removing whitespace
   *  as it goes.  No checks are made on the format of the sequence, apart
   *  from checking that the stream contains only letters.
   **/
  private void readSequence(final LinePushBackReader in_stream)
      throws IOException 
  {

    // initialise these here because this method is called before class
    // variables are initialised
    fasta_header_positions = new Vector<Integer>();
    fasta_header_strings   = new Vector<String>();

    final int buffer_capacity = 5000;

    // we buffer up the sequence bases then assign them to sequence once all
    // bases are read
    setSequencePackingCapacity(buffer_capacity);

    String line;
    int nbase = 0;
    boolean validSequenceCheck = true;
    String hdrLine = null;
    while((line = in_stream.readLine()) !=null) 
    {
      if(line.startsWith(">")) 
      {
        storeHeader(line, nbase);
        validSequenceCheck = true;
        hdrLine = line;
        continue;
      }

      line = line.trim().toLowerCase();
      
      if(validSequenceCheck)
      {
        if(BasePattern.patternType(line) == BasePattern.ILLEGAL_PATTERN)
        {
          // ignore non-nucleotide sequence
          if(hdrLine != null)
          {
            System.err.println(
                "Warning:: ignore non-nucleotide sequence found in "+hdrLine.substring(1));
            fasta_header_strings.remove(hdrLine.substring(1));
            fasta_header_positions.remove(new Integer(nbase));
          }

          while((line = in_stream.readLine()) !=null) 
          {
            if(line.startsWith(">")) 
            {
              storeHeader(line, nbase);
              hdrLine = line;
              break;
            }
          }
          continue;
        }
        validSequenceCheck = false;
      }

      if(line.length() > 0)
        appendChar(line.toCharArray());
      nbase += line.length();
      hdrLine = null;
    }

    setCounts();
  }
  
  private void storeHeader(String line, int nbase)
  {
    fasta_header_strings.addElement(line.substring(1));
    fasta_header_positions.addElement(new Integer(nbase));
  }

  /**
   *  Write this Sequence to the given stream.
   *  @param writer The stream to write to.
   **/
  public void writeToStream(final Writer writer)
      throws IOException 
  {
    final StringBuffer line_buffer = new StringBuffer(90);
    final String sequence = new String(getCharSequence());

    final int SEQUENCE_LINE_BASE_COUNT = 60;

    int header_counter  = 0;
    final int [] header_positions = getFastaHeaderPositions();

    int [] header_positions_sorted = new int[header_positions.length];
    System.arraycopy(header_positions, 0,
                     header_positions_sorted, 0,
                     header_positions.length);
    java.util.Arrays.sort(header_positions_sorted);

    final String [] header_strings = getFastaHeaderStrings();

    int i = 0;

    while(i < sequence.length()) 
    {
      if(header_counter < header_positions.length) 
      {
        if(i == header_positions_sorted[header_counter]) 
        {
          // dump a header
          String header = "";
          for(int j = 0; j<header_positions.length; j++)
          {
            if(header_positions_sorted[header_counter] ==
               header_positions[j])
            {
              header = header_strings[j];
              continue;
            }
          }

          writer.write(">" + header + "\n");
          ++header_counter;
        }
      }

      // get the bases in chunks of at most 60

      int this_line_length;

      if(sequence.length() - i < SEQUENCE_LINE_BASE_COUNT) 
        this_line_length = sequence.length() - i;
      else 
        this_line_length = SEQUENCE_LINE_BASE_COUNT;

      if(header_counter < header_positions.length) 
      {
        if(i + this_line_length > header_positions_sorted[header_counter]) 
          this_line_length = header_positions_sorted[header_counter] - i;
      }

      line_buffer.setLength(0);
      line_buffer.append(sequence.substring(i, i + this_line_length));
      line_buffer.append("\n");

      writer.write(line_buffer.toString());

      if((i / SEQUENCE_LINE_BASE_COUNT) % 100 == 0) 
        Thread.yield();

      if(header_counter < header_positions.length) 
      {
        if(header_positions_sorted[header_counter] < i + SEQUENCE_LINE_BASE_COUNT) 
        {
          i = header_positions_sorted[header_counter];
          continue;
        }
      }

      i += SEQUENCE_LINE_BASE_COUNT;
    }
  }

  /**
  *
  * Reset the header positions. This is used when contigs a reordered
  * by a SequenceChangeEvent.CONTIG_REORDER event.
  *
  */
  public void setFastaHeaderPosition(final int old_position[], 
                                     final int new_position[])
  {
    if(old_position == new_position)
      return;

    if(fasta_header_positions != null && fasta_header_positions.size() > 0)
    {
      Vector<Integer> seen = new Vector<Integer>(fasta_header_positions.size());
      for(int i = 0 ; i < fasta_header_positions.size(); ++i)
      {
        int current_position = ((Integer)fasta_header_positions.elementAt(i)).intValue();
        
        for(int j = 0; j < old_position.length; ++j)
        {
          if(current_position == old_position[j] &&
             !seen.contains(new Integer(j)))
          {
            fasta_header_positions.set(i, new Integer(new_position[j]));
//          System.out.println("CHANGED current_position="+current_position+
//                             "  old_position[i]="+old_position[i]+
//                             "  new_position[i]="+new_position[i]);
            seen.add(new Integer(j));
            break;
          }
        }
      }
    }
  }
  
  /**
   * Set the fasta header positions when the complete sequence is reverse complemented.
   * @param contigRanges
   */
  public void setFastaHeaderPositionsOnReverseComplement(final RangeVector contigRanges)
  {
    if(fasta_header_positions != null && fasta_header_positions.size() > 0)
    {
      int length = length();

      for(int i = 0 ; i < fasta_header_positions.size(); ++i)
      {
        int current_position = ((Integer)fasta_header_positions.elementAt(i)).intValue();
        for(int j=0; j<contigRanges.size(); j++)
        {
          Range range = (Range) contigRanges.get(j);
          int start = range.getStart()-1;
          if(start == current_position)
            fasta_header_positions.set(i, new Integer(length-range.getEnd()));
        }
      }
    }
  }


  /**
   *  Return an array containing the character positions of the fasta header
   *  lines.  The positions are returned in the same order as the strings from
   *  getFastaHeaderStrings().
   **/
  int [] getFastaHeaderPositions() 
  {
    if(fasta_header_positions != null && fasta_header_positions.size() > 0) 
    {
      final int [] return_value = new int [fasta_header_positions.size()];

      for(int i = 0 ; i < return_value.length ; ++i) 
      {
        return_value[i] =
                ((Integer)fasta_header_positions.elementAt(i)).intValue();
      }

      return return_value;
    } 
    else 
      return new int [0];
  }

  /**
   *  Return an array containing the fasta headers for the input sequence.
   *  The positions are returned in the same order as the strings from
   *  getFastaHeaderPositions().
   **/
  String [] getFastaHeaderStrings() 
  {
    if(fasta_header_strings != null && fasta_header_strings.size() > 0) 
    {
      final String [] return_value = new String [fasta_header_strings.size()];

      for(int i = 0 ; i < return_value.length ; ++i) 
        return_value[i] =(String)fasta_header_strings.elementAt(i);

      return return_value;
    } 
    else 
      return new String [0];
  }

}