/*
 * Created on 17-May-2005
 *
 * TODO To change the template for this generated file go to
 * Window - Preferences - Java - Code Style - Code Templates
 */
package org.vamsas.objects.utils;

import java.io.BufferedWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.util.regex.Pattern;

import org.vamsas.objects.core.AlignmentSequence;
import org.vamsas.objects.core.Sequence;
import org.vamsas.objects.core.SequenceType;

/**
 * @author jimp
 *
 * TODO To change the template for this generated type comment go to
 * Window - Preferences - Java - Code Style - Code Templates
 */
public class Seq {

	public static void write_PirSeq(OutputStream os, SequenceType seq, int wid) throws IOException {
	  	BufferedWriter pir_out = new BufferedWriter(new OutputStreamWriter(os));
		pir_out.write(">P1;"+seq.getName()+"\n");
		int width = (wid<1) ? 80 : wid;
  		for (int j=0,k=seq.getSequence().length(); j<k; j+=width)
  			if (j+width<k)
  				pir_out.write(seq.getSequence().substring(j,j+width)+"\n");
  			else
  				pir_out.write(seq.getSequence().substring(j)+"\n");
		pir_out.flush();
	  }
  
	public static void write_FastaSeq(OutputStream os, SequenceType seq) throws IOException {
	  	BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
		fasta_out.write(">"+seq.getName()+"\n");
		fasta_out.write(seq.getSequence()+"\n");
		fasta_out.flush();
	  }

	public static void write_FastaSeq(OutputStream os, SequenceType seq, int wid) throws IOException {
	  	BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
		fasta_out.write(">"+seq.getName()+"\n");
		int width = (wid<1) ? 80 : wid;
  		for (int j=0,k=seq.getSequence().length(); j<k; j+=width)
  			if (j+width<k)
  				fasta_out.write(seq.getSequence().substring(j,j+width)+"\n");
  			else
  				fasta_out.write(seq.getSequence().substring(j)+"\n");
		fasta_out.flush();
	  }
	/**
   *validate a SequenceType object as an info:iubmb.org/aminoacid SequenceType
   *This version resolves references to Sequence objects from AlignmentSequence
   *TODO: Define info: urn for dictionary string (could also be regex of valid characters!)
   * @param s
	 * @param dict TODO
   * @return true if a valid amino acid sequence object
	 */
	private static boolean valid_aadictionary_string(String s, String dict) {
    if (s==null)
      return false;
    // validate against dictionary
    // TODO generalise to resolve dictionary against info: urn for dictionary type
      Pattern aa_repl = Pattern.compile("[ARNDCQEGHILKMFPSTWYVUX]+", Pattern.CASE_INSENSITIVE);
      String remnants = aa_repl.matcher(s).replaceAll("");
      return !remnants.matches("//S+");
  }

  public static Sequence newSequence(String Name, String Sequence, String Dictionary, int start, int end) {
    //TODO: make hierarchy reflecting the SeqType object.
    Sequence seq= new Sequence();
     seq.setDictionary(Dictionary);
     seq.setName(Name);
     seq.setSequence(Sequence);
     seq.setStart(start);
     if (start<=end) {
       if ((end-start)!=Sequence.length())
         seq.setEnd(start+Sequence.length());
     } else {
       // reverse topology mapping. TODO: VAMSAS: decide if allowed to do start>end on Sequence object
       if ((start-end)!=Sequence.length())
         seq.setEnd(end+Sequence.length());
     }
     return seq;
  }

  public static boolean is_valid_aa_seq(SequenceType s) {
    Sequence q;
    boolean validref=false;
    if (s instanceof Sequence) {
      q=(Sequence) s;
      if (q.getDictionary()!=null 
    
        && q.getDictionary().length()>0
        || !q.getDictionary().equals(SymbolDictionary.STANDARD_AA))
        return false;
      return valid_aadictionary_string(q.getSequence(), SymbolDictionary.STANDARD_AA);
    }
    
    // follow references
    if (s instanceof AlignmentSequence) {
      Object w = (((AlignmentSequence) s).getRefid());
      if (w!=null && w!=s && w instanceof SequenceType)
        return is_valid_aa_seq((SequenceType) w) 
        && valid_aadictionary_string(((AlignmentSequence) s).getSequence(), SymbolDictionary.STANDARD_AA);
    }
    
    return false;
  }
}