package jalview.io;

import jalview.datamodel.*;
import jalview.analysis.*;

import java.io.*;
import java.util.*;

public class FastaFile extends AlignFile {

  public FastaFile()
  {}

  public FastaFile(String inStr) {
    super(inStr);
  }

  public FastaFile(String inFile, String type) throws IOException {
    super(inFile,type);
  }

  public void parse() throws IOException
  {

    String       id    = "";
    StringBuffer seq   = new StringBuffer();
    int          count = 0;
    boolean      flag  = false;

    int          sstart = 0;
    int          send   = 0;

    String line;

      while ((line = nextLine()) != null) {

	if (line.length() > 0) {

	  // Do we have an id line?

	  if (line.substring(0,1).equals(">")) {

	    if (count != 0) {
	      if (sstart != 0) {
		seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),sstart,send));
	      } else {
		seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),1,seq.length()));
	      }
	    }

	    count++;

	    StringTokenizer str = new StringTokenizer(line," ");

	    id = str.nextToken();
	    id = id.substring(1);

	    if (id.indexOf("/") > 0 ) {

	      StringTokenizer st = new StringTokenizer(id,"/");
	      if (st.countTokens() == 2) {
		id = st.nextToken();
		String tmp = st.nextToken();

		st = new StringTokenizer(tmp,"-");

		if (st.countTokens() == 2) {
		  sstart = Integer.valueOf(st.nextToken()).intValue();
		  send   = Integer.valueOf(st.nextToken()).intValue();
		}
	      }
	    }

	    seq = new StringBuffer();

	  } else {
	    seq = seq.append(line);
	  }
	}
      }
      if (count > 0) {

        if(!isValidProteinSequence(seq.toString().toUpperCase()))
          throw new IOException("Invalid protein sequence");

	if (sstart != 0) {
	  seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),sstart,send));
	} else {
	  seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),1,seq.length()));
	}
      }

  }

  public static String print(SequenceI[] s) {
    return print(s,72);
  }
  public static String print(SequenceI[] s, int len) {
    return print(s,len,true);
  }
  public static String print(SequenceI[] s, int len,boolean gaps) {
    StringBuffer out = new StringBuffer();
    int i = 0;
    while (i < s.length && s[i] != null) {
      String seq = "";
      if (gaps) {
        seq = s[i].getSequence();
      } else {
        seq = AlignSeq.extractGaps("-. ",s[i].getSequence());
      }

      out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd() + "\n");

      int nochunks = seq.length() / len + 1;

      for (int j = 0; j < nochunks; j++) {
        int start = j*len;
        int end = start + len;

        if (end < seq.length()) {
          out.append(seq.substring(start,end) + "\n");
        } else if (start < seq.length()) {
          out.append(seq.substring(start) + "\n");
        }
      }
      i++;
    }
    return out.toString();
  }

  public String print() {
    return print(getSeqsAsArray());
  }
}