/*
 * 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.BufferedOutputStream;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Hashtable;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.regex.Pattern;

import vamsas.objects.simple.Alignment;
import vamsas.objects.simple.Sequence;
import vamsas.objects.simple.SequenceSet;

/**
 * @author jimp
 *
 * TODO To change the template for this generated type comment go to
 * Window - Preferences - Java - Code Style - Code Templates
 */
public class SeqAln extends vamsas.objects.simple.Alignment {
	
	public static Sequence[] ReadClustalFile(InputStream os) throws Exception {

		Pattern nonGap = Pattern.compile("[A-Z*0-9]", Pattern.CASE_INSENSITIVE);	
	  	String gapchars = "";
	  	char gapchar='-';
	
		int     i    = 0;
	    boolean flag = false;
	    
	    Vector    headers = new Vector();
	    Hashtable seqhash = new Hashtable();
	    Sequence[] seqs=null;
	    int noSeqs = 0;
	    String line;

	    try {
	    	BufferedReader ins = new BufferedReader(new InputStreamReader(os));
	    	while ((line = ins.readLine()) != null) {
	    		if (line.indexOf(" ") != 0) {
	    			java.util.StringTokenizer str = new StringTokenizer(line," ");
	    			String id = "";
	    			
	    			if (str.hasMoreTokens()) {
	    				id = str.nextToken();
	    				if (id.equals("CLUSTAL")) {
	    					flag = true;
	    				} else {
	    					if (flag) {
	    						StringBuffer tempseq;
	    						if (seqhash.containsKey(id)) {
	    							tempseq = (StringBuffer)seqhash.get(id);
	    						} else {
	    							tempseq = new StringBuffer();
	    							seqhash.put(id,tempseq);
	    						}
	    						
	    						if (!(headers.contains(id))) {
	    							headers.addElement(id);
	    						}
	    						
	    						tempseq.append(str.nextToken());
	    					}
	    				}
	    			}
	    		}
	    	}
	    	
	    } catch (IOException e) {
	    	throw(new Exception("Exception parsing clustal file ",e));
	    }
	    
	    if (flag) {
	    	noSeqs = headers.size();
	    	
	    	//Add sequences to the hash
	    	seqs = new Sequence[headers.size()];
	      for (i = 0; i < headers.size(); i++ ) {
	        if ( seqhash.get(headers.elementAt(i)) != null) {
	        	
	        	Sequence newSeq = new Sequence(headers.elementAt(i).toString(),
	                                         seqhash.get(headers.elementAt(i).toString()).toString());
	        	
	        	seqs[i]=newSeq;

	        } else {
	          throw(new Exception("Bizarreness! Can't find sequence for " + headers.elementAt(i)));
	        }
	      }
	    }
	    return seqs;
	  }

	  public static void WriteClustalWAlignment(java.io.OutputStream os, Alignment seqAl) throws IOException {
	  	Sequence[] s = seqAl.getSeqs().getSeqs();
	  	
	  	java.io.BufferedWriter out = new BufferedWriter(new java.io.OutputStreamWriter(os));
	  	
	  	out.write("CLUSTAL\n\n");

	    int max = 0;
	    int maxid = 0;

	    int i = 0;

	    while (i < s.length && s[i] != null) {
	      String tmp = s[i].getId();

	      if (s[i].getSeq().length() > max) {
	        max = s[i].getSeq().length();
	      }
	      if (tmp.length() > maxid) {
	        maxid = tmp.length();
	      }
	      i++;
	    }

	    if (maxid < 15) {
	      maxid = 15;
	    }
	    maxid++;
	    int len = 60;
	    int nochunks =  max / len + 1;

	    for (i = 0; i < nochunks; i++) {
	      int j = 0;
	      while ( j < s.length && s[j] != null) {
	        out.write(new Format("%-" + maxid + "s").form(s[j].getId()+" "));
	        int start = i*len;
	        int end = start + len;

	        if (end < s[j].getSeq().length() && start < s[j].getSeq().length() ) {
	          out.write(s[j].getSeq().substring(start,end) + "\n");
	        } else {
	          if (start < s[j].getSeq().length()) {
	            out.write(s[j].getSeq().substring(start) + "\n");
	          }
	        }
	        j++;
	      }
	      out.write("\n");

	    }
	 }


	  public static Alignment make_Alignment(vamsas.objects.simple.Action origin, Sequence[] seqs, String[] source) throws Exception {
	  	Pattern nonGap = Pattern.compile("[A-Z*0-9]", Pattern.CASE_INSENSITIVE);	
	  	boolean gapsset = false;
	  	char gapchar='-';
	  	int seqLength = 0;
	  	
	  	
	  	for (int i=0, nseq=seqs.length; i<nseq; i++) {
	  		String seq = seqs[i].getSeq();
	  		String gaps = nonGap.matcher(seq).replaceAll("");
  			if (seqLength==0) {
	  			seqLength=seq.length();
  			} else 
	  			if (seqLength!=seq.length())
	  				throw(new Exception(i+"th Sequence (>"+seqs[i].getId()+") is not aligned.\n"));//TODO: move this to assertions part of Alignment
	  		
	  		// common check for any sequence...
	  		if (gaps!=null && gaps.length()>0) {
	  			if (!gapsset)
	  				gapchar = gaps.charAt(0);
	  			for (int c=0, gc=gaps.length(); c<gc; c++) {
	  				if (gapchar!=gaps.charAt(c)) {
	  					throw(new IOException("Inconsistent gap characters in sequence "+i+": '"+seq+"'"));
	  				}
	  			}
	  		}
	  	}

	  	return new Alignment(origin, new SequenceSet(seqs), source, new String(""+gapchar));
	  }
	  
	  public static Alignment read_FastaAlignment(InputStream os, String[] source) throws Exception {
	  	Sequence[] seqs;
	  	try {
	  		seqs = SeqSet.read_SeqFasta(os);
	  		if (seqs==null)
	  			throw(new Exception("Empty alignment stream!\n"));
	  	} catch (Exception e) {
	  		throw new Exception("Invalid fasta alignment\n",e);
	  	}
	  	
	  	return make_Alignment(new vamsas.objects.simple.Action(source[0]), seqs, source);
	  }
	  public static Alignment read_ClustalAlignment(InputStream os, String[] source) throws Exception {
	  	Sequence[] seqs;
	  	try {
	  		seqs = SeqAln.ReadClustalFile(os);
	  		if (seqs==null)
	  			throw(new Exception("Empty alignment stream!\n"));
	  	} catch (Exception e) {
	  		throw new Exception("Invalid fasta alignment\n",e);
	  	}
	  	
	  	return make_Alignment(new vamsas.objects.simple.Action(source[0]), seqs, source);
	  }
}