package jalview.analysis;

import jalview.datamodel.*;
import jalview.io.*;

import java.util.*;

public class CompareAlignments {

    Vector align;
    String refId;
    Vector ids;

    public CompareAlignments(Vector align) {

	this.align = align;

	ids = new Vector();

	Alignment al0 = (Alignment)align.elementAt(0);

	for (int i = 0; i < al0.getHeight(); i++) {
	    SequenceI seq = al0.getSequenceAt(i);

	    ids.addElement(seq.getName());

	    if (i == 0) {
		setReferenceId(seq.getName());
	    }
	}

    }

    public void compare() {

	Hashtable positions = new Hashtable();

	for (int k = 0; k < ids.size(); k++) {

	    String id = (String)ids.elementAt(k);

	    System.out.println("Ids " + id + " " + refId);

	    if (!id.equals(refId)) {

		Hashtable fullhash = new Hashtable();

		for (int i = 0; i < align.size(); i++) {
		    System.out.println("Alignment " + i);

		    Alignment al = (Alignment)align.elementAt(i);

		    SequenceI refseq = null;

		    for (int j = 0; j < al.getHeight(); j++) {
			if (((SequenceI)al.getSequenceAt(j)).getName().equals(refId)) {
			    refseq = (SequenceI)al.getSequenceAt(j);
			}
		    }

		    if (refseq != null) {

			System.out.println("Refseq " + refseq.getName());

			for (int jj = 0; jj < al.getHeight(); jj++) {
			    SequenceI seq = (SequenceI)al.getSequenceAt(jj);

			    if (seq.getName().equals(id)) {
				Hashtable hash = getAlignPositions(seq,refseq);

				Enumeration keys = hash.keys();

				while (keys.hasMoreElements()) {
				    Integer key = (Integer)keys.nextElement();
				    //				System.out.println(key + " " + hash.get(key));
				    if (fullhash.get(key) == null) {
					fullhash.put(key,new Vector());
				    }

				    Vector tmp = (Vector)fullhash.get(key);

				    tmp.addElement(hash.get(key));
				}
			    }

			}
		    }
		}

		System.out.println ("\nId " + id);

		Enumeration keys = fullhash.keys();


		int totdiff = 0;
		while (keys.hasMoreElements()) {
		    Integer key = (Integer)keys.nextElement();

		    Vector tmp = (Vector)fullhash.get(key);



		    int diff0 = ((Integer)tmp.elementAt(0)).intValue();;
		    int diff = 0;

		    for (int l = 1; l < tmp.size(); l++) {
			diff += Math.abs(diff0 - ((Integer)tmp.elementAt(l)).intValue());

		    }

		    if (diff > 0) {
			totdiff++;
			System.out.print(id + " Ref pos " + key + " : " + diff0 + " " + diff + " : ");

			for (int l = 1; l < tmp.size(); l++) {
			    System.out.print(diff0 - ((Integer)tmp.elementAt(l)).intValue() + " ");
			}
			System.out.println();
		    }
		}

		System.out.println("Total " + id + " " + totdiff);

	    }
	}
    }


    public void setReferenceId(String id) {
	this.refId = id;
    }

    public Hashtable getAlignPositions(SequenceI seq1, SequenceI seq2) {

	Hashtable hash = new Hashtable();

	int i = 0;

	int pos1 = 0;
	int pos2 = 0;

	while (i < seq1.getLength()) {

	    char c1 = seq1.getCharAt(i);
	    char c2 = seq2.getCharAt(i);

	    if (c1 != '-') {
		pos1++;
	    }

	    if (c2 != '-') {
		pos2++;
	    }

	    if (c1 != '-') {
		hash.put(new Integer(pos1),new Integer(pos2));
	    }

	    i++;
	}
	return hash;
    }



}