/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/
package jalview.io;

import jalview.datamodel.*;

import jalview.util.*;

import java.io.*;

import java.util.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class MSFfile extends AlignFile
{


    /**
     * Creates a new MSFfile object.
     */
    public MSFfile()
    {
    }

    /**
     * Creates a new MSFfile object.
     *
     * @param inStr DOCUMENT ME!
     */
    public MSFfile(String inStr)
    {
        super(inStr);
    }

    /**
     * Creates a new MSFfile object.
     *
     * @param inFile DOCUMENT ME!
     * @param type DOCUMENT ME!
     *
     * @throws IOException DOCUMENT ME!
     */
    public MSFfile(String inFile, String type) throws IOException
    {
        super(inFile, type);
    }

    /**
     * DOCUMENT ME!
     */
    public void parse()
    {
        int i = 0;
        boolean seqFlag = false;
        String key = new String();
        Vector headers = new Vector();
        Hashtable seqhash = new Hashtable();
        String line;

        try
        {
            while ((line = nextLine()) != null)
            {
                StringTokenizer str = new StringTokenizer(line);

                while (str.hasMoreTokens())
                {
                    String inStr = str.nextToken();

                    //If line has header information add to the headers vector
                    if (inStr.indexOf("Name:") != -1)
                    {
                        key = str.nextToken();
                        headers.addElement(key);
                    }

                    //if line has // set SeqFlag to 1 so we know sequences are coming
                    if (inStr.indexOf("//") != -1)
                    {
                        seqFlag = true;
                    }

                    //Process lines as sequence lines if seqFlag is set
                    if ((inStr.indexOf("//") == -1) && (seqFlag == true))
                    {
                        //seqeunce id is the first field
                        key = inStr;

                        StringBuffer tempseq;

                        //Get sequence from hash if it exists
                        if (seqhash.containsKey(key))
                        {
                            tempseq = (StringBuffer) seqhash.get(key);
                        }
                        else
                        {
                            tempseq = new StringBuffer();
                            seqhash.put(key, tempseq);
                        }

                        //loop through the rest of the words
                        while (str.hasMoreTokens())
                        {
                            //append the word to the sequence
                            tempseq.append(str.nextToken());
                        }
                    }
                }
            }
        }
        catch (IOException e)
        {
            System.err.println("Exception parsing MSFFile " + e);
            e.printStackTrace();
        }

        this.noSeqs = headers.size();

        //Add sequences to the hash
        for (i = 0; i < headers.size(); i++)
        {
            if (seqhash.get(headers.elementAt(i)) != null)
            {
                String head = headers.elementAt(i).toString();
                String seq = seqhash.get(head).toString();

                int start = -1;
                int end =  -1;

                if (maxLength < head.length())
                {
                    maxLength = head.length();
                }

                if (head.indexOf("/") > 0)
                {
                    StringTokenizer st = new StringTokenizer(head, "/");

                    if (st.countTokens() == 2)
                    {
                        head = st.nextToken();

                        String tmp = st.nextToken();
                        st = new StringTokenizer(tmp, "-");

                        if (st.countTokens() == 2)
                        {
                            start = Integer.valueOf(st.nextToken()).intValue();
                            end = Integer.valueOf(st.nextToken()).intValue();
                        }
                    }
                }


                // Replace ~ with a sensible gap character
                seq = seq.replace('~', '-');

                Sequence newSeq = new Sequence(head, seq, start, end);

                seqs.addElement(newSeq);
            }
            else
            {
                System.err.println("MSFFile Parser: Can't find sequence for " +
                    headers.elementAt(i));
            }
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param seq DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public static int checkSum(String seq)
    {
        int check = 0;
        String sequence = seq.toUpperCase();

        for (int i = 0; i < sequence.length(); i++)
        {
            try
            {

                    int value = sequence.charAt(i);
                    if (value!=-1)
                    {
                        check += (i % 57 +1) * value;
                    }
            }
            catch (Exception e)
            {
                System.err.println("Exception during MSF Checksum calculation");
                e.printStackTrace();
            }
        }

        return check % 10000;
    }

    /**
     * DOCUMENT ME!
     *
     * @param s DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public static String print(SequenceI[] s)
    {
        return print(s, false);
    }

    /**
     * DOCUMENT ME!
     *
     * @param s DOCUMENT ME!
     * @param is_NA DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public static String print(SequenceI[] seqs, boolean is_NA)
    {

      SequenceI [] s = new SequenceI[seqs.length];

        StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +
                "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.

        int max = 0;
        int maxid = 0;
        int i = 0;

        while ((i < seqs.length) && (seqs[i] != null))
        {
          // Replace all internal gaps with . and external spaces with ~
          s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequence().replace('-', '.'));

          StringBuffer sb = new StringBuffer(s[i].getSequence());
          for (int ii = 0; ii < sb.length(); ii++)
          {
            if (sb.charAt(ii) == '.')
            {
              sb.replace(ii, ii + 1, "~");
            }
            else
              break;
          }

          for (int ii = sb.length() - 1; ii > 0; ii--)
          {
            if (sb.charAt(ii) == '.')
            {
              sb.replace(ii, ii + 1, "~");
            }
            else
              break;
          }

            s[i].setSequence(sb.toString());

            if (s[i].getSequence().length() > max)
            {
                max = s[i].getSequence().length();
            }

            i++;
        }

        Format maxLenpad = new Format("%" + (new String("" + max)).length() +
                "d");
        Format maxChkpad = new Format("%" + (new String("1" + max)).length() +
                "d");
        i = 0;

        int bigChecksum = 0;
        int [] checksums = new int[s.length];
        while ( i < s.length )
        {
          checksums[i] = checkSum(s[i].getSequence());
          bigChecksum += checksums[i];
          i++;
        }

        long maxNB = 0;
        out.append("   MSF: " + s[0].getSequence().length() + "   Type: " +
            (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum%10000) + "   ..\n\n\n");

        String[] nameBlock = new String[s.length];
        String[] idBlock = new String[s.length];

        i=0;
        while ((i < s.length) && (s[i] != null))
        {
            nameBlock[i] = new String("  Name: " + s[i].getName() + " ");
            idBlock[i] = new String("Len: " +
                    maxLenpad.form(s[i].getSequence().length()) + "  Check: " +
                    maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");

            if (s[i].getName().length() > maxid)
            {
                maxid = s[i].getName().length();
            }

            if (nameBlock[i].length() > maxNB)
            {
                maxNB = nameBlock[i].length();
            }

            i++;
        }

        if (maxid < 10)
        {
            maxid = 10;
        }

        if (maxNB < 15)
        {
            maxNB = 15;
        }

        Format nbFormat = new Format("%-" + maxNB + "s");

        for (i = 0; (i < s.length) && (s[i] != null); i++)
        {
            out.append(nbFormat.form(nameBlock[i]) + idBlock[i]);
        }

        maxid++;
        out.append("\n\n//\n\n");

        int len = 50;

        int nochunks = (max / len) + 1;

        if ((max % len) == 0)
        {
            nochunks--;
        }

        for (i = 0; i < nochunks; i++)
        {
            int j = 0;

            while ((j < s.length) && (s[j] != null))
            {
                String name = s[j].getName();
                out.append(new Format("%-" + maxid + "s").form(name)+ " ");

                for (int k = 0; k < 5; k++)
                {
                    int start = (i * 50) + (k * 10);
                    int end = start + 10;

                    if ((end < s[j].getSequence().length()) &&
                            (start < s[j].getSequence().length()))
                    {
                        out.append(s[j].getSequence().substring(start, end));

                        if (k < 4)
                        {
                             out.append(" ");
                        }
                        else
                        {
                            out.append("\n");
                        }
                    }
                    else
                    {
                        if (start < s[j].getSequence().length())
                        {
                            out.append(s[j].getSequence().substring(start));
                            out.append("\n");
                        }
                        else
                        {
                            if (k == 0)
                            {
                                out.append("\n");
                            }
                        }
                    }
                }

                j++;
            }

            out.append("\n");
        }

        return out.toString();
    }

    /**
     * DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String print()
    {
        return print(getSeqsAsArray());
    }
}