/*
* 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.analysis.*;

import jalview.datamodel.*;

import java.io.*;

import java.util.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class FastaFile extends AlignFile
{
    /**
     * Creates a new FastaFile object.
     */
    public FastaFile()
    {
    }

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

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

    /**
     * DOCUMENT ME!
     *
     * @throws IOException DOCUMENT ME!
     */
    public void parse() throws IOException
    {
        String id = "";
        StringBuffer seq = new StringBuffer();
        int count = 0;

        int sstart = 0;
        int send = 0;

        String line;

        while ((line = nextLine()) != null)
        {
            if (line.length() > 0)
            {
                // Do we have an id line?
                // JBPNote - this code needs to be standardised to EBI/whatever for the
                // >dbref/dbref/dbref|refid1|refid2|refid3 'human-readable' style of naming (should it really exist)
                if (line.substring(0, 1).equals(">"))
                {
                    if (count != 0)
                    {
                        if (sstart != 0)
                        {
                            seqs.addElement(new Sequence(id, seq.toString(),
                                    sstart, send));
                        }
                        else
                        {
                            seqs.addElement(new Sequence(id, seq.toString(), 1,
                                    seq.length()));
                        }
                    }

                    count++;

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

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

                    com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex(
                            "[A-Za-z-]+/?[A-Za-z-]+\\|(\\w+)\\|(.+)");

                    // JBPNote At the moment - we don't get rid of the friendly names but this
                    // behaviour is probably wrong in the long run.
                    if (dbId.search(id))
                    {
                        String dbid = dbId.stringMatched(1);
                        String idname = dbId.stringMatched(2);

                        if ((idname.length() > 0) &&
                                (idname.indexOf("_") > -1))
                        {
                            id = idname; // use the friendly name - apparently no dbid
                        }
                        else if (dbid.length() > 1)
                        {
                            id = dbid; // ignore the friendly name - we lose uniprot accession ID otherwise
                        }
                    }

                    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()));
            }
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param s DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public static String print(SequenceI[] s)
    {
        return print(s, 72);
    }

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

    /**
     * DOCUMENT ME!
     *
     * @param s DOCUMENT ME!
     * @param len DOCUMENT ME!
     * @param gaps DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public static String print(SequenceI[] s, int len, boolean gaps)
    {
        return print(s, len, gaps, true);
    }

    /**
     * DOCUMENT ME!
     *
     * @param s DOCUMENT ME!
     * @param len DOCUMENT ME!
     * @param gaps DOCUMENT ME!
     * @param displayId DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public static String print(SequenceI[] s, int len, boolean gaps,
        boolean displayId)
    {
        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());
            }

            // used to always put this here: + "/" + s[i].getStart() + "-" + s[i].getEnd() +
            out.append(">" +
                ((displayId) ? s[i].getDisplayId() : s[i].getName()) + "\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();
    }

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