/*
* 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.*;


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);

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

                    if (dbId.search(id)) {
                        String dbid = dbId.stringMatched(1);
                        String idname = dbId.stringMatched(2);

                        if ((idname.length() > 0) &&
                                (idname.indexOf("_") > -1)) {
                            id = idname; // just use friendly name // JBPNote: we may lose uniprot standardised ID here.
                        } else {
                            id = dbid; // use dbid to ensure sensible queries
                        }
                    }

                    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) {
        return print(s, len, gaps, true);
    }

    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();
    }

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