/*
* 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.*;


public class ClustalFile extends AlignFile {
    Vector ids;

    public ClustalFile() {
    }

    public ClustalFile(String inStr) {
        super(inStr);
    }

    public ClustalFile(String inFile, String type) throws IOException {
        super(inFile, type);
    }

    public void initData() {
        super.initData();
        ids = new Vector();
    }

    public void parse() {
        int i = 0;
        boolean flag = false;

        Vector headers = new Vector();
        Hashtable seqhash = new Hashtable();

        String line;

        try {
            while ((line = nextLine()) != null) {
                if (line.indexOf(" ") != 0) {
                    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);
                                }

                                if (str.hasMoreTokens()) {
                                    tempseq.append(str.nextToken());
                                }
                            }
                        }
                    }
                }
            }
        } catch (IOException e) {
            System.err.println("Exception parsing clustal file " + e);
            e.printStackTrace();
        }

        if (flag) {
            this.noSeqs = headers.size();

            //Add sequences to the hash
            for (i = 0; i < headers.size(); i++) {
                int start = -1;
                int end = -1;

                if (seqhash.get(headers.elementAt(i)) != null) {
                    if (maxLength < seqhash.get(headers.elementAt(i)).toString()
                                               .length()) {
                        maxLength = seqhash.get(headers.elementAt(i)).toString()
                                           .length();
                    }

                    String head = headers.elementAt(i).toString();
                    start = 1;
                    end = seqhash.get(headers.elementAt(i)).toString().length();

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

                        if (st.countTokens() == 2) {
                            ids.addElement(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();
                            }
                        } else {
                            ids.addElement(headers.elementAt(i));
                        }
                    } else {
                        ids.addElement(headers.elementAt(i));
                    }

                    Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
                            seqhash.get(headers.elementAt(i).toString())
                                   .toString(), start, end);

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

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

    public static String print(SequenceI[] s) {
        StringBuffer out = new StringBuffer("CLUSTAL\n\n");

        int max = 0;
        int maxid = 0;

        int i = 0;

        while ((i < s.length) && (s[i] != null)) {
            String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +
                s[i].getEnd();

            if (s[i].getSequence().length() > max) {
                max = s[i].getSequence().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.append(new Format("%-" + maxid + "s").form(s[j].getName() +
                        "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");

                int start = i * len;
                int end = start + len;

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

                out.append("\n");
                j++;
            }

            out.append("\n");
        }

        return out.toString();
    }
}