001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021/**
022 *
023 */
024package org.biojava.nbio.core.sequence.io;
025
026import org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface;
027import org.biojava.nbio.core.sequence.template.Compound;
028import org.biojava.nbio.core.sequence.template.Sequence;
029import org.biojava.nbio.core.util.StringManipulationHelper;
030
031import java.io.OutputStream;
032import java.io.PrintWriter;
033import java.util.Collection;
034
035
036/**
037 * @author mckeee1
038 *
039 */
040public class GenbankWriter<S extends Sequence<?>, C extends Compound> {
041        int SEQUENCE_INDENT = 9;
042
043        OutputStream os;
044        Collection<S> sequences;
045        GenbankHeaderFormatInterface<S, C> headerFormat;
046        private int lineLength = 60;
047
048        // byte[] lineSep = System.getProperty("line.separator").getBytes();
049        /**
050         * Use default line length of 60
051         *
052         * @param os
053         * @param sequences
054         * @param headerFormat
055         */
056        public GenbankWriter(OutputStream os, Collection<S> sequences,
057                        GenbankHeaderFormatInterface<S, C> headerFormat) {
058
059                this.os = os;
060                this.sequences = sequences;
061                this.headerFormat = headerFormat;
062        }
063
064        /**
065         * Set custom lineLength
066         *
067         * @param os
068         * @param sequences
069         * @param headerFormat
070         * @param lineLength
071         */
072
073        public GenbankWriter(OutputStream os, Collection<S> sequences,
074                        GenbankHeaderFormatInterface<S, C> headerFormat, int lineLength) {
075                this.os = os;
076                this.sequences = sequences;
077                this.headerFormat = headerFormat;
078                this.lineLength = lineLength;
079        }
080
081        /**
082         * Allow an override of operating system line separator for programs that
083         * needs a specific CRLF or CR or LF option
084         *
085         * @param lineSeparator
086         */
087
088        public void process() throws Exception {
089                // Loosely based on code from Howard Salis
090                // TODO - Force lower case?
091                // boolean closeit = false;
092                PrintWriter writer = new PrintWriter(os);
093                for (S sequence : sequences) {
094                        String header = headerFormat.getHeader(sequence);
095                        writer.print(header);
096                        writer.println();
097                        // os.write(lineSep);                   
098                        /*
099                         * if isinstance(record.seq, UnknownSeq): #We have already recorded
100                         * the length, and there is no need #to record a long sequence of
101                         * NNNNNNN...NNN or whatever. if "contig" in record.annotations:
102                         * self._write_contig(record) else: self.handle.write("ORIGIN\n")
103                         * return
104                         */
105
106                        String data = sequence.getSequenceAsString().toLowerCase();
107                        int seq_len = data.length();
108                        writer.println("ORIGIN");
109                        // os.write(lineSep);
110
111                        for (int line_number = 0; line_number < seq_len; line_number += lineLength) {
112                                writer.print(StringManipulationHelper.padLeft(
113                                                Integer.toString(line_number + 1), SEQUENCE_INDENT));
114                                for (int words = line_number; words < Math.min(line_number
115                                                + lineLength, seq_len); words += 10) {
116                                        if ((words + 10) > data.length()) {
117                                                writer.print((" " + data.substring(words)));
118                                        } else {
119                                                writer.print((" " + data.substring(words, words + 10)));
120                                        }
121                                }
122                                // os.write(lineSep);
123                                writer.println();
124                        }
125
126                        writer.println("//");
127
128                }
129
130                writer.flush();
131
132        }
133
134        /**
135         * @return the lineLength
136         */
137        public int getLineLength() {
138                return lineLength;
139        }
140
141        /**
142         * @param lineLength
143         *            the lineLength to set
144         */
145        public void setLineLength(int lineLength) {
146                this.lineLength = lineLength;
147        }
148
149}