eu.eubrazilcc.lvl.core.io.FastaWriter.java Source code

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Here is the source code for eu.eubrazilcc.lvl.core.io.FastaWriter.java

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/*
 * Copyright 2014 EUBrazilCC (EU?Brazil Cloud Connect)
 * 
 * Licensed under the EUPL, Version 1.1 or - as soon they will be approved by 
 * the European Commission - subsequent versions of the EUPL (the "Licence");
 * You may not use this work except in compliance with the Licence.
 * You may obtain a copy of the Licence at:
 * 
 *   http://ec.europa.eu/idabc/eupl
 * 
 * Unless required by applicable law or agreed to in writing, software 
 * distributed under the Licence is distributed on an "AS IS" basis,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the Licence for the specific language governing permissions and 
 * limitations under the Licence.
 * 
 * This product combines work with different licenses. See the "NOTICE" text
 * file for details on the various modules and licenses.
 * The "NOTICE" text file is part of the distribution. Any derivative works
 * that you distribute must include a readable copy of the "NOTICE" text file.
 */

package eu.eubrazilcc.lvl.core.io;

import static eu.eubrazilcc.lvl.core.DataSource.GENBANK_SHORT;
import static org.apache.commons.lang.StringUtils.trimToEmpty;

import java.io.IOException;
import java.io.OutputStream;

import eu.eubrazilcc.lvl.core.xml.ncbi.gb.GBSeq;

/**
 * Writes a sequence to a file or an output stream. Headers are generated using the NCBI format.
 * @author Erik Torres <ertorser@upv.es>
 * @see <a href="http://www.ncbi.nlm.nih.gov/books/NBK21097/#A631">The NCBI Handbook, Chapter 16: Appendix 1 - FASTA identifiers</a>
 */
public class FastaWriter {

    public static final char HEADER_FIELD_SEPARATOR = '|';
    public static final char FASTA_BEGIN = '>';
    public static final int LINE_LENGTH = 70;

    private static final byte[] LINE_SEPARATOR = System.getProperty("line.separator").getBytes();

    public static void writeFasta(final OutputStream os, final GBSeq gbSeq) throws IOException {
        final String header = fastaHeader(gbSeq);
        os.write(FASTA_BEGIN);
        os.write(header.getBytes());
        os.write(LINE_SEPARATOR);

        int compoundCount = 0;
        final String sequence = trimToEmpty(gbSeq.getGBSeqSequence()).toUpperCase();
        for (int i = 0; i < sequence.length(); i++) {
            os.write(sequence.charAt(i));
            compoundCount++;
            if (compoundCount == LINE_LENGTH) {
                os.write(LINE_SEPARATOR);
                compoundCount = 0;
            }
        }

        if ((sequence.length() % LINE_LENGTH) != 0) {
            os.write(LINE_SEPARATOR);
        }
    }

    public static String fastaHeader(final GBSeq gbSeq) {
        return GENBANK_SHORT + HEADER_FIELD_SEPARATOR + trimToEmpty(gbSeq.getGBSeqAccessionVersion())
                + HEADER_FIELD_SEPARATOR + trimToEmpty(gbSeq.getGBSeqLocus());
    }

}