biospectra.lucene.SequenceCompressFilter.java Source code

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Here is the source code for biospectra.lucene.SequenceCompressFilter.java

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/*
 * Copyright 2015 iychoi.
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package biospectra.lucene;

import biospectra.utils.SequenceHelper;
import java.io.IOException;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.lucene.analysis.TokenFilter;
import org.apache.lucene.analysis.TokenStream;
import org.apache.lucene.analysis.tokenattributes.CharTermAttribute;

/**
 *
 * @author iychoi
 */
public final class SequenceCompressFilter extends TokenFilter {

    private static final Log LOG = LogFactory.getLog(SequenceCompressFilter.class);

    private final CharTermAttribute termAtt = addAttribute(CharTermAttribute.class);
    private boolean base64Compress = true;
    private boolean minStrand = false;

    public SequenceCompressFilter(TokenStream in) {
        super(in);
    }

    public SequenceCompressFilter(TokenStream in, boolean base64Compress, boolean minStrand) {
        super(in);

        this.base64Compress = base64Compress;
        this.minStrand = minStrand;
    }

    @Override
    public boolean incrementToken() throws IOException {
        if (this.input.incrementToken()) {
            char[] buffer = this.termAtt.buffer();
            final int length = this.termAtt.length();

            if (this.minStrand) {
                char[] reverseComplement = SequenceHelper.getReverseComplement(buffer, length);

                String originalSeq = String.valueOf(buffer, 0, length);
                String revcompSeq = String.valueOf(reverseComplement);

                if (originalSeq.compareTo(revcompSeq) > 0) {
                    // use reverse-complement sequence
                    for (int i = 0; i < length; i++) {
                        buffer[i] = reverseComplement[i];
                    }
                }
            }

            if (this.base64Compress) {
                byte[] compressed = SequenceHelper.compress(buffer, length);
                byte[] encoded = Base64.encodeBase64(compressed);

                buffer = this.termAtt.resizeBuffer(encoded.length);

                for (int i = 0; i < buffer.length; i++) {
                    if (i < encoded.length) {
                        buffer[i] = (char) encoded[i];
                    } else {
                        buffer[i] = 0;
                    }
                }

                this.termAtt.setLength(encoded.length);
                //System.out.println("comp: " + String.valueOf(buffer));
            }
            return true;
        } else {
            return false;
        }
    }

}