htsjdk.samtools.tabix.GFFAlignmentContextEncoder.java Source code

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Here is the source code for htsjdk.samtools.tabix.GFFAlignmentContextEncoder.java

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package htsjdk.samtools.tabix;

import java.io.IOException;
import java.io.Writer;
import org.apache.commons.lang3.StringUtils;

/**
 *
 * @author Soma
 */
public class GFFAlignmentContextEncoder implements AlignmentContextEncoder {

    Writer w;

    public GFFAlignmentContextEncoder(Writer out) {
        w = out;
    }

    @Override
    public void encode(AlignmentContext context) throws IOException {
        w.write(String.format(
                "%s\t" + "CGV\t" + "chain\t" + "%d\t" + "%d\t" + "%f\t" + "+\t" + ".\t" + "id \"%s\"; "
                        + "targetChr \"%s\"; " + "targetStart \"%d\"; " + "targetEnd \"%d\"; "
                        + "toNegativeStrand \"%b\"; " + "queryStarts \"%s\"; " + "targetStarts \"%s\"; "
                        + "blockLengths \"%s\";" + "\n",
                context.getChr(), context.getStart(), context.getEnd(), context.getScore(), context.getId(),
                context.getTargetChr(), context.getTargetStart(), context.getTargetEnd(),
                context.getToNegativeStrand(), StringUtils.join(context.getQueryStarts(), ','),
                StringUtils.join(context.getTargetStarts(), ','),
                StringUtils.join(context.getBlockLengths(), ',')));
    }

    @Override
    public void close() throws IOException {
        w.close();
    }

}