41 lines
1.3 KiB
Java
41 lines
1.3 KiB
Java
package org.broadinstitute.sting.gatk.refdata;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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/**
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* Created by IntelliJ IDEA.
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* User: mdepristo
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* Date: Feb 27, 2009
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* Time: 10:49:47 AM
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* To change this template use File | Settings | File Templates.
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*/
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public interface ReferenceOrderedDatum extends Comparable<ReferenceOrderedDatum> {
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public String getName();
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public boolean parseLine(final Object header, final String[] parts) throws IOException;
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public String toString();
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public String toSimpleString();
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public String repl();
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/**
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* Used by the ROD system to determine how to split input lines
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* @return Regex string delimiter separating fields
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*/
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public String delimiterRegex();
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public GenomeLoc getLocation();
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public int compareTo( ReferenceOrderedDatum that );
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/**
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* Backdoor hook to read header, meta-data, etc. associated with the file. Will be
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* called by the ROD system before streaming starts
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*
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* @param source source data file on disk from which this rod stream will be pulled
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* @return a header object that will be passed to parseLine command
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*/
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public Object initialize(final File source) throws FileNotFoundException;
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}
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