29 lines
940 B
Java
29 lines
940 B
Java
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package edu.mit.broad.picard.reference;
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import java.io.File;
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/**
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* Factory class for creating ReferenceSequenceFile instances for reading reference
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* sequences store in various formats.
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*
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* @author Tim Fennell
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*/
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public class ReferenceSequenceFileFactory {
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/**
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* Attempts to determine the type of the reference file and return an instance
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* of ReferenceSequenceFile that is appropriate to read it.
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*
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* @param file the reference sequence file on disk
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*/
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public static ReferenceSequenceFile getReferenceSequenceFile(File file) {
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String name = file.getName();
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if (name.endsWith(".fasta") || name.endsWith("fasta.gz") || name.endsWith(".txt") || name.endsWith(".txt.gz")) {
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return new FastaSequenceFile(file);
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}
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else {
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throw new IllegalArgumentException("File is not a supported reference file type: " + file.getAbsolutePath());
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}
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}
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}
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