49 lines
1.6 KiB
Java
49 lines
1.6 KiB
Java
package edu.mit.broad.picard.reference;
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/**
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* Wrapper around a reference sequence that has been read from a reference file.
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*
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* @author Tim Fennell
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*/
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public class ReferenceSequence {
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private String name;
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private byte[] bases;
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private int contigIndex;
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private int length;
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/**
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* Package level constructor that creates a fully formed ReferenceSequence
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*
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* @param name the name of the sequence from the source file
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* @param index the zero based index of this contig in the source file
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* @param bases the bases themselves stored as one-byte characters
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*/
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ReferenceSequence(String name, int index, byte[] bases) {
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this.name = name;
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this.contigIndex = index;
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this.bases = bases;
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this.length = bases.length;
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}
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/** Gets the set of names given to this sequence in the source file. */
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public String getName() { return name; }
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/**
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* Gets the array of bases that define this sequence. The bases can include any
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* letter and possibly include masking information in the form of lower case
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* letters. This array is mutable (obviously!) and it NOT a clone of the array
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* held interally. Do not modify it!!!
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*/
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public byte[] getBases() { return bases; }
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/** Gets the 0-based index of this contig in the source file from which it came. */
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public int getContigIndex() { return contigIndex; }
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/** Gets the length of this reference sequence in bases. */
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public int length() { return length; }
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public String toString() {
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return "ReferenceSequence " + getName();
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}
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}
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