35 lines
932 B
Java
35 lines
932 B
Java
package org.broadinstitute.sting.bwa;
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/**
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* An in-memory representation of a suffix array.
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*
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* @author mhanna
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* @version 0.1
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*/
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public class SuffixArray {
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public final int inverseSA0;
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public final int[] occurrences;
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public final int[] sequence;
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/**
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* Creates a new sequence array with the given inverse SA, occurrences, and values.
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* @param inverseSA0 Inverse SA entry for the first element.
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* @param occurrences Cumulative number of occurrences of A,C,G,T, in order.
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* @param sequence The full suffix array.
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*/
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public SuffixArray(int inverseSA0, int[] occurrences, int[] sequence) {
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this.inverseSA0 = inverseSA0;
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this.occurrences = occurrences;
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this.sequence = sequence;
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}
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/**
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* Retrieves the length of the sequence array.
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* @return Length of the suffix array.
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*/
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public int length() {
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return sequence.length;
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}
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}
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