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SuffixArrayFast.java
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SuffixArrayFast.java
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/**
* Suffix array construction implementation.
*
* <p>Time Complexity: O(nlog(n))
*
* @author William Fiset, william.alexandre.fiset@gmail.com
*/
package com.williamfiset.algorithms.datastructures.suffixarray;
public class SuffixArrayFast extends SuffixArray {
private static final int DEFAULT_ALPHABET_SIZE = 256;
int alphabetSize;
int[] sa2, rank, tmp, c;
public SuffixArrayFast(String text) {
this(toIntArray(text), DEFAULT_ALPHABET_SIZE);
}
public SuffixArrayFast(int[] text) {
this(text, DEFAULT_ALPHABET_SIZE);
}
// Designated constructor
public SuffixArrayFast(int[] text, int alphabetSize) {
super(text);
this.alphabetSize = alphabetSize;
}
@Override
protected void construct() {
sa = new int[N];
sa2 = new int[N];
rank = new int[N];
c = new int[Math.max(alphabetSize, N)];
int i, p, r;
for (i = 0; i < N; ++i) c[rank[i] = T[i]]++;
for (i = 1; i < alphabetSize; ++i) c[i] += c[i - 1];
for (i = N - 1; i >= 0; --i) sa[--c[T[i]]] = i;
for (p = 1; p < N; p <<= 1) {
for (r = 0, i = N - p; i < N; ++i) sa2[r++] = i;
for (i = 0; i < N; ++i) if (sa[i] >= p) sa2[r++] = sa[i] - p;
java.util.Arrays.fill(c, 0, alphabetSize, 0);
for (i = 0; i < N; ++i) c[rank[i]]++;
for (i = 1; i < alphabetSize; ++i) c[i] += c[i - 1];
for (i = N - 1; i >= 0; --i) sa[--c[rank[sa2[i]]]] = sa2[i];
for (sa2[sa[0]] = r = 0, i = 1; i < N; ++i) {
if (!(rank[sa[i - 1]] == rank[sa[i]]
&& sa[i - 1] + p < N
&& sa[i] + p < N
&& rank[sa[i - 1] + p] == rank[sa[i] + p])) r++;
sa2[sa[i]] = r;
}
tmp = rank;
rank = sa2;
sa2 = tmp;
if (r == N - 1) break;
alphabetSize = r + 1;
}
}
public static void main(String[] args) {
SuffixArrayFast sa = new SuffixArrayFast("ABBABAABAA");
System.out.println(sa);
}
}