package org.gbif.checklistbank.authorship;
/*************************************************************************
* Compilation: javac SuffixArray.java
* Execution: java SuffixArray < input.txt
* A data type that computes the suffix array of a string.
* % java SuffixArray < abra.txt
* i ind lcp rnk select
* ---------------------------
* 0 11 - 0 "!"
* 1 10 0 1 "A!"
* 2 7 1 2 "ABRA!"
* 3 0 4 3 "ABRACADABRA!"
* 4 3 1 4 "ACADABRA!"
* 5 5 1 5 "ADABRA!"
* 6 8 0 6 "BRA!"
* 7 1 3 7 "BRACADABRA!"
* 8 4 0 8 "CADABRA!"
* 9 6 0 9 "DABRA!"
* 10 9 0 10 "RA!"
* 11 2 2 11 "RACADABRA!"
* See SuffixArrayX.java for an optimized version that uses 3-way
* radix quicksort and does not use the nested class Suffix.
*************************************************************************/
import java.util.Arrays;
/**
* The <tt>SuffixArray</tt> class represents a suffix array of a string of
* length <em>N</em>.
* It supports the <em>selecting</em> the <em>i</em>th smallest suffix,
* getting the <em>index</em> of the <em>i</em>th smallest suffix,
* computing the length of the <em>longest common prefix</em> between the
* <em>i</em>th smallest suffix and the <em>i</em>-1st smallest suffix,
* and determining the <em>rank</em> of a query string (which is the number
* of suffixes strictly less than the query string).
* This implementation uses a nested class <tt>Suffix</tt> to represent
* a suffix of a string (using constant time and space) and
* <tt>Arrays.sort()</tt> to sort the array of suffixes.
* For alternate implementations of the same API, see
* {@link SuffixArrayX}, which is faster in practice (uses 3-way radix quicksort)
* and uses less memory (does not create <tt>Suffix</tt> objects).
* The <em>index</em> and <em>length</em> operations takes constant time
* in the worst case. The <em>lcp</em> operation takes time proportional to the
* length of the longest common prefix.
* The <em>select</em> operation takes time proportional
* to the length of the suffix and should be used primarily for debugging.
* For additional documentation, see <a href="http://algs4.cs.princeton.edu/63suffix">Section 6.3</a> of
* <i>Algorithms, 4th Edition</i> by Robert Sedgewick and Kevin Wayne.
*/
public class SuffixArray {
private Suffix[] suffixes;
/**
* Initializes a suffix array for the given <tt>text</tt> string.
*
* @param text the input string
*/
public SuffixArray(String text) {
int N = text.length();
this.suffixes = new Suffix[N];
for (int i = 0; i < N; i++) {
suffixes[i] = new Suffix(text, i);
}
Arrays.sort(suffixes);
}
private static class Suffix implements Comparable<Suffix> {
private final String text;
private final int index;
private Suffix(String text, int index) {
this.text = text;
this.index = index;
}
private int length() {
return text.length() - index;
}
private char charAt(int i) {
return text.charAt(index + i);
}
public int compareTo(Suffix that) {
if (this == that) return 0; // optimization
int N = Math.min(this.length(), that.length());
for (int i = 0; i < N; i++) {
if (this.charAt(i) < that.charAt(i)) return -1;
if (this.charAt(i) > that.charAt(i)) return +1;
}
return this.length() - that.length();
}
public String toString() {
return text.substring(index);
}
}
/**
* Returns the length of the input string.
*
* @return the length of the input string
*/
public int length() {
return suffixes.length;
}
/**
* Returns the index into the original string of the <em>i</em>th smallest suffix.
* That is, <tt>text.substring(sa.index(i))</tt> is the <em>i</em>th smallest suffix.
*
* @param i an integer between 0 and <em>N</em>-1
*
* @return the index into the original string of the <em>i</em>th smallest suffix
*
* @throws IndexOutOfBoundsException unless 0 ≤ <em>i</em> < <Em>N</em>
*/
public int index(int i) {
if (i < 0 || i >= suffixes.length) throw new IndexOutOfBoundsException();
return suffixes[i].index;
}
/**
* Returns the length of the longest common prefix of the <em>i</em>th
* smallest suffix and the <em>i</em>-1st smallest suffix.
*
* @param i an integer between 1 and <em>N</em>-1
*
* @return the length of the longest common prefix of the <em>i</em>th
* smallest suffix and the <em>i</em>-1st smallest suffix.
*
* @throws IndexOutOfBoundsException unless 1 ≤ <em>i</em> < <em>N</em>
*/
public int lcp(int i) {
if (i < 1 || i >= suffixes.length) throw new IndexOutOfBoundsException();
return lcp(suffixes[i], suffixes[i - 1]);
}
// longest common prefix of s and t
private static int lcp(Suffix s, Suffix t) {
int N = Math.min(s.length(), t.length());
for (int i = 0; i < N; i++) {
if (s.charAt(i) != t.charAt(i)) return i;
}
return N;
}
/**
* Returns the <em>i</em>th smallest suffix as a string.
*
* @param i the index
*
* @return the <em>i</em> smallest suffix as a string
*
* @throws IndexOutOfBoundsException unless 0 ≤ <em>i</em> < <Em>N</em>
*/
public String select(int i) {
if (i < 0 || i >= suffixes.length) throw new IndexOutOfBoundsException();
return suffixes[i].toString();
}
/**
* Returns the number of suffixes strictly less than the <tt>query</tt> string.
* We note that <tt>rank(select(i))</tt> compareStrict <tt>i</tt> for each <tt>i</tt>
* between 0 and <em>N</em>-1.
*
* @param query the query string
*
* @return the number of suffixes strictly less than <tt>query</tt>
*/
public int rank(String query) {
int lo = 0, hi = suffixes.length - 1;
while (lo <= hi) {
int mid = lo + (hi - lo) / 2;
int cmp = compare(query, suffixes[mid]);
if (cmp < 0) {
hi = mid - 1;
} else if (cmp > 0) {
lo = mid + 1;
} else {
return mid;
}
}
return lo;
}
// compare query string to suffix
private static int compare(String query, Suffix suffix) {
int N = Math.min(query.length(), suffix.length());
for (int i = 0; i < N; i++) {
if (query.charAt(i) < suffix.charAt(i)) return -1;
if (query.charAt(i) > suffix.charAt(i)) return +1;
}
return query.length() - suffix.length();
}
}