helper class. array-like random access and fast shift. good for sliding windows (e.g. keeping coverage over last 100 bases while sliding along the reference)
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package org.broadinstitute.sting.playground.utils;
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import org.broadinstitute.sting.utils.StingException;
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/** This class, closely resembling a deque (except that it is not dynamically grown),
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* provides an object with array-like interface and efficient
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* implementation of shift operation. Use this class when some kind of sliding window is required:
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* e.g. an array (window) is populated from some stream of data, and then the window is shifted.
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* If most of the data in the window remains the same so that only a few old elements sjould be popped from
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* and a few new elements pushed onto the array, both re-populating the whole array from the data and
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* shifting a regular array would be grossly inefficient. Instead, shiftData(int N) method of circular array
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* efficiently pops out N first elements and makes last N elements available.
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*
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* Consider an example of reading a character stream A,B,C,D,....,Z into an array with requirement of keeping
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* last 5 letters. First, we would read first 5 letters same way as we would with a regular array:<br><br>
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*
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* <code>
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* CircularArray a(5);<br>
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* for ( int i = 0; i < 5; i++ ) a.set(i, readChar());<br>
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* </code>
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* <br>
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* and then on the arrival of each next character we shift the array:<br><br>
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*
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* <code>
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* a.shiftData(1); a.set(4, readChar() );<br>
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* </code>
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* <br>
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* After the lines from the above example are executed, the array will <i>logically</i> look as:<br>
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*
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* B,C,D,E,F,<br><br>
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*
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* e.g. as if we had a regular array, shifted it one element down and added new element on the top.
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*
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*
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* @author asivache
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*
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*/
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public class CircularArray <T> {
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private Object[] data ;
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private int offset;
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/** Creates an array of fixed length */
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public CircularArray(int length) {
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if ( length <= 0 ) throw new StingException("CircularArray length must be positive. Passed: "+length);
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data = new Object[length];
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offset = 0;
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}
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/** Returns length of the array */
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public int length() {
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return data.length;
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}
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/** Gets i-th element of the array
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*
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* @throws IndexOutOfBoundsException if value of i is illegal
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*/
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@SuppressWarnings("unchecked")
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public T get(int i) {
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if ( i < 0 || i >= data.length )
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throw new IndexOutOfBoundsException("Length of CircularArray: "+data.length+"; element requested: "+i);
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return (T)(data [ ( offset + i ) % data.length ]);
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}
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/** Sets i-th element of the array to the specified value.
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*
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* @throws IndexOutOfBoundsException if value of i is illegal
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*/
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public void set(int i, T value) {
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if ( i < 0 || i >= data.length )
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throw new IndexOutOfBoundsException("Length of CircularArray: "+data.length+"; set element request at: "+i);
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data [ ( offset + i ) % data.length ] = value;
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}
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/** Set all elements to null.
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*
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*/
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public void clear() {
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for ( int i = 0 ; i < data.length ; i++ ) data[i] = null;
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offset = 0;
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}
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/** Efficient shift-down of the array data. After this operation, array.get(0), array.get(1), etc will
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* be returning what array.get(shift), array.get(shift+1),... were returning before the shift was performed,
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* and last shift elements of the array will be reset to 0.
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* @param shift
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*/
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public void shiftData(int shift) {
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if ( shift >= data.length ) {
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// if we shift by more than the length of stored data, we lose
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// all that data completely, so we just re-initialize the array.
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// This is not the operating mode CircularArray is intended for
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// but we can handle it, just in case.
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for ( int i = 0 ; i < data.length ; i++ ) data[i] = null;
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offset = 0;
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return;
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}
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// shift < data.length, so at least some data should be preserved
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final int newOffset = ( offset+shift ) % data.length;
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if ( newOffset < offset ) {
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// wrap-around!
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for ( int i = offset ; i < data.length ; i++ ) data[i] = null;
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for ( int i = 0; i < newOffset ; i++ ) data[i] = null;
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} else {
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for ( int i = offset ; i < newOffset ; i++ ) data[i] = null;
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}
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offset = newOffset;
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}
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/** Implements primitive int type-based circular array. See CircularArray for details.
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*
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* @author asivache
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*
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*/
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public static class Int {
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private int [] data ;
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private int offset;
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/** Creates an array of fixed length */
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public Int(int length) {
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if ( length <= 0 ) throw new StingException("CircularArray length must be positive. Passed: "+length);
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data = new int[length]; // automaticaly initialized to zeros
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offset = 0;
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}
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/** Returns length of the array */
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public int length() {
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return data.length;
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}
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/** Gets i-th element of the array
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*
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* @throws IndexOutOfBoundsException if value of i is illegal
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*/
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public int get(int i) {
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if ( i < 0 || i >= data.length )
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throw new IndexOutOfBoundsException("Length of CircularArray: "+data.length+"; element requested: "+i);
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return data [ ( offset + i ) % data.length ];
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}
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/** Sets i-th element of the array to the specified value.
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*
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* @throws IndexOutOfBoundsException if value of i is illegal
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*/
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public void set(int i, int value) {
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if ( i < 0 || i >= data.length )
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throw new IndexOutOfBoundsException("Length of CircularArray: "+data.length+"; set element request at: "+i);
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data [ ( offset + i ) % data.length ] = value;
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}
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/** Increments i-th element of the array by the specified value (value can be negative).
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*
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* @throws IndexOutOfBoundsException if i is illegal
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*/
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public void increment(int i, int value) {
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if ( i < 0 || i >= data.length )
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throw new IndexOutOfBoundsException("Length of CircularArray: "+data.length+"; increment element request at: "+i);
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data [ ( offset + i ) % data.length ] += value;
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}
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/** Set all elements to 0.
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*
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*/
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public void clear() {
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for ( int i = 0 ; i < data.length ; i++ ) data[i] = 0;
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offset = 0;
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}
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/** Efficient shift-down of the array data. After this operation, array.get(0), array.get(1), etc will
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* be returning what array.get(shift), array.get(shift+1),... were returning before the shift was performed,
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* and last shift elements of the array will be reset to 0.
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* @param shift
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*/
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public void shiftData(int shift) {
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if ( shift >= data.length ) {
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// if we shift by more than the length of stored data, we lose
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// all that data completely, so we just re-initialize the array.
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// This is not the operating mode CircularArray is intended for
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// but we can handle it, just in case.
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for ( int i = 0 ; i < data.length ; i++ ) data[i] = 0;
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offset = 0;
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return;
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}
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// shift < data.length, so at least some data should be preserved
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final int newOffset = ( offset+shift ) % data.length;
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if ( newOffset < offset ) {
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// wrap-around!
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for ( int i = offset ; i < data.length ; i++ ) data[i] = 0;
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for ( int i = 0; i < newOffset ; i++ ) data[i] = 0;
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} else {
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for ( int i = offset ; i < newOffset ; i++ ) data[i] = 0;
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}
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offset = newOffset;
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}
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}
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}
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