88 lines
3.0 KiB
Java
88 lines
3.0 KiB
Java
package org.broadinstitute.sting.playground.indels;
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/**
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* Created by IntelliJ IDEA.
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* User: asivache
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* Date: Mar 22, 2009
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* Time: 3:43:05 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class SymmetricMatrix {
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protected double [] data;
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protected int size;
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public SymmetricMatrix(int dimension) {
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assert dimension >= 0 : "Matrix size can not be negative";
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if ( dimension % 2 == 0 ) {
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int k = dimension >> 1; // dimension/2
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data = new double[k*(dimension+1)];
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} else {
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int k = ( dimension + 1 ) >> 1; // (dimension + 1)/2
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data = new double[k*dimension];
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}
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size = dimension;
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}
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public double get(int i, int j) {
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assert (i < size) && ( j < size) : "Out of bound index into matrix detected";
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if ( i >= j ) return data[linearOffset(j,i)]; // we store only the upper triangle in memory
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return data[ linearOffset(i,j) ];
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}
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public void set(int i, int j, double value) {
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assert (i < size) && (j < size) : "Out of bound index into matrix detected";
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if ( i >= j ) data[ linearOffset(j,i) ] = value;
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else data[ linearOffset(i,j) ] = value;
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}
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public int size() { return size; }
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public int nRows() { return size; }
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public int nCols() { return size; }
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/** Returns ready-to-print string representing the full matrix (don't use for 1000x1000 matrices!!);
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* each element is formatted according to a default format.
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* @return
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* @see #format(String f)
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*/
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public String format() {
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return format("%6.3f ");
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}
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/** Returns ready-to-print string representing the full matrix (don't use for 1000x1000 matrices!!);
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* each element is formatted according to a specified format string (note: format string must include all desired
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* whitespaces before and/or after an element, as this method itself does not add any spaces between the formatted elements).
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* @return
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* @see #format()
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*/
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public String format(String f) {
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StringBuilder b = new StringBuilder();
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java.util.Formatter frm = new java.util.Formatter(b);
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for ( int i = 0 ; i < size ; i++ ) {
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for ( int j = 0 ; j < size ; j++ ) {
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frm.format(f, get(i,j));
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}
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b.append('\n');
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}
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return b.toString();
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}
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/** Computes linear offset into the internal array that keeps actual data, given "row" and "column" indices
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* into the matrix; this method is unchecked, but it expects i <= j otherwise the result is unspecified.
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* @param i row index
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* @param j column index
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* @return linear offset into the data[] member of this class
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*/
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private int linearOffset(int i, int j) {
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int k = (( size << 1 ) - i + 1)*i; // [ 2*d - (i+1) ] * i
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k >>= 1; // k/=2
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// now k is the offset of the first stored element in row i
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return ( k + j - i );
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}
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}
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