60 lines
2.4 KiB
Java
60 lines
2.4 KiB
Java
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/*
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The Broad Institute
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SOFTWARE COPYRIGHT NOTICE AGREEMENT
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This software and its documentation are copyright 2005 by the
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Broad Institute/Massachusetts Institute of Technology. All rights are
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reserved.
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This software is supplied without any warranty or guaranteed support
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whatsoever. Neither the Broad Institute nor MIT can be responsible for its
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use, misuse, or functionality.
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*/
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package edu.mit.broad.picard.util;
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/**
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* Basic coordinate-based math utils, so it's encapsulated in one place! Assumes
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* a one-based coordinate system and then 'end' is always inclusive
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*/
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public class CoordMath {
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/** Gets the length of an interval given the start and the end. */
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public static int getLength(int start, int end) { return (end - start) + 1; }
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/** Gets the start of an interval given the end and the length. */
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public static int getStart(int end, int length) { return end - length + 1; }
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/** Gets the end of an interval given the start and the length. */
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public static int getEnd(int start, int length) { return start + length - 1; }
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/** Checks to see if the two sets of coordinates have any overlap. */
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public static boolean overlaps(int start, int end, int start2, int end2) {
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return (start2 >= start && start2 <= end) || (end2 >=start && end2 <= end) ||
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encloses(start2, end2, start, end);
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}
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/** Returns true if the "inner" coords and totally enclosed by the "outer" coords. */
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public static boolean encloses(int outerStart, int outerEnd, int innerStart, int innerEnd) {
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return innerStart >= outerStart && innerEnd <= outerEnd;
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}
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/**
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* Determines the amount of overlap between two coordinate ranges. Assumes that the two ranges
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* actually do overlap and therefore may produce strange results when they do not!
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*/
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public static int getOverlap(int start, int end, int start2, int end2) {
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return getLength(Math.max(start, start2), Math.min(end, end2));
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}
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/**
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* Determines the read cycle number for the base
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*
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* @param isNegativeStrand true if the read is negative strand
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* @param readLength
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* @param readBaseIndex the 0-based index of the read base in question
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*/
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public static int getCycle(boolean isNegativeStrand, int readLength, final int readBaseIndex) {
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return isNegativeStrand ? readLength - readBaseIndex : readBaseIndex + 1;
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}
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}
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