76 lines
2.8 KiB
Java
76 lines
2.8 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 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package edu.mit.broad.sam.util;
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public class CoordMath {
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public static long getLength(final long start, final long end) {
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return (end - start) + 1;
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}
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public static long getStart(final long end, final long length) {
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return end - length + 1;
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}
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public static long getEnd(final long start, final long length) {
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return start + length - 1;
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}
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/**
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* Offsets are meant to exclude the 'offset' number of bases
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*/
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public static long getStartFromOffset(final long offset, final long length) {
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return offset + 1;
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}
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public static long getEndFromOffset(final long offset, final long length) {
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return length - offset;
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}
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public static long getLengthFromOffsets(final long startOffset, final long endOffset, final long length) {
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return getLength(getStartFromOffset(startOffset, length),
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getEndFromOffset(endOffset, length));
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}
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/**
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* Gets a sub-sequence from a java.lang.String (which is zero based) using one based
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* sequence coordinated. The base at the end coordinate will be included.
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*
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* @param sequence The String of base pairs
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* @param begin The one based start coordinate
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* @param end The one based end coordinate
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* @return The subsequence specified
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*/
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public static String getSubsequence(final String sequence, final int begin, final int end) {
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return sequence.substring(begin-1, end);
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}
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/**
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* Checks to see if the two sets of coordinates have any overlap.
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*/
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public static boolean overlaps(final long start, final long end, final long start2, final long 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(final long outerStart, final long outerEnd, final long innerStart, final long 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 long getOverlap(final long start, final long end, final long start2, final long 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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