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