/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.util;
/**
* Static methods that encapsulate the standard SAM way of storing ranges: one-based, with both ends
* inclusive.
*/
public class CoordMath {
public static int getLength(final int start, final int end) {
return (end - start) + 1;
}
public static int getStart(final int end, final int length) {
return end - length + 1;
}
public static int getEnd(final int start, final int length) {
return start + length - 1;
}
/**
* Checks to see if the two sets of coordinates have any overlap.
*/
public static boolean overlaps(final int start, final int end, final int start2, final 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(final int outerStart, final int outerEnd, final int innerStart, final 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(final int start, final int end, final int start2, final 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;
}
}