public class CoordMath
extends java.lang.Object
Constructor and Description |
---|
CoordMath() |
Modifier and Type | Method and Description |
---|---|
static boolean |
encloses(int outerStart,
int outerEnd,
int innerStart,
int innerEnd)
Returns true if the "inner" coords and totally enclosed by the "outer" coords.
|
static int |
getCycle(boolean isNegativeStrand,
int readLength,
int readBaseIndex)
Determines the read cycle number for the base
|
static int |
getEnd(int start,
int length) |
static int |
getLength(int start,
int end) |
static int |
getOverlap(int start,
int end,
int start2,
int end2)
Determines the amount of overlap between two coordinate ranges.
|
static int |
getStart(int end,
int length) |
static boolean |
overlaps(int start,
int end,
int start2,
int end2)
Checks to see if the two sets of coordinates have any overlap.
|
public static int getLength(int start, int end)
public static int getStart(int end, int length)
public static int getEnd(int start, int length)
public static boolean overlaps(int start, int end, int start2, int end2)
public static boolean encloses(int outerStart, int outerEnd, int innerStart, int innerEnd)
public static int getOverlap(int start, int end, int start2, int end2)
public static int getCycle(boolean isNegativeStrand, int readLength, int readBaseIndex)
isNegativeStrand
- true if the read is negative strandreadLength
- readBaseIndex
- the 0-based index of the read base in question