htsjdk.variant.utils

Class GeneralUtils

java.lang.Object

htsjdk.variant.utils.GeneralUtils

public class GeneralUtils
extends java.lang.Object

Constants and utility methods used throughout the VCF/BCF/VariantContext classes

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	DEBUG_MODE_ENABLED Setting this to true causes the VCF/BCF/VariantContext classes to emit debugging information to standard error
static double	LOG10_P_OF_ZERO The smallest log10 value we'll emit from normalizeFromLog10 and other functions where the real-space value is 0.0.

Constructor Summary

Constructors

Constructor and Description
GeneralUtils()

Method Summary

Methods

Modifier and Type	Method and Description
static double	arrayMax(double[] array)
static byte	compareDoubles(double a, double b) Compares double values for equality (within 1e-6), or inequality.
static byte	compareDoubles(double a, double b, double epsilon) Compares double values for equality (within epsilon), or inequality.
static <T> java.util.List<T>	cons(T elt, java.util.List<T> l)
static <T> java.lang.String	join(java.lang.String separator, java.util.Collection<T> objects) Returns a string of the form elt1.toString() [sep elt2.toString() ...
static <T> java.util.List<java.util.List<T>>	makePermutations(java.util.List<T> objects, int n, boolean withReplacement) Make all combinations of N size of objects if objects = [A, B, C] if N = 1 => [[A], [B], [C]] if N = 2 => [[A, A], [B, A], [C, A], [A, B], [B, B], [C, B], [A, C], [B, C], [C, C]]
static int	maxElementIndex(double[] array)
static int	maxElementIndex(double[] array, int endIndex)
static double[]	normalizeFromLog10(double[] array) normalizes the log10-based array.
static double[]	normalizeFromLog10(double[] array, boolean takeLog10OfOutput) normalizes the log10-based array.
static double[]	normalizeFromLog10(double[] array, boolean takeLog10OfOutput, boolean keepInLogSpace) See #normalizeFromLog10 but with the additional option to use an approximation that keeps the calculation always in log-space
static <T> java.util.List<T>	reverse(java.util.List<T> l)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEBUG_MODE_ENABLED

public static final boolean DEBUG_MODE_ENABLED

Setting this to true causes the VCF/BCF/VariantContext classes to emit debugging information to standard error

See Also:

Constant Field Values

LOG10_P_OF_ZERO

public static final double LOG10_P_OF_ZERO

The smallest log10 value we'll emit from normalizeFromLog10 and other functions where the real-space value is 0.0.

See Also:

Constant Field Values

Constructor Detail

GeneralUtils

public GeneralUtils()

Method Detail

join

public static <T> java.lang.String join(java.lang.String separator,
                        java.util.Collection<T> objects)

Returns a string of the form elt1.toString() [sep elt2.toString() ... sep elt.toString()] for a collection of elti objects (note there's no actual space between sep and the elti elements). Returns "" if collection is empty. If collection contains just elt, then returns elt.toString()

Type Parameters:

T - the type of the objects

Parameters:

separator - the string to use to separate objects

objects - a collection of objects. the element order is defined by the iterator over objects

Returns:

a non-null string

normalizeFromLog10

public static double[] normalizeFromLog10(double[] array)

normalizes the log10-based array. ASSUMES THAT ALL ARRAY ENTRIES ARE <= 0 (<= 1 IN REAL-SPACE).

Parameters:

array - the array to be normalized

Returns:

a newly allocated array corresponding the normalized values in array

normalizeFromLog10

public static double[] normalizeFromLog10(double[] array,
                          boolean takeLog10OfOutput)

normalizes the log10-based array. ASSUMES THAT ALL ARRAY ENTRIES ARE <= 0 (<= 1 IN REAL-SPACE).

Parameters:

array - the array to be normalized

takeLog10OfOutput - if true, the output will be transformed back into log10 units

Returns:

a newly allocated array corresponding the normalized values in array, maybe log10 transformed

normalizeFromLog10

public static double[] normalizeFromLog10(double[] array,
                          boolean takeLog10OfOutput,
                          boolean keepInLogSpace)

See #normalizeFromLog10 but with the additional option to use an approximation that keeps the calculation always in log-space

Parameters:

array -

takeLog10OfOutput -

keepInLogSpace -

Returns:

arrayMax

public static double arrayMax(double[] array)

maxElementIndex

public static int maxElementIndex(double[] array)

maxElementIndex

public static int maxElementIndex(double[] array,
                  int endIndex)

cons

public static <T> java.util.List<T> cons(T elt,
                         java.util.List<T> l)

makePermutations

public static <T> java.util.List<java.util.List<T>> makePermutations(java.util.List<T> objects,
                                                     int n,
                                                     boolean withReplacement)

Make all combinations of N size of objects if objects = [A, B, C] if N = 1 => [[A], [B], [C]] if N = 2 => [[A, A], [B, A], [C, A], [A, B], [B, B], [C, B], [A, C], [B, C], [C, C]]

Type Parameters:

T -

Parameters:

objects -

n -

withReplacement - if false, the resulting permutations will only contain unique objects from objects

Returns:

compareDoubles

public static byte compareDoubles(double a,
                  double b)

Compares double values for equality (within 1e-6), or inequality.

Parameters:

a - the first double value

b - the second double value

Returns:

-1 if a is greater than b, 0 if a is equal to be within 1e-6, 1 if b is greater than a.

compareDoubles

public static byte compareDoubles(double a,
                  double b,
                  double epsilon)

Compares double values for equality (within epsilon), or inequality.

Parameters:

a - the first double value

b - the second double value

epsilon - the precision within which two double values will be considered equal

Returns:

-1 if a is greater than b, 0 if a is equal to be within epsilon, 1 if b is greater than a.

reverse

public static final <T> java.util.List<T> reverse(java.util.List<T> l)