net.maizegenetics.util

Class BitUtil

net.maizegenetics.util.BitUtil

public class BitUtil

A variety of high efficiency bit twiddling routines.

Field Detail

ntzTable

public static kotlin.Array[] ntzTable

table of number of trailing zeros in a byte

Method Detail

pop

public static int pop(long x)

Returns the number of bits set in the long

pop_array_to_index

public static long pop_array_to_index(kotlin.Array[] A,
                                      int index)

pop_array

public static long pop_array(kotlin.Array[] A,
                             int wordOffset,
                             int numWords)

* Returns the number of set bits in an array of longs.

pop_intersect

public static long pop_intersect(kotlin.Array[] A,
                                 kotlin.Array[] B,
                                 int wordOffset,
                                 int numWords)

Returns the popcount or cardinality of the two sets after an intersection. Neither array is modified.

pop_union

public static long pop_union(kotlin.Array[] A,
                             kotlin.Array[] B,
                             int wordOffset,
                             int numWords)

Returns the popcount or cardinality of the union of two sets. Neither array is modified.

pop_andnot

public static long pop_andnot(kotlin.Array[] A,
                              kotlin.Array[] B,
                              int wordOffset,
                              int numWords)

Returns the popcount or cardinality of A & ~B Neither array is modified.

pop_xor

public static long pop_xor(kotlin.Array[] A,
                           kotlin.Array[] B,
                           int wordOffset,
                           int numWords)

ntz

public static int ntz(long val)

Returns number of trailing zeros in a 64 bit long value.

ntz

public static int ntz(int val)

Returns number of trailing zeros in a 32 bit int value.

ntz2

public static int ntz2(long x)

returns 0 based index of first set bit (only works for x!=0)
This is an alternate implementation of ntz()

ntz3

public static int ntz3(long x)

returns 0 based index of first set bit
This is an alternate implementation of ntz()

isPowerOfTwo

public static boolean isPowerOfTwo(int v)

returns true if v is a power of two or zero

isPowerOfTwo

public static boolean isPowerOfTwo(long v)

returns true if v is a power of two or zero

nextHighestPowerOfTwo

public static int nextHighestPowerOfTwo(int v)

returns the next highest power of two, or the current value if it's already a power of two or zero

nextHighestPowerOfTwo

public static long nextHighestPowerOfTwo(long v)

returns the next highest power of two, or the current value if it's already a power of two or zero

transpose

public static BitSet[] transpose(BitSet[] matrix,
                                 int numDataRows,
                                 int numRows,
                                 int numColumns,
                                 ProgressListener listener)

This converts taxa optimized Bit Sets to site optimized Bit Sets and vice versa.

Parameters:

matrix - matrix to convert

numDataRows - number data rows (i.e. max num alleles + rare?)

numRows - number rows (i.e. number taxa)

numColumns - number columns (i.e. number sites)

Returns:

org.jetbrains.dokka.NodeRenderContent@3ac50329: transposed Bit Sets

bits2words

public static int bits2words(long numBits)

returns the number of 64 bit words it would take to hold numBits

transpose

public static kotlin.Array[] transpose(kotlin.Array[] orig)

Transposes 64 x 64 bit matrix. The below before and after locations. 1 2 4 2 3 4 3 1

Parameters:

orig - original

Returns:

org.jetbrains.dokka.NodeRenderContent@184db5e: transposed matrix

printBitLong

public static void printBitLong(long A)

toPadString

public static java.lang.String toPadString(long A)

toPadStringLowSiteToHighSite

public static java.lang.String toPadStringLowSiteToHighSite(long A)

Returns the bits in the same order that we store them for TASSEL

Parameters:

A -

Returns:

org.jetbrains.dokka.NodeRenderContent@eac4be8:

printBitMatrix

public static void printBitMatrix(kotlin.Array[] A)

toReadableString

public static java.lang.String toReadableString(BitSet bitSet)