Package ubic.basecode.dataStructure.matrix

Class MatrixUtil

java.lang.Object

ubic.basecode.dataStructure.matrix.MatrixUtil

public class MatrixUtil
extends Object

Author:

Paul

Constructor Summary

Constructors

Constructor	Description
MatrixUtil()

Method Summary

Modifier and Type	Method	Description
static cern.colt.matrix.DoubleMatrix1D	applyToIndicesMatchingCriteria(cern.colt.matrix.DoubleMatrix1D x, DoubleFunction<Boolean> criterion, DoubleFunction<Double> action)
static cern.colt.list.BooleanArrayList	conjunction(cern.colt.list.BooleanArrayList a, cern.colt.list.BooleanArrayList b)	Compute the conjuction (logical 'and') of two boolean vectors
static boolean	containsNearlyZeros(cern.colt.matrix.DoubleMatrix1D d)
static cern.colt.matrix.DoubleMatrix1D	diagonal(cern.colt.matrix.DoubleMatrix2D matrix)	Extract the diagonal from a matrix.
static cern.colt.matrix.DoubleMatrix2D	dropColumn(cern.colt.matrix.DoubleMatrix2D n, int indexToDrop)
static cern.colt.matrix.DoubleMatrix2D	dropColumns(cern.colt.matrix.DoubleMatrix2D n, Collection<Integer> droppedColumns)
static cern.colt.matrix.DoubleMatrix1D	fromList(cern.colt.list.DoubleArrayList list)	Makes a copy
static <R,C,V> V	getObject(Matrix2D<R,C,V> matrix, int rowIndex, int colIndex)
static <R,C,V> V[]	getRow(Matrix2D<R,C,V> matrix, int rowIndex)
static void	maskMissing(cern.colt.matrix.DoubleMatrix2D source, cern.colt.matrix.DoubleMatrix2D target)
static cern.colt.list.BooleanArrayList	matchingCriteria(cern.colt.matrix.DoubleMatrix1D x, DoubleFunction<Boolean> criterion)
static cern.colt.matrix.DoubleMatrix1D	multWithMissing(cern.colt.matrix.DoubleMatrix1D a, cern.colt.matrix.DoubleMatrix2D b)
static cern.colt.matrix.DoubleMatrix1D	multWithMissing(cern.colt.matrix.DoubleMatrix2D a, cern.colt.matrix.DoubleMatrix1D b)
static cern.colt.matrix.DoubleMatrix2D	multWithMissing(cern.colt.matrix.DoubleMatrix2D a, cern.colt.matrix.DoubleMatrix2D b)	Multiple two matrices, tolerate missing values.
static List<Integer>	notNearlyZeroIndices(cern.colt.matrix.DoubleMatrix1D d)
static cern.colt.matrix.DoubleMatrix1D	removeMissing(cern.colt.matrix.DoubleMatrix1D x)
static cern.colt.matrix.DoubleMatrix1D	removeMissingOrInfinite(cern.colt.matrix.DoubleMatrix1D data)
static cern.colt.matrix.DoubleMatrix1D	removeMissingOrInfinite(cern.colt.matrix.DoubleMatrix1D reference, cern.colt.matrix.DoubleMatrix1D data)	Remove values from data corresponding to missing values in reference.
static void	replaceValues(cern.colt.matrix.DoubleMatrix1D x, cern.colt.list.BooleanArrayList toReplace, cern.colt.matrix.DoubleMatrix1D replacements)	Perform the awkward operation of substituting certain values in a vector from values in another vector.
static cern.colt.matrix.DoubleMatrix1D	select(cern.colt.matrix.DoubleMatrix1D v, Collection<Integer> selected)
static cern.colt.matrix.DoubleMatrix2D	selectColumns(cern.colt.matrix.DoubleMatrix2D n, Collection<Integer> selected)
static cern.colt.matrix.DoubleMatrix2D	selectColumnsAndRows(cern.colt.matrix.DoubleMatrix2D n, Collection<Integer> selected)
static cern.colt.matrix.DoubleMatrix2D	selectRows(cern.colt.matrix.DoubleMatrix2D n, Collection<Integer> selected)
static int	sizeWithoutMissingValues(cern.colt.matrix.DoubleMatrix1D list)
static cern.colt.matrix.DoubleMatrix1D	stripByCriterion(cern.colt.matrix.DoubleMatrix1D x, DoubleFunction<Boolean> criterion)
static cern.colt.matrix.DoubleMatrix1D	stripNegative(cern.colt.matrix.DoubleMatrix1D x)
static cern.colt.matrix.DoubleMatrix1D	stripNonOK(cern.colt.matrix.DoubleMatrix1D x, cern.colt.list.BooleanArrayList ok)
static cern.colt.list.DoubleArrayList	toList(cern.colt.matrix.DoubleMatrix1D vector)	Makes a copy

Methods inherited from class java.lang.Object

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

Constructor Detail

MatrixUtil

public MatrixUtil()

Method Detail

containsNearlyZeros

public static boolean containsNearlyZeros(cern.colt.matrix.DoubleMatrix1D d)

Parameters:

d -

Returns:

true if any of the values are very close to zero.

diagonal

public static cern.colt.matrix.DoubleMatrix1D diagonal(cern.colt.matrix.DoubleMatrix2D matrix)

Extract the diagonal from a matrix.

Parameters:

matrix -

Returns:

dropColumn

public static cern.colt.matrix.DoubleMatrix2D dropColumn(cern.colt.matrix.DoubleMatrix2D n,
                                                         int indexToDrop)

Parameters:

n -

indexToDrop -

Returns:

dropColumns

public static cern.colt.matrix.DoubleMatrix2D dropColumns(cern.colt.matrix.DoubleMatrix2D n,
                                                          Collection<Integer> droppedColumns)

Parameters:

n -

droppedColumns -

fromList

public static cern.colt.matrix.DoubleMatrix1D fromList(cern.colt.list.DoubleArrayList list)

Makes a copy

Parameters:

list -

Returns:

getObject

public static <R,C,V> V getObject(Matrix2D<R,C,V> matrix,
                                              int rowIndex,
                                              int colIndex)

Type Parameters:

R -

C -

V -

Parameters:

matrix -

rowIndex -

colIndex -

Returns:

getRow

public static <R,C,V> V[] getRow(Matrix2D<R,C,V> matrix,
                                             int rowIndex)

Type Parameters:

R -

C -

V -

Parameters:

matrix -

rowIndex -

Returns:

maskMissing

public static void maskMissing(cern.colt.matrix.DoubleMatrix2D source,
                               cern.colt.matrix.DoubleMatrix2D target)

Parameters:

source - the source of information about missing values

target - the target where we want to convert values to missing

multWithMissing

public static cern.colt.matrix.DoubleMatrix1D multWithMissing(cern.colt.matrix.DoubleMatrix1D a,
                                                              cern.colt.matrix.DoubleMatrix2D b)

multWithMissing

public static cern.colt.matrix.DoubleMatrix1D multWithMissing(cern.colt.matrix.DoubleMatrix2D a,
                                                              cern.colt.matrix.DoubleMatrix1D b)

Parameters:

a -

b -

Returns:

multWithMissing

public static cern.colt.matrix.DoubleMatrix2D multWithMissing(cern.colt.matrix.DoubleMatrix2D a,
                                                              cern.colt.matrix.DoubleMatrix2D b)

Multiple two matrices, tolerate missing values.

Parameters:

a -

b -

Returns:

notNearlyZeroIndices

public static List<Integer> notNearlyZeroIndices(cern.colt.matrix.DoubleMatrix1D d)

removeMissingOrInfinite

public static cern.colt.matrix.DoubleMatrix1D removeMissingOrInfinite(cern.colt.matrix.DoubleMatrix1D data)

Parameters:

data -

Returns:

a copy of the data with missing or infinite values removed (might be empty!)

removeMissing

public static final cern.colt.matrix.DoubleMatrix1D removeMissing(cern.colt.matrix.DoubleMatrix1D x)

Parameters:

x -

Returns:

a copy of x with missing values removed

removeMissingOrInfinite

public static cern.colt.matrix.DoubleMatrix1D removeMissingOrInfinite(cern.colt.matrix.DoubleMatrix1D reference,
                                                                      cern.colt.matrix.DoubleMatrix1D data)

Remove values from data corresponding to missing values in reference.

Parameters:

reference -

data -

Returns:

stripNegative

public static final cern.colt.matrix.DoubleMatrix1D stripNegative(cern.colt.matrix.DoubleMatrix1D x)

stripByCriterion

public static final cern.colt.matrix.DoubleMatrix1D stripByCriterion(cern.colt.matrix.DoubleMatrix1D x,
                                                                     DoubleFunction<Boolean> criterion)

conjunction

public static final cern.colt.list.BooleanArrayList conjunction(cern.colt.list.BooleanArrayList a,
                                                                cern.colt.list.BooleanArrayList b)

Compute the conjuction (logical 'and') of two boolean vectors

Parameters:

a -

b -

Returns:

conjunction of a and b

matchingCriteria

public static cern.colt.list.BooleanArrayList matchingCriteria(cern.colt.matrix.DoubleMatrix1D x,
                                                               DoubleFunction<Boolean> criterion)

Parameters:

x - vector to be operated on

criterion - a function that returns a boolean if a double matches the desired criteria

Returns:

booleans indicating which values in x match the criterion func

applyToIndicesMatchingCriteria

public static cern.colt.matrix.DoubleMatrix1D applyToIndicesMatchingCriteria(cern.colt.matrix.DoubleMatrix1D x,
                                                                             DoubleFunction<Boolean> criterion,
                                                                             DoubleFunction<Double> action)

Parameters:

x - vector to be operated on

criterion - criterion used to test values if they should be acted on.

action - function applied to values if they match the criterion

Returns:

copy of x in which the values meeting the criterion have been replaced with the return value of action, otherwise unchanged from the original x

stripNonOK

public static final cern.colt.matrix.DoubleMatrix1D stripNonOK(cern.colt.matrix.DoubleMatrix1D x,
                                                               cern.colt.list.BooleanArrayList ok)

Parameters:

x - a vector of values to be filtered

ok - a list of booleans defining which values are "ok".

Returns:

A copy of x that has the non-ok values removed.

replaceValues

public static void replaceValues(cern.colt.matrix.DoubleMatrix1D x,
                                 cern.colt.list.BooleanArrayList toReplace,
                                 cern.colt.matrix.DoubleMatrix1D replacements)

Perform the awkward operation of substituting certain values in a vector from values in another vector.

Parameters:

x - vector to be operated on in place (it will be modified).

toReplace - boolean indicators of same length of x, 'true' indicates a value to be replaced in x with a value from 'replacements'; 'false' will be unmodified in x.

replacements - the replacements, in order, to be substituted in x where toReplace(i) is true. This vector can be shorter than x.

select

public static cern.colt.matrix.DoubleMatrix1D select(cern.colt.matrix.DoubleMatrix1D v,
                                                     Collection<Integer> selected)

selectColumns

public static cern.colt.matrix.DoubleMatrix2D selectColumns(cern.colt.matrix.DoubleMatrix2D n,
                                                            Collection<Integer> selected)

selectColumnsAndRows

public static cern.colt.matrix.DoubleMatrix2D selectColumnsAndRows(cern.colt.matrix.DoubleMatrix2D n,
                                                                   Collection<Integer> selected)

Parameters:

n - square matrix

selected -

Returns:

selectRows

public static cern.colt.matrix.DoubleMatrix2D selectRows(cern.colt.matrix.DoubleMatrix2D n,
                                                         Collection<Integer> selected)

sizeWithoutMissingValues

public static int sizeWithoutMissingValues(cern.colt.matrix.DoubleMatrix1D list)

toList

public static cern.colt.list.DoubleArrayList toList(cern.colt.matrix.DoubleMatrix1D vector)

Makes a copy

Parameters:

vector -

Returns: