ch.systemsx.cisd.base.mdarray

Class MDAbstractArray<T>

java.lang.Object

ch.systemsx.cisd.base.mdarray.MDAbstractArray<T>

All Implemented Interfaces:

java.io.Serializable, java.lang.Iterable<MDAbstractArray.ArrayEntry>

Direct Known Subclasses:

HDF5TimeDurationMDArray, MDArray, MDByteArray, MDDoubleArray, MDFloatArray, MDIntArray, MDLongArray, MDShortArray

public abstract class MDAbstractArray<T>
extends java.lang.Object
implements java.io.Serializable, java.lang.Iterable<MDAbstractArray.ArrayEntry>

Base class of a multi-dimensional array. The dimensions of an array are provided separately from the data as a int[].

The array can grow or shrink in the first dimension (dimensions[0]). Dimensions 1...n are static. They are said to form a hyper-row.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	MDAbstractArray.ArrayEntry A class to represent an entry (index and value) of a MDArray, used for iteration.

Method Summary

Methods

Modifier and Type	Method and Description
abstract int	capacity() Returns the capacity of elements in the array.
int	computeIndex(int... indices) Computes the linear index for the multi-dimensional indices provided.
int	computeIndex(int indexX, int indexY) Computes the linear index for the two-dimensional (indexX, indexY) provided.
int	computeIndex(int indexX, int indexY, int indexZ) Computes the linear index for the three-dimensional (indexX, indexY, indexZ) provided.
int[]	computeReverseIndex(int linearIndex) Computes the multi-dimensional index from the linearIndex.
int	decNumberOfHyperRows(int count) Decrease the number of hyper-rows by count.
int[]	dimensions() Returns a copy of the dimensions of the multi-dimensional array.
abstract java.lang.Object	getAsFlatArray() Returns the array in flattened form.
abstract T	getAsObject(int... indices) Return an object which has the same value as the element of the array specified by indices.
abstract T	getAsObject(int linearIndex) Return an object which has the same value as the element of the array specified by linearIndex.
abstract java.lang.Object	getCopyAsFlatArray() Returns a copy of the array in flattened form.
static int	getLength(int[] dimensions) Returns the one-dimensional length of the multi-dimensional array defined by dimensions.
static int	getLength(int[] dimensions, int capacityHyperRows) Returns the one-dimensional length of the multi-dimensional array defined by dimensions.
static int	getLength(long[] dimensions) Returns the one-dimensional length of the multi-dimensional array defined by dimensions.
static int	getLength(long[] dimensions, long capacityHyperRows) Returns the one-dimensional length of the multi-dimensional array defined by dimensions.
int	incNumberOfHyperRows(int count) Increase the number of hyper-rows by count.
java.util.Iterator<MDAbstractArray.ArrayEntry>	iterator()
long[]	longDimensions() Returns a copy of the dimensions of the multi-dimensional array as long[].
int	numberOfHyperRows() Returns the current number of hyper rows of of this array.
int	rank() Returns the rank of the array.
abstract void	setToObject(T value, int... indices) Sets the element of the array specified by indices to the particular value.
abstract void	setToObject(T value, int linearIndex) Sets the element of the array specified by linearIndex to the particular value.
int	size() Returns the number of elements in the array.
int	size(int dim) Returns the extent of the array along its dim-th axis.
static int[]	toInt(long[] dimensions) Converts the dimensions from long[] to int[].
static long[]	toLong(int[] dimensions) Converts the dimensions from int[] to long[].
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Method Detail

rank

public int rank()

Returns the rank of the array.

size

public int size(int dim)

Returns the extent of the array along its dim-th axis.

dimensions

public int[] dimensions()

Returns a copy of the dimensions of the multi-dimensional array.

longDimensions

public long[] longDimensions()

Returns a copy of the dimensions of the multi-dimensional array as long[].

size

public int size()

Returns the number of elements in the array.

numberOfHyperRows

public int numberOfHyperRows()

Returns the current number of hyper rows of of this array.

getAsObject

public abstract T getAsObject(int linearIndex)

Return an object which has the same value as the element of the array specified by linearIndex.

Parameters:

linearIndex - The index in the linear array returned by getAsFlatArray().

Returns:

The value at the specified index.

getAsObject

public abstract T getAsObject(int... indices)

Return an object which has the same value as the element of the array specified by indices.

setToObject

public abstract void setToObject(T value,
               int... indices)

Sets the element of the array specified by indices to the particular value.

setToObject

public abstract void setToObject(T value,
               int linearIndex)

Sets the element of the array specified by linearIndex to the particular value.

Parameters:

value - The new value to set.

linearIndex - The index in the linear array returned by getAsFlatArray().

getAsFlatArray

public abstract java.lang.Object getAsFlatArray()

Returns the array in flattened form. Changes to the returned object will change the multi-dimensional array directly.

getCopyAsFlatArray

public abstract java.lang.Object getCopyAsFlatArray()

Returns a copy of the array in flattened form. Changes to the returned object will not change the multi-dimensional array directly.

capacity

public abstract int capacity()

Returns the capacity of elements in the array.

incNumberOfHyperRows

public int incNumberOfHyperRows(int count)

Increase the number of hyper-rows by count. Doubles the capacity if needed.

Returns:

The new number of rows.

decNumberOfHyperRows

public int decNumberOfHyperRows(int count)

Decrease the number of hyper-rows by count.

Returns:

The new number of rows.

computeIndex

public int computeIndex(int... indices)

Computes the linear index for the multi-dimensional indices provided.

computeReverseIndex

public int[] computeReverseIndex(int linearIndex)

Computes the multi-dimensional index from the linearIndex.

computeIndex

public int computeIndex(int indexX,
               int indexY)

Computes the linear index for the two-dimensional (indexX, indexY) provided.

computeIndex

public int computeIndex(int indexX,
               int indexY,
               int indexZ)

Computes the linear index for the three-dimensional (indexX, indexY, indexZ) provided.

toInt

public static int[] toInt(long[] dimensions)

Converts the dimensions from long[] to int[].

toLong

public static long[] toLong(int[] dimensions)

Converts the dimensions from int[] to long[].

getLength

public static int getLength(int[] dimensions)

Returns the one-dimensional length of the multi-dimensional array defined by dimensions.

Throws:

java.lang.IllegalArgumentException - If dimensions overflow the int type.

getLength

public static int getLength(int[] dimensions,
            int capacityHyperRows)

Returns the one-dimensional length of the multi-dimensional array defined by dimensions. If capacityHyperRows > dimensions[0], then it will replace dimensions[0] by capacityHyperRows

Throws:

java.lang.IllegalArgumentException - If dimensions overflow the int type.

getLength

public static int getLength(long[] dimensions)

Returns the one-dimensional length of the multi-dimensional array defined by dimensions.

Throws:

java.lang.IllegalArgumentException - If dimensions overflow the int type.

getLength

public static int getLength(long[] dimensions,
            long capacityHyperRows)

Returns the one-dimensional length of the multi-dimensional array defined by dimensions. If capacityHyperRows > dimensions[0], then it will replace dimensions[0] by capacityHyperRows

Throws:

java.lang.IllegalArgumentException - If dimensions overflow the int type.

iterator

public java.util.Iterator<MDAbstractArray.ArrayEntry> iterator()

Specified by:

iterator in interface java.lang.Iterable<MDAbstractArray.ArrayEntry>

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object