jigcell.compare.data
Class PackedDoubleDataElement

java.lang.Object
  javax.swing.TransferHandler
      jigcell.compare.impl.Transferer
          jigcell.compare.data.DataElement
              jigcell.compare.data.EditableDataElement
                  jigcell.compare.data.PackedDoubleDataElement

All Implemented Interfaces:

java.awt.datatransfer.Transferable, java.io.Serializable, IDataElement, IEditableDataElement

public class PackedDoubleDataElement
extends EditableDataElement

An implementation of EditableDataElement that uses an array of doubles to store values. Only real values may be placed in this element. This structure is faster and smaller than a PackedTreeDataElement. Removing values from this element does not decrease the memory used until trimToSize (int) is called. PackedDoubleDataElement does not protect against concurrent edits. This element cannot index past 2^31-1. The maximum number of values this element can contain is approximately 2^29, but is likely to fail before then.

This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.

Author:

Nicholas Allen

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class jigcell.compare.data.EditableDataElement

EditableDataElement.EditableDataElementDelegate

Nested classes/interfaces inherited from interface jigcell.compare.IDataElement

IDataElement.Type

Field Summary

private int	length Element length
protected static java.lang.String	MESSAGE_CHUNKSIZEERROR Error message when the chunk size is too small
protected static java.lang.Double	NAN NaN
private java.lang.Double	scalar Placeholder for scalar value
private int	size Element pack size
protected static int	SIZE_DEFAULTPACK Size of default element pack
private double[]	values Element values

Fields inherited from class jigcell.compare.data.EditableDataElement

DOUBLE_NaN, DOUBLE_NINFINITY, DOUBLE_PINFINITY, MESSAGE_PARSEBLOCKERROR, MESSAGE_PARSEERROR, MESSAGE_PARSEEXTRAERROR, MESSAGE_PARSELITERALERROR, PATTERN_FP, prototypeChild, TOKEN_ALL, TOKEN_BLOCKELEMENT, TOKEN_BLOCKEND, TOKEN_BLOCKSTART, TOKEN_LITERAL

Fields inherited from class jigcell.compare.data.DataElement

lockCount, LONGPOOL, PATTERN_FALSE, PATTERN_NAN, PATTERN_NINFINITY, PATTERN_NINFINITY2, PATTERN_NULL, PATTERN_PINFINITY, PATTERN_PINFINITY2, PATTERN_TRUE, PATTERN_VOID, SIZE_LONGPOOL

Fields inherited from class jigcell.compare.impl.Transferer

CSV_FOOTER, CSV_LINEPOSTPEND, CSV_LINEPREPEND, CSV_LINESEPARATOR, HTML_FOOTER, HTML_HEADPOSTPEND, HTML_HEADPREPEND, HTML_HEADSEPARATOR, HTML_LINEPOSTPEND, HTML_LINEPREPEND, HTML_LINESEPARATOR

Fields inherited from class javax.swing.TransferHandler

COPY, COPY_OR_MOVE, MOVE, NONE

Constructor Summary

PackedDoubleDataElement()
Creates a new data element backed by an array of doubles.

PackedDoubleDataElement(int size)
Creates a new data element with packed storage.

Method Summary

void	clear() Deletes all values in this element.
protected EditableDataElement	constructNew() Constructs a new element of the same type as this element.
static IEditableDataElement	createElement(java.io.Reader reader) Generates a PackedDoubleDataElement from streaming input.
static IEditableDataElement	createElementSafe(java.io.Reader reader) Generates a PackedDoubleDataElement from streaming input.
protected java.lang.Object	getDirect(long pos) Gets the value at a position.
long	getLength() The number of elements in this element, or 0 if this element is scalar.
double[]	getSlice(double[] slice, long start, int length, long stride) A dense, homogeneous subset of this element represented as a real list. If slice cannot hold the requested range, a new array is created and returned. Slice may be null. If the given start or length has no valid meaning for this element, the value is null. If the subset is not a dense list of reals or slices are not available, the value is null. Position 0 in the returned slice corresponds to position start in the original element.
double[]	getValues() The underlying array of this element.
boolean	isAvailable() Whether the element data can currently be worked with. Editing the internal state of a data generator while locked may cause subsequent calls to isAvailable to incorrectly report that the element data is available. The array store of this element is always available.
void	memoryLock() Forces the element to guarantee that the element data can currently be worked with. Implementations may or may not support reentrancy or other forms of multiple locking. Editing the internal state of a data generator while locked may cause subsequent calls to memoryLock to incorrectly terminate without guarantee that the element data can currently be worked with. Locking is unnecessary for this element.
void	memoryUnlock() Releases the element from the guarantee that the element data can currently be worked with. Implementations may or may not support reentrancy or other forms of multiple locking. Locking is unnecessary for this element.
protected void	putDirect(long pos, java.lang.Object value) Sets the value at a position.
protected void	removeDirect(long pos) Removes the value at a position.
protected void	setLengthDirect(long length) Sets the known length of an element.
void	setValue(IDataElement value) Sets the element to a list.
void	setValues(double[] values, int length) Sets the underlying array of this element.
void	trimToSize(int size) Trims the underlying array to a particular size.

Methods inherited from class jigcell.compare.data.EditableDataElement

copyValue, createElement, createElement, createElement, createElementSafe, createElementSafe, createScalarElement, createScalarElement, createScalarElement, createScalarElement, forceSlice, forceSlice, forceSlice, forceSlice, getBooleanValue, getChecked, getIntegralValue, getListValue, getLiteralValue, getPrototypeChild, getRealValue, getType, getType, makeList, moveValue, putChecked, setPrototypeChild, setValue, setValue, setValue, setValue, setValue, setValue, setValue, setValue, setValue, setValueInterpreted, setValueInterpreted, swapValues, unsetValue

Methods inherited from class jigcell.compare.data.DataElement

forceBooleanValue, forceBooleanValue, forceIntegralValue, forceIntegralValue, forceListValue, forceLiteralValue, forceLiteralValue, forceRealValue, forceRealValue, forceSlice, getBooleanValue, getIntegralValue, getLiteralValue, getLongObject, getRealValue, getSlice, getSlice, getSlice, getSlice, getTransferData, isScalar, isSpecialNonNumeric, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString, toString

Methods inherited from class jigcell.compare.impl.Transferer

addExtension, addFlavor, createCSVTable, createFormattedTable, createHTMLTable, getExceptionRecorder, getExpectedClasses, getExpectedClasses, getExpectedClasses, getFlavors, getFlavors, getPreferredExtensions, getPreferredExtensions, getTransferClass, getTransferDataFlavors, getTransferFlavor, isDataFlavorSupported, transfer

Methods inherited from class javax.swing.TransferHandler

canImport, createTransferable, exportAsDrag, exportDone, exportToClipboard, getCopyAction, getCutAction, getPasteAction, getSourceActions, getVisualRepresentation, importData

Methods inherited from class java.lang.Object

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

Methods inherited from interface jigcell.compare.IDataElement

forceBooleanValue, forceBooleanValue, forceIntegralValue, forceIntegralValue, forceListValue, forceLiteralValue, forceLiteralValue, forceRealValue, forceRealValue, forceSlice, getBooleanValue, getIntegralValue, getLiteralValue, getRealValue, getSlice, getSlice, getSlice, getSlice, isScalar, toString, toString, toString, toString, toString, toString, toString

Methods inherited from interface java.awt.datatransfer.Transferable

getTransferData, getTransferDataFlavors, isDataFlavorSupported

Field Detail

NAN

protected static final java.lang.Double NAN

NaN

SIZE_DEFAULTPACK

protected static final int SIZE_DEFAULTPACK

Size of default element pack

See Also:

Constant Field Values

MESSAGE_CHUNKSIZEERROR

protected static final java.lang.String MESSAGE_CHUNKSIZEERROR

Error message when the chunk size is too small

See Also:

Constant Field Values

values

private double[] values

Element values

scalar

private java.lang.Double scalar

Placeholder for scalar value

length

private int length

Element length

size

private int size

Element pack size

Constructor Detail

PackedDoubleDataElement

public PackedDoubleDataElement()

Creates a new data element backed by an array of doubles.

PackedDoubleDataElement

public PackedDoubleDataElement(int size)

Creates a new data element with packed storage.

Parameters:

size - Pack size

Method Detail

createElement

public static IEditableDataElement createElement(java.io.Reader reader)

Generates a PackedDoubleDataElement from streaming input.

Parameters:

reader - Reader

createElementSafe

public static IEditableDataElement createElementSafe(java.io.Reader reader)

Generates a PackedDoubleDataElement from streaming input. If an element cannot be created, an empty element in returned.

Parameters:

reader - Reader

clear

public void clear()

Deletes all values in this element.

getLength

public long getLength()

The number of elements in this element, or 0 if this element is scalar.

Specified by:

getLength in interface IDataElement

Overrides:

getLength in class DataElement

getSlice

public double[] getSlice(double[] slice,
                         long start,
                         int length,
                         long stride)

A dense, homogeneous subset of this element represented as a real list. If slice cannot hold the requested range, a new array is created and returned. Slice may be null. If the given start or length has no valid meaning for this element, the value is null. If the subset is not a dense list of reals or slices are not available, the value is null. Position 0 in the returned slice corresponds to position start in the original element.

Specified by:

getSlice in interface IDataElement

Overrides:

getSlice in class DataElement

Parameters:

slice - Suggested container for the slice

start - First position to pull

length - Number of positions to pull

stride - Interval between positions to pull

getValues

public double[] getValues()

The underlying array of this element.

isAvailable

public boolean isAvailable()

Whether the element data can currently be worked with. Editing the internal state of a data generator while locked may cause subsequent calls to isAvailable to incorrectly report that the element data is available. The array store of this element is always available.

Specified by:

isAvailable in interface IDataElement

Overrides:

isAvailable in class DataElement

memoryLock

public void memoryLock()

Forces the element to guarantee that the element data can currently be worked with. Implementations may or may not support reentrancy or other forms of multiple locking. Editing the internal state of a data generator while locked may cause subsequent calls to memoryLock to incorrectly terminate without guarantee that the element data can currently be worked with. Locking is unnecessary for this element.

Specified by:

memoryLock in interface IDataElement

Overrides:

memoryLock in class DataElement

memoryUnlock

public void memoryUnlock()

Releases the element from the guarantee that the element data can currently be worked with. Implementations may or may not support reentrancy or other forms of multiple locking. Locking is unnecessary for this element.

Specified by:

memoryUnlock in interface IDataElement

Overrides:

memoryUnlock in class DataElement

setValue

public void setValue(IDataElement value)

Sets the element to a list.

Specified by:

setValue in interface IEditableDataElement

Overrides:

setValue in class EditableDataElement

Parameters:

value - Value

setValues

public void setValues(double[] values,
                      int length)

Sets the underlying array of this element.

Parameters:

values - Underlying array

trimToSize

public void trimToSize(int size)

Trims the underlying array to a particular size. If the trimmed size is smaller than the current length, the length will be reduced. This does nothing if the underlying array is smaller than the requested size.

Parameters:

size - Size

constructNew

protected EditableDataElement constructNew()

Constructs a new element of the same type as this element.

Specified by:

constructNew in class EditableDataElement

getDirect

protected java.lang.Object getDirect(long pos)

Gets the value at a position. Boolean values are represented by Boolean. Empty values are represented by null. Integral values are represented by Integer. Literal values are represented by String. Multiple values are represented by DataElement. Real values are represented by Double. The position of the object may be anything.

Specified by:

getDirect in class EditableDataElement

Parameters:

pos - Position

putDirect

protected void putDirect(long pos,
                         java.lang.Object value)

Sets the value at a position. Boolean values are represented by Boolean. Empty values are represented by null. Integral values are represented by Integer. Literal values are represented by String. Multiple values are represented by DataElement. Real values are represented by Double. The position of the object may be anything.

Specified by:

putDirect in class EditableDataElement

Parameters:

pos - Position

value - Value

removeDirect

protected void removeDirect(long pos)

Removes the value at a position. The position of the object may be anything.

Specified by:

removeDirect in class EditableDataElement

Parameters:

pos - Position

setLengthDirect

protected void setLengthDirect(long length)

Sets the known length of an element. The length of the object may be anything.

Specified by:

setLengthDirect in class EditableDataElement

Parameters:

length - Length of element