jigcell.compare.data
Class PackedTreeDataElement

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

All Implemented Interfaces:

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

Direct Known Subclasses:

PackedTreeDataElement2

public class PackedTreeDataElement
extends TreeDataElement

An implementation of EditableDataElement that uses a red-black tree to store values. The tree keys are boxed. Each key can hold a pack of values so this structure uses less memory than SparseTreeDataElement for dense collections. The size of the pack is adjustable. PackedTreeDataElement does not protect against concurrent edits. The maximum number of values this element can contain is approximately 2^60, 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

protected static java.lang.String	MESSAGE_CHUNKSIZEERROR Error message when the chunk size is too small
protected static java.lang.String	MESSAGE_LASTERROR Error message when the last value in a pack is incorrect
protected long	size Element packing size
protected static int	SIZE_DEFAULTPACK Size of default element pack

Fields inherited from class jigcell.compare.data.TreeDataElement

length, 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

PackedTreeDataElement()
Creates a new data element backed by a tree with packed storage.

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

Method Summary

protected EditableDataElement	constructNew() Constructs a new element of the same type as this element.
static IEditableDataElement	createElement(java.io.Reader reader) Generates a PackedTreeDataElement from streaming input.
static IEditableDataElement	createElementSafe(java.io.Reader reader) Generates a PackedTreeDataElement from streaming input.
protected java.lang.Object	getDirect(long pos) Gets the value at a position.
protected long	lastValue() Finds the last defined value.
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.

Methods inherited from class jigcell.compare.data.TreeDataElement

clear, getLength, getValues, isAvailable, memoryLock, memoryUnlock, setLengthDirect, setValue, setValues, unsetValue

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

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, 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, getSlice, isScalar, toString, toString, toString, toString, toString, toString, toString

Methods inherited from interface java.awt.datatransfer.Transferable

getTransferData, getTransferDataFlavors, isDataFlavorSupported

Field Detail

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

MESSAGE_LASTERROR

protected static final java.lang.String MESSAGE_LASTERROR

Error message when the last value in a pack is incorrect

See Also:

Constant Field Values

size

protected long size

Element packing size

Constructor Detail

PackedTreeDataElement

public PackedTreeDataElement()

Creates a new data element backed by a tree with packed storage.

PackedTreeDataElement

public PackedTreeDataElement(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 PackedTreeDataElement from streaming input.

Parameters:

reader - Reader

createElementSafe

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

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

Parameters:

reader - Reader

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

lastValue

protected long lastValue()

Finds the last defined value.

Specified by:

lastValue in class TreeDataElement

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