write vtkTree data to PhyloXML format. More...

#include <vtkPhyloXMLTreeWriter.h>

Inheritance diagram for vtkPhyloXMLTreeWriter:

Collaboration diagram for vtkPhyloXMLTreeWriter:

Public Types
typedef vtkXMLWriter	Superclass

Public Types inherited from vtkXMLWriter
enum	{ Int32 =32, Int64 =64 }

enum	CompressorType { NONE, ZLIB }

typedef vtkAlgorithm	Superclass

enum	{ BigEndian, LittleEndian }

enum	{ Ascii, Binary, Appended }

enum	{ UInt32 =32, UInt64 =64 }

Public Types inherited from vtkAlgorithm
typedef vtkObject	Superclass

enum	DesiredOutputPrecision { SINGLE_PRECISION, DOUBLE_PRECISION, DEFAULT_PRECISION }

Public Types inherited from vtkObject
typedef vtkObjectBase	Superclass

Public Member Functions
virtual int	IsA (const char *type)

vtkPhyloXMLTreeWriter *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent)

virtual const char *	GetDefaultFileExtension ()

void	IgnoreArray (const char *arrayName)


vtkTree *	GetInput ()

vtkTree *	GetInput (int port)


virtual vtkStdString	GetEdgeWeightArrayName ()

virtual void	SetEdgeWeightArrayName (vtkStdString)


virtual vtkStdString	GetNodeNameArrayName ()

virtual void	SetNodeNameArrayName (vtkStdString)

Public Member Functions inherited from vtkXMLWriter
vtkXMLWriter *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent)

int	Write ()

virtual int	ProcessRequest (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)

virtual void	SetByteOrder (int)

virtual int	GetByteOrder ()

void	SetByteOrderToBigEndian ()

void	SetByteOrderToLittleEndian ()

virtual void	SetHeaderType (int)

virtual int	GetHeaderType ()

void	SetHeaderTypeToUInt32 ()

void	SetHeaderTypeToUInt64 ()

virtual void	SetIdType (int)

virtual int	GetIdType ()

void	SetIdTypeToInt32 ()

void	SetIdTypeToInt64 ()

virtual void	SetFileName (const char *)

virtual char *	GetFileName ()

virtual void	SetWriteToOutputString (int)

virtual int	GetWriteToOutputString ()

virtual void	WriteToOutputStringOn ()

virtual void	WriteToOutputStringOff ()

std::string	GetOutputString ()

virtual void	SetCompressor (vtkDataCompressor *)

virtual vtkDataCompressor *	GetCompressor ()

void	SetCompressorType (int compressorType)

void	SetCompressorTypeToNone ()

void	SetCompressorTypeToZLib ()

virtual void	SetBlockSize (size_t blockSize)

virtual size_t	GetBlockSize ()

virtual void	SetDataMode (int)

virtual int	GetDataMode ()

void	SetDataModeToAscii ()

void	SetDataModeToBinary ()

void	SetDataModeToAppended ()

virtual void	SetEncodeAppendedData (int)

virtual int	GetEncodeAppendedData ()

virtual void	EncodeAppendedDataOn ()

virtual void	EncodeAppendedDataOff ()

void	SetInputData (vtkDataObject *)

void	SetInputData (int, vtkDataObject *)

vtkDataObject *	GetInput (int port)

vtkDataObject *	GetInput ()

virtual void	SetTimeStep (int)

virtual int	GetTimeStep ()

virtual int *	GetTimeStepRange ()

virtual void	GetTimeStepRange (int &, int &)

virtual void	GetTimeStepRange (int[2])

virtual void	SetTimeStepRange (int, int)

void	SetTimeStepRange (int[2])

virtual int	GetNumberOfTimeSteps ()

virtual void	SetNumberOfTimeSteps (int)

void	Start ()

void	Stop ()

void	WriteNextTime (double time)

Public Member Functions inherited from vtkAlgorithm
vtkAlgorithm *	NewInstance () const

int	HasExecutive ()

vtkExecutive *	GetExecutive ()

virtual void	SetExecutive (vtkExecutive *executive)

virtual int	ModifyRequest (vtkInformation *request, int when)

vtkInformation *	GetInputPortInformation (int port)

vtkInformation *	GetOutputPortInformation (int port)

int	GetNumberOfInputPorts ()

int	GetNumberOfOutputPorts ()

void	UpdateProgress (double amount)

vtkInformation *	GetInputArrayInformation (int idx)

void	RemoveAllInputs ()

vtkDataObject *	GetOutputDataObject (int port)

virtual void	RemoveInputConnection (int port, vtkAlgorithmOutput *input)

virtual void	RemoveInputConnection (int port, int idx)

virtual void	RemoveAllInputConnections (int port)

int	GetNumberOfInputConnections (int port)

int	GetTotalNumberOfInputConnections ()

vtkAlgorithmOutput *	GetInputConnection (int port, int index)

vtkAlgorithm *	GetInputAlgorithm (int port, int index, int &algPort)

vtkAlgorithm *	GetInputAlgorithm (int port, int index)

vtkExecutive *	GetInputExecutive (int port, int index)

vtkInformation *	GetInputInformation (int port, int index)

vtkInformation *	GetOutputInformation (int port)

virtual void	UpdateInformation ()

virtual void	UpdateDataObject ()

virtual void	PropagateUpdateExtent ()

virtual void	UpdateWholeExtent ()

void	ConvertTotalInputToPortConnection (int ind, int &port, int &conn)

int	SetUpdateExtentToWholeExtent (int port)

int	SetUpdateExtentToWholeExtent ()

void	SetUpdateExtent (int port, int extent[6])

int	ProcessRequest (vtkInformation request, vtkCollection inInfo, vtkInformationVector *outInfo)

virtual int	ComputePipelineMTime (vtkInformation request, vtkInformationVector inInfoVec, vtkInformationVector outInfoVec, int requestFromOutputPort, unsigned long *mtime)

virtual vtkInformation *	GetInformation ()

virtual void	SetInformation (vtkInformation *)

virtual void	Register (vtkObjectBase *o)

virtual void	UnRegister (vtkObjectBase *o)

virtual void	SetAbortExecute (int)

virtual int	GetAbortExecute ()

virtual void	AbortExecuteOn ()

virtual void	AbortExecuteOff ()

virtual void	SetProgress (double)

virtual double	GetProgress ()

void	SetProgressText (const char *ptext)

virtual char *	GetProgressText ()

virtual unsigned long	GetErrorCode ()

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, const char *name)

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, int fieldAttributeType)

virtual void	SetInputArrayToProcess (int idx, vtkInformation *info)

virtual void	SetInputArrayToProcess (int idx, int port, int connection, const char fieldAssociation, const char attributeTypeorName)

vtkDataObject *	GetInputDataObject (int port, int connection)

virtual void	SetInputConnection (int port, vtkAlgorithmOutput *input)

virtual void	SetInputConnection (vtkAlgorithmOutput *input)

virtual void	AddInputConnection (int port, vtkAlgorithmOutput *input)

virtual void	AddInputConnection (vtkAlgorithmOutput *input)

virtual void	SetInputDataObject (int port, vtkDataObject *data)

virtual void	SetInputDataObject (vtkDataObject *data)

virtual void	AddInputDataObject (int port, vtkDataObject *data)

virtual void	AddInputDataObject (vtkDataObject *data)

vtkAlgorithmOutput *	GetOutputPort (int index)

vtkAlgorithmOutput *	GetOutputPort ()

vtkAlgorithm *	GetInputAlgorithm ()

vtkExecutive *	GetInputExecutive ()

vtkInformation *	GetInputInformation ()

virtual void	Update (int port)

virtual void	Update ()

virtual void	SetReleaseDataFlag (int)

virtual int	GetReleaseDataFlag ()

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

int	UpdateExtentIsEmpty (vtkInformation pinfo, vtkDataObject output)

int	UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)

void	SetUpdateExtent (int port, int piece, int numPieces, int ghostLevel)

void	SetUpdateExtent (int piece, int numPieces, int ghostLevel)

void	SetUpdateExtent (int extent[6])

int *	GetUpdateExtent ()

int *	GetUpdateExtent (int port)

void	GetUpdateExtent (int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)

void	GetUpdateExtent (int port, int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)

void	GetUpdateExtent (int extent[6])

void	GetUpdateExtent (int port, int extent[6])

int	GetUpdatePiece ()

int	GetUpdatePiece (int port)

int	GetUpdateNumberOfPieces ()

int	GetUpdateNumberOfPieces (int port)

int	GetUpdateGhostLevel ()

int	GetUpdateGhostLevel (int port)

void	SetProgressObserver (vtkProgressObserver *)

virtual vtkProgressObserver *	GetProgressObserver ()

Public Member Functions inherited from vtkObject
vtkObject *	NewInstance () const

virtual void	DebugOn ()

virtual void	DebugOff ()

bool	GetDebug ()

void	SetDebug (bool debugFlag)

virtual void	Modified ()

virtual unsigned long	GetMTime ()

unsigned long	AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)

unsigned long	AddObserver (const char event, vtkCommand , float priority=0.0f)

vtkCommand *	GetCommand (unsigned long tag)

void	RemoveObserver (vtkCommand *)

void	RemoveObservers (unsigned long event, vtkCommand *)

void	RemoveObservers (const char event, vtkCommand )

int	HasObserver (unsigned long event, vtkCommand *)

int	HasObserver (const char event, vtkCommand )

void	RemoveObserver (unsigned long tag)

void	RemoveObservers (unsigned long event)

void	RemoveObservers (const char *event)

void	RemoveAllObservers ()

int	HasObserver (unsigned long event)

int	HasObserver (const char *event)

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::*callback)(), float priority=0.0f)

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, bool(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)

int	InvokeEvent (unsigned long event, void *callData)

int	InvokeEvent (const char event, void callData)

int	InvokeEvent (unsigned long event)

int	InvokeEvent (const char *event)

Public Member Functions inherited from vtkObjectBase
const char *	GetClassName () const

virtual void	Delete ()

virtual void	FastDelete ()

void	Print (ostream &os)

void	SetReferenceCount (int)

void	PrintRevisions (ostream &)

virtual void	PrintHeader (ostream &os, vtkIndent indent)

virtual void	PrintTrailer (ostream &os, vtkIndent indent)

int	GetReferenceCount ()

Static Public Member Functions
static vtkPhyloXMLTreeWriter *	New ()

static int	IsTypeOf (const char *type)

static vtkPhyloXMLTreeWriter *	SafeDownCast (vtkObjectBase *o)

Static Public Member Functions inherited from vtkXMLWriter
static int	IsTypeOf (const char *type)

static vtkXMLWriter *	SafeDownCast (vtkObjectBase *o)

Static Public Member Functions inherited from vtkAlgorithm
static vtkAlgorithm *	New ()

static int	IsTypeOf (const char *type)

static vtkAlgorithm *	SafeDownCast (vtkObjectBase *o)

static vtkInformationIntegerKey *	INPUT_IS_OPTIONAL ()

static vtkInformationIntegerKey *	INPUT_IS_REPEATABLE ()

static vtkInformationInformationVectorKey *	INPUT_REQUIRED_FIELDS ()

static vtkInformationStringVectorKey *	INPUT_REQUIRED_DATA_TYPE ()

static vtkInformationInformationVectorKey *	INPUT_ARRAYS_TO_PROCESS ()

static vtkInformationIntegerKey *	INPUT_PORT ()

static vtkInformationIntegerKey *	INPUT_CONNECTION ()

static vtkInformationIntegerKey *	CAN_PRODUCE_SUB_EXTENT ()

static vtkInformationIntegerKey *	CAN_HANDLE_PIECE_REQUEST ()

static void	SetDefaultExecutivePrototype (vtkExecutive *proto)

Static Public Member Functions inherited from vtkObject
static int	IsTypeOf (const char *type)

static vtkObject *	SafeDownCast (vtkObjectBase *o)

static vtkObject *	New ()

static void	BreakOnError ()

static void	SetGlobalWarningDisplay (int val)

static void	GlobalWarningDisplayOn ()

static void	GlobalWarningDisplayOff ()

static int	GetGlobalWarningDisplay ()

Static Public Member Functions inherited from vtkObjectBase
static int	IsTypeOf (const char *name)

static vtkObjectBase *	New ()

Protected Member Functions
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkPhyloXMLTreeWriter ()

	~vtkPhyloXMLTreeWriter ()

virtual int	WriteData ()

virtual const char *	GetDataSetName ()

virtual int	StartFile ()

virtual int	EndFile ()

void	WriteTreeLevelProperties (vtkTree input, vtkXMLDataElement rootElement)

void	WriteNameElement (vtkIdType vertex, vtkXMLDataElement *element)

virtual int	FillInputPortInformation (int port, vtkInformation *info)


void	WriteTreeLevelElement (vtkTree input, vtkXMLDataElement rootElement, const char elementName, const char attributeName)


void	WriteCladeElement (vtkTree const input, vtkIdType vertex, vtkXMLDataElement parentElement)


void	WriteBranchLengthAttribute (vtkTree const input, vtkIdType vertex, vtkXMLDataElement element)


void	WriteConfidenceElement (vtkTree const input, vtkIdType vertex, vtkXMLDataElement element)


void	WriteColorElement (vtkTree const input, vtkIdType vertex, vtkXMLDataElement element)


void	WritePropertyElement (vtkAbstractArray array, vtkIdType vertex, vtkXMLDataElement element)


const char *	GetArrayAttribute (vtkAbstractArray array, const char attributeName)

Protected Member Functions inherited from vtkXMLWriter
	vtkXMLWriter ()

	~vtkXMLWriter ()

virtual int	RequestInformation (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)

virtual int	RequestData (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)

virtual void	SetDataStream (vtkOutputStream *)

virtual vtkOutputStream *	GetDataStream ()

virtual int	WriteInternal ()

virtual int	GetDataSetMajorVersion ()

virtual int	GetDataSetMinorVersion ()

vtkDataSet *	GetInputAsDataSet ()

virtual void	WriteFileAttributes ()

void	DeleteAFile ()

void	DeleteAFile (const char *name)

virtual int	WritePrimaryElement (ostream &os, vtkIndent indent)

virtual void	WritePrimaryElementAttributes (ostream &os, vtkIndent indent)

void	StartAppendedData ()

void	EndAppendedData ()

vtkTypeInt64	ReserveAttributeSpace (const char *attr, size_t length=20)

vtkTypeInt64	GetAppendedDataOffset ()

void	WriteAppendedDataOffset (vtkTypeInt64 streamPos, vtkTypeInt64 &lastoffset, const char *attr=0)

void	ForwardAppendedDataOffset (vtkTypeInt64 streamPos, vtkTypeInt64 offset, const char *attr=0)

void	ForwardAppendedDataDouble (vtkTypeInt64 streamPos, double value, const char *attr)

int	WriteScalarAttribute (const char *name, int data)

int	WriteScalarAttribute (const char *name, float data)

int	WriteScalarAttribute (const char *name, double data)

int	WriteVectorAttribute (const char name, int length, int data)

int	WriteVectorAttribute (const char name, int length, float data)

int	WriteVectorAttribute (const char name, int length, double data)

int	WriteDataModeAttribute (const char *name)

int	WriteWordTypeAttribute (const char *name, int dataType)

int	WriteStringAttribute (const char name, const char value)

void	WriteArrayHeader (vtkAbstractArray a, vtkIndent indent, const char alternateName, int writeNumTuples, int timestep)

virtual void	WriteArrayFooter (ostream &os, vtkIndent indent, vtkAbstractArray *a, int shortFormat)

virtual void	WriteArrayInline (vtkAbstractArray a, vtkIndent indent, const char alternateName=0, int writeNumTuples=0)

virtual void	WriteInlineData (vtkAbstractArray *a, vtkIndent indent)

void	WriteArrayAppended (vtkAbstractArray a, vtkIndent indent, OffsetsManager &offs, const char alternateName=0, int writeNumTuples=0, int timestep=0)

int	WriteAsciiData (vtkAbstractArray *a, vtkIndent indent)

int	WriteBinaryData (vtkAbstractArray *a)

int	WriteBinaryDataInternal (vtkAbstractArray *a)

void	WriteArrayAppendedData (vtkAbstractArray *a, vtkTypeInt64 pos, vtkTypeInt64 &lastoffset)

void	WriteFieldData (vtkIndent indent)

void	WriteFieldDataInline (vtkFieldData *fd, vtkIndent indent)

void	WritePointDataInline (vtkPointData *pd, vtkIndent indent)

void	WriteCellDataInline (vtkCellData *cd, vtkIndent indent)

void	WriteFieldDataAppended (vtkFieldData fd, vtkIndent indent, OffsetsManagerGroup fdManager)

void	WriteFieldDataAppendedData (vtkFieldData fd, int timestep, OffsetsManagerGroup fdManager)

void	WritePointDataAppended (vtkPointData pd, vtkIndent indent, OffsetsManagerGroup pdManager)

void	WritePointDataAppendedData (vtkPointData pd, int timestep, OffsetsManagerGroup pdManager)

void	WriteCellDataAppended (vtkCellData cd, vtkIndent indent, OffsetsManagerGroup cdManager)

void	WriteCellDataAppendedData (vtkCellData cd, int timestep, OffsetsManagerGroup cdManager)

void	WriteAttributeIndices (vtkDataSetAttributes dsa, char *names)

void	WritePointsAppended (vtkPoints points, vtkIndent indent, OffsetsManager manager)

void	WritePointsAppendedData (vtkPoints points, int timestep, OffsetsManager pdManager)

void	WritePointsInline (vtkPoints *points, vtkIndent indent)

void	WriteCoordinatesInline (vtkDataArray xc, vtkDataArray yc, vtkDataArray *zc, vtkIndent indent)

void	WriteCoordinatesAppended (vtkDataArray xc, vtkDataArray yc, vtkDataArray zc, vtkIndent indent, OffsetsManagerGroup coordManager)

void	WriteCoordinatesAppendedData (vtkDataArray xc, vtkDataArray yc, vtkDataArray zc, int timestep, OffsetsManagerGroup coordManager)

void	WritePPointData (vtkPointData *pd, vtkIndent indent)

void	WritePCellData (vtkCellData *cd, vtkIndent indent)

void	WritePPoints (vtkPoints *points, vtkIndent indent)

void	WritePArray (vtkAbstractArray a, vtkIndent indent, const char alternateName=0)

void	WritePCoordinates (vtkDataArray xc, vtkDataArray yc, vtkDataArray *zc, vtkIndent indent)

int	WriteBinaryDataBlock (unsigned char *in_data, size_t numWords, int wordType)

void	PerformByteSwap (void *data, size_t numWords, size_t wordSize)

int	CreateCompressionHeader (size_t size)

int	WriteCompressionBlock (unsigned char *data, size_t size)

int	WriteCompressionHeader ()

size_t	GetWordTypeSize (int dataType)

const char *	GetWordTypeName (int dataType)

size_t	GetOutputWordTypeSize (int dataType)

char **	CreateStringArray (int numStrings)

void	DestroyStringArray (int numStrings, char **strings)

virtual void	GetProgressRange (float range[2])

virtual void	SetProgressRange (const float range[2], int curStep, int numSteps)

virtual void	SetProgressRange (const float range[2], int curStep, const float *fractions)

virtual void	SetProgressPartial (float fraction)

virtual void	UpdateProgressDiscrete (float progress)

int	OpenStream ()

int	OpenFile ()

int	OpenString ()

void	CloseStream ()

void	CloseFile ()

void	CloseString ()

Protected Member Functions inherited from vtkAlgorithm
	vtkAlgorithm ()

	~vtkAlgorithm ()

virtual int	FillOutputPortInformation (int port, vtkInformation *info)

virtual void	SetNumberOfInputPorts (int n)

virtual void	SetNumberOfOutputPorts (int n)

int	InputPortIndexInRange (int index, const char *action)

int	OutputPortIndexInRange (int index, const char *action)

int	GetInputArrayAssociation (int idx, vtkInformationVector **inputVector)

virtual vtkExecutive *	CreateDefaultExecutive ()

virtual void	ReportReferences (vtkGarbageCollector *)

virtual void	SetNumberOfInputConnections (int port, int n)

int	GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector)

int	GetInputArrayAssociation (int idx, vtkDataObject *input)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input)

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input, int &association)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input)

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association)

vtkInformation *	GetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector)

virtual void	SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input)

void	SetInputDataInternal (int port, vtkDataObject *input)

void	AddInputDataInternal (int port, vtkDataObject *input)

virtual void	SetErrorCode (unsigned long)

Protected Member Functions inherited from vtkObject
	vtkObject ()

virtual	~vtkObject ()

virtual void	RegisterInternal (vtkObjectBase *, int check)

virtual void	UnRegisterInternal (vtkObjectBase *, int check)

void	InternalGrabFocus (vtkCommand mouseEvents, vtkCommand keypressEvents=NULL)

void	InternalReleaseFocus ()

Protected Member Functions inherited from vtkObjectBase
	vtkObjectBase ()

virtual	~vtkObjectBase ()

virtual void	CollectRevisions (ostream &)

	vtkObjectBase (const vtkObjectBase &)

void	operator= (const vtkObjectBase &)

Protected Attributes
vtkInformation *	InputInformation

vtkStdString	EdgeWeightArrayName

vtkStdString	NodeNameArrayName

vtkAbstractArray *	EdgeWeightArray

vtkAbstractArray *	NodeNameArray

vtkSmartPointer< vtkStringArray >	Blacklist

Protected Attributes inherited from vtkXMLWriter
char *	FileName

ostream *	Stream

int	WriteToOutputString

std::string	OutputString

int	ByteOrder

int	HeaderType

int	IdType

int	DataMode

int	EncodeAppendedData

vtkTypeInt64	AppendedDataPosition

OffsetsManagerGroup *	FieldDataOM

Int32IdType *	Int32IdTypeBuffer

unsigned char *	ByteSwapBuffer

vtkDataCompressor *	Compressor

size_t	BlockSize

size_t	CompressionBlockNumber

vtkXMLDataHeader *	CompressionHeader

vtkTypeInt64	CompressionHeaderPosition

vtkOutputStream *	DataStream

float	ProgressRange [2]

ofstream *	OutFile

std::ostringstream *	OutStringStream

int	TimeStep

int	CurrentTimeIndex

int	NumberOfTimeSteps

int	TimeStepRange [2]

int	UserContinueExecuting

bool	UsePreviousVersion

vtkTypeInt64 *	NumberOfTimeValues

Protected Attributes inherited from vtkAlgorithm
vtkInformation *	Information

double	Progress

char *	ProgressText

vtkProgressObserver *	ProgressObserver

unsigned long	ErrorCode

Protected Attributes inherited from vtkObject
bool	Debug

vtkTimeStamp	MTime

vtkSubjectHelper *	SubjectHelper

Protected Attributes inherited from vtkObjectBase
vtkAtomicInt32	ReferenceCount

vtkWeakPointerBase **	WeakPointers

Additional Inherited Members
Public Attributes inherited from vtkAlgorithm
int	AbortExecute

Static Protected Member Functions inherited from vtkAlgorithm
static vtkInformationIntegerKey *	PORT_REQUIREMENTS_FILLED ()

Static Protected Attributes inherited from vtkAlgorithm
static vtkExecutive *	DefaultExecutivePrototype

Detailed Description

write vtkTree data to PhyloXML format.

vtkPhyloXMLTreeWriter is writes a vtkTree to a PhyloXML formatted file or string.

Tests:: vtkPhyloXMLTreeWriter (Tests)

Definition at line 37 of file vtkPhyloXMLTreeWriter.h.

Member Typedef Documentation

typedef vtkXMLWriter vtkPhyloXMLTreeWriter::Superclass

Definition at line 41 of file vtkPhyloXMLTreeWriter.h.

Constructor & Destructor Documentation

vtkPhyloXMLTreeWriter::vtkPhyloXMLTreeWriter ( )

protected

vtkPhyloXMLTreeWriter::~vtkPhyloXMLTreeWriter ( )

inlineprotected

Definition at line 78 of file vtkPhyloXMLTreeWriter.h.

Member Function Documentation

static vtkPhyloXMLTreeWriter* vtkPhyloXMLTreeWriter::New ( )

static

static int vtkPhyloXMLTreeWriter::IsTypeOf ( const char * type )

static

virtual int vtkPhyloXMLTreeWriter::IsA ( const char * name )

virtual

Return 1 if this class is the same type of (or a subclass of) the named class. Returns 0 otherwise. This method works in combination with vtkTypeMacro found in vtkSetGet.h.

Reimplemented from vtkXMLWriter.

static vtkPhyloXMLTreeWriter* vtkPhyloXMLTreeWriter::SafeDownCast ( vtkObjectBase * o )

static

virtual vtkObjectBase* vtkPhyloXMLTreeWriter::NewInstanceInternal ( ) const

protectedvirtual

Reimplemented from vtkXMLWriter.

vtkPhyloXMLTreeWriter* vtkPhyloXMLTreeWriter::NewInstance ( ) const

void vtkPhyloXMLTreeWriter::PrintSelf	(	ostream &	os,
		vtkIndent	indent
	)

virtual

Methods invoked by print to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from vtkAlgorithm.

vtkTree* vtkPhyloXMLTreeWriter::GetInput ( )

Get the input to this writer.

vtkTree* vtkPhyloXMLTreeWriter::GetInput ( int port )

Get the input to this writer.

virtual const char* vtkPhyloXMLTreeWriter::GetDefaultFileExtension ( )

virtual

Get the default file extension for files written by this writer.

Implements vtkXMLWriter.

virtual vtkStdString vtkPhyloXMLTreeWriter::GetEdgeWeightArrayName ( )

virtual

Get/Set the name of the input's tree edge weight array. This array must be part of the input tree's EdgeData. The default name is "weight". If this array cannot be found, then no edge weights will be included in the output of this writer.

virtual void vtkPhyloXMLTreeWriter::SetEdgeWeightArrayName ( vtkStdString )

virtual

Get/Set the name of the input's tree edge weight array. This array must be part of the input tree's EdgeData. The default name is "weight". If this array cannot be found, then no edge weights will be included in the output of this writer.

virtual vtkStdString vtkPhyloXMLTreeWriter::GetNodeNameArrayName ( )

virtual

Get/Set the name of the input's tree node name array. This array must be part of the input tree's VertexData. The default name is "node name". If this array cannot be found, then no node names will be included in the output of this writer.

virtual void vtkPhyloXMLTreeWriter::SetNodeNameArrayName ( vtkStdString )

virtual

Get/Set the name of the input's tree node name array. This array must be part of the input tree's VertexData. The default name is "node name". If this array cannot be found, then no node names will be included in the output of this writer.

void vtkPhyloXMLTreeWriter::IgnoreArray ( const char * arrayName )

Do not include name the VertexData array in the PhyloXML output of this writer. Call this function once for each array that you wish to ignore.

virtual int vtkPhyloXMLTreeWriter::WriteData ( )

protectedvirtual

Reimplemented from vtkXMLWriter.

virtual const char* vtkPhyloXMLTreeWriter::GetDataSetName ( )

protectedvirtual

Implements vtkXMLWriter.

virtual int vtkPhyloXMLTreeWriter::StartFile ( )

protectedvirtual

Reimplemented from vtkXMLWriter.

virtual int vtkPhyloXMLTreeWriter::EndFile ( )

protectedvirtual

Reimplemented from vtkXMLWriter.

void vtkPhyloXMLTreeWriter::WriteTreeLevelElement	(	vtkTree *	input,
		vtkXMLDataElement *	rootElement,
		const char *	elementName,
		const char *	attributeName
	)

protected

Check for an optional, tree-level element and write it out if it is found.

void vtkPhyloXMLTreeWriter::WriteTreeLevelProperties	(	vtkTree *	input,
		vtkXMLDataElement *	rootElement
	)

protected

Search for any tree-level properties and write them out if they are found.

void vtkPhyloXMLTreeWriter::WriteCladeElement	(	vtkTree *const	input,
		vtkIdType	vertex,
		vtkXMLDataElement *	parentElement
	)

protected

Convert one vertex to PhyloXML. This function calls itself recursively for any children of the input vertex.

void vtkPhyloXMLTreeWriter::WriteBranchLengthAttribute	(	vtkTree *const	input,
		vtkIdType	vertex,
		vtkXMLDataElement *	element
	)

protected

Write the branch length attribute for the specified vertex.

void vtkPhyloXMLTreeWriter::WriteNameElement	(	vtkIdType	vertex,
		vtkXMLDataElement *	element
	)

protected

Write the name element for the specified vertex.

void vtkPhyloXMLTreeWriter::WriteConfidenceElement	(	vtkTree *const	input,
		vtkIdType	vertex,
		vtkXMLDataElement *	element
	)

protected

Write the confidence element for the specified vertex.

void vtkPhyloXMLTreeWriter::WriteColorElement	(	vtkTree *const	input,
		vtkIdType	vertex,
		vtkXMLDataElement *	element
	)

protected

Write the color element and its subelements (red, green, blue) for the specified vertex.

void vtkPhyloXMLTreeWriter::WritePropertyElement	(	vtkAbstractArray *	array,
		vtkIdType	vertex,
		vtkXMLDataElement *	element
	)

protected

Write a property element as a child of the specified vtkXMLDataElement.

const char* vtkPhyloXMLTreeWriter::GetArrayAttribute	(	vtkAbstractArray *	array,
		const char *	attributeName
	)

protected

Get the value of the requested attribute from the specified array's vtkInformation.

virtual int vtkPhyloXMLTreeWriter::FillInputPortInformation	(	int	port,
		vtkInformation *	info
	)

protectedvirtual

Fill the input port information objects for this algorithm. This is invoked by the first call to GetInputPortInformation for each port so subclasses can specify what they can handle.

Reimplemented from vtkAlgorithm.

Member Data Documentation

vtkInformation* vtkPhyloXMLTreeWriter::InputInformation

protected

Definition at line 144 of file vtkPhyloXMLTreeWriter.h.

vtkStdString vtkPhyloXMLTreeWriter::EdgeWeightArrayName

protected

Definition at line 146 of file vtkPhyloXMLTreeWriter.h.

vtkStdString vtkPhyloXMLTreeWriter::NodeNameArrayName

protected

Definition at line 147 of file vtkPhyloXMLTreeWriter.h.

vtkAbstractArray* vtkPhyloXMLTreeWriter::EdgeWeightArray

protected

Definition at line 149 of file vtkPhyloXMLTreeWriter.h.

vtkAbstractArray* vtkPhyloXMLTreeWriter::NodeNameArray

protected

Definition at line 150 of file vtkPhyloXMLTreeWriter.h.

vtkSmartPointer<vtkStringArray> vtkPhyloXMLTreeWriter::Blacklist

protected

Definition at line 151 of file vtkPhyloXMLTreeWriter.h.

The documentation for this class was generated from the following file:

dox/IO/Infovis/vtkPhyloXMLTreeWriter.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation