read vtkTree from PhyloXML formatted file More...

#include <vtkPhyloXMLTreeReader.h>

Inheritance diagram for vtkPhyloXMLTreeReader:

Collaboration diagram for vtkPhyloXMLTreeReader:

Public Types
typedef vtkXMLReader	Superclass

Public Types inherited from vtkXMLReader
typedef vtkAlgorithm	Superclass

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)

vtkPhyloXMLTreeReader *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent)


vtkTree *	GetOutput ()

vtkTree *	GetOutput (int idx)

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

void	PrintSelf (ostream &os, vtkIndent indent)

virtual int	CanReadFile (const char *name)

virtual void	CopyOutputInformation (vtkInformation *vtkNotUsed(outInfo), int vtkNotUsed(port))

virtual int	GetNumberOfTimeSteps ()

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

virtual void	SetFileName (const char *)

virtual char *	GetFileName ()

virtual void	SetReadFromInputString (int)

virtual int	GetReadFromInputString ()

virtual void	ReadFromInputStringOn ()

virtual void	ReadFromInputStringOff ()

void	SetInputString (std::string s)

vtkDataSet *	GetOutputAsDataSet ()

vtkDataSet *	GetOutputAsDataSet (int index)

virtual vtkDataArraySelection *	GetPointDataArraySelection ()

virtual vtkDataArraySelection *	GetCellDataArraySelection ()

int	GetNumberOfPointArrays ()

int	GetNumberOfCellArrays ()

const char *	GetPointArrayName (int index)

const char *	GetCellArrayName (int index)

int	GetPointArrayStatus (const char *name)

int	GetCellArrayStatus (const char *name)

void	SetPointArrayStatus (const char *name, int status)

void	SetCellArrayStatus (const char *name, int status)

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])

vtkXMLDataParser *	GetXMLParser ()

void	SetReaderErrorObserver (vtkCommand *)

virtual vtkCommand *	GetReaderErrorObserver ()

void	SetParserErrorObserver (vtkCommand *)

virtual vtkCommand *	GetParserErrorObserver ()

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 vtkPhyloXMLTreeReader *	New ()

static int	IsTypeOf (const char *type)

static vtkPhyloXMLTreeReader *	SafeDownCast (vtkObjectBase *o)

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

static vtkXMLReader *	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

	vtkPhyloXMLTreeReader ()

	~vtkPhyloXMLTreeReader ()

virtual void	ReadXMLData ()

void	PropagateBranchColor (vtkTree *tree)

void	CountNodes (vtkXMLDataElement *element)

std::string	GetTrimmedString (const char *input)

std::string	GetStringBeforeColon (const char *input)

std::string	GetStringAfterColon (const char *input)

virtual int	FillOutputPortInformation (int, vtkInformation *)

virtual const char *	GetDataSetName ()

void	SetOutput (vtkTree *output)

virtual void	SetupEmptyOutput ()


void	ReadXMLElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)


vtkIdType	ReadCladeElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType parent)


void	ReadNameElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)


void	ReadDescriptionElement (vtkXMLDataElement element, vtkMutableDirectedGraph g)


void	ReadPropertyElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)


void	ReadBranchLengthElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)


void	ReadConfidenceElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)


void	ReadColorElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)

Protected Member Functions inherited from vtkXMLReader
	vtkXMLReader ()

	~vtkXMLReader ()

virtual int	ReadXMLInformation ()

virtual int	CanReadFileVersion (int major, int minor)

virtual void	SetupOutputInformation (vtkInformation *vtkNotUsed(outInfo))

virtual void	SetupOutputData ()

virtual int	ReadPrimaryElement (vtkXMLDataElement *ePrimary)

virtual int	ReadVTKFile (vtkXMLDataElement *eVTKFile)

vtkAbstractArray *	CreateArray (vtkXMLDataElement *da)

int	CreateInformationKey (vtkXMLDataElement eInfoKey, vtkInformation info)

virtual int	OpenStream ()

virtual void	CloseStream ()

virtual int	OpenVTKFile ()

virtual void	CloseVTKFile ()

virtual int	OpenVTKString ()

virtual void	CloseVTKString ()

virtual void	CreateXMLParser ()

virtual void	DestroyXMLParser ()

void	SetupCompressor (const char *type)

int	CanReadFileVersionString (const char *version)

virtual int	CanReadFileWithDataType (const char *dsname)

virtual int	GetFileMajorVersion ()

virtual int	GetFileMinorVersion ()

int	IntersectExtents (int extent1, int extent2, int *result)

int	Min (int a, int b)

int	Max (int a, int b)

void	ComputePointDimensions (int extent, int dimensions)

void	ComputePointIncrements (int extent, vtkIdType increments)

void	ComputeCellDimensions (int extent, int dimensions)

void	ComputeCellIncrements (int extent, vtkIdType increments)

vtkIdType	GetStartTuple (int extent, vtkIdType increments, int i, int j, int k)

void	ReadAttributeIndices (vtkXMLDataElement eDSA, vtkDataSetAttributes dsa)

char **	CreateStringArray (int numStrings)

void	DestroyStringArray (int numStrings, char **strings)

void	SetDataArraySelections (vtkXMLDataElement eDSA, vtkDataArraySelection sel)

int	SetFieldDataInfo (vtkXMLDataElement eDSA, int association, int numTuples, vtkInformationVector (&infoVector))

int	PointDataArrayIsEnabled (vtkXMLDataElement *ePDA)

int	CellDataArrayIsEnabled (vtkXMLDataElement *eCDA)

virtual void	GetProgressRange (float *range)

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	UpdateProgressDiscrete (float progress)

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

virtual int	RequestDataObject (vtkInformation vtkNotUsed(request), vtkInformationVector vtkNotUsed(inputVector), vtkInformationVector vtkNotUsed(outputVector))

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

void	SetNumberOfTimeSteps (int num)

vtkDataObject *	GetCurrentOutput ()

vtkInformation *	GetCurrentOutputInformation ()

Protected Member Functions inherited from vtkAlgorithm
	vtkAlgorithm ()

	~vtkAlgorithm ()

virtual int	FillInputPortInformation (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 &)

Additional Inherited Members
Public Attributes inherited from vtkAlgorithm
int	AbortExecute

Static Protected Member Functions inherited from vtkXMLReader
static void	SelectionModifiedCallback (vtkObject caller, unsigned long eid, void clientdata, void *calldata)

static int	IsTimeStepInArray (int timestep, int *timesteps, int length)

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

Protected Attributes inherited from vtkXMLReader
vtkXMLDataParser *	XMLParser

vtkXMLDataElement *	FieldDataElement

char *	FileName

istream *	Stream

int	ReadFromInputString

std::string	InputString

vtkDataArraySelection *	PointDataArraySelection

vtkDataArraySelection *	CellDataArraySelection

vtkCallbackCommand *	SelectionObserver

int	InformationError

int	DataError

float	ProgressRange [2]

vtkTimeStamp	ReadMTime

int	ReadError

int	AxesEmpty [3]

int	TimeStep

int	CurrentTimeStep

int	NumberOfTimeSteps

int *	TimeSteps

int	TimeStepRange [2]

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

Static Protected Attributes inherited from vtkAlgorithm
static vtkExecutive *	DefaultExecutivePrototype

Detailed Description

read vtkTree from PhyloXML formatted file

vtkPhyloXMLTreeReader is a source object that reads PhyloXML tree format files. The output of this reader is a single vtkTree data object.

Warning: This reader does not implement the entire PhyloXML specification. It currently only supports the following tags: phylogeny, name, description, confidence, property, clade, branch_length, color, red, green, and blue. This reader also only supports a single phylogeny per file.

See also: vtkTree vtkXMLReader vtkPhyloXMLTreeWriter

Tests:: vtkPhyloXMLTreeReader (Tests)

Definition at line 49 of file vtkPhyloXMLTreeReader.h.

Member Typedef Documentation

typedef vtkXMLReader vtkPhyloXMLTreeReader::Superclass

Definition at line 53 of file vtkPhyloXMLTreeReader.h.

Constructor & Destructor Documentation

vtkPhyloXMLTreeReader::vtkPhyloXMLTreeReader ( )

protected

vtkPhyloXMLTreeReader::~vtkPhyloXMLTreeReader ( )

protected

Member Function Documentation

static vtkPhyloXMLTreeReader* vtkPhyloXMLTreeReader::New ( )

static

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

static

virtual int vtkPhyloXMLTreeReader::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 vtkXMLReader.

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

static

virtual vtkObjectBase* vtkPhyloXMLTreeReader::NewInstanceInternal ( ) const

protectedvirtual

Reimplemented from vtkXMLReader.

vtkPhyloXMLTreeReader* vtkPhyloXMLTreeReader::NewInstance ( ) const

void vtkPhyloXMLTreeReader::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* vtkPhyloXMLTreeReader::GetOutput ( )

Get the output of this reader.

vtkTree* vtkPhyloXMLTreeReader::GetOutput ( int idx )

Get the output of this reader.

virtual void vtkPhyloXMLTreeReader::ReadXMLData ( )

protectedvirtual

Read the input PhyloXML and populate our output vtkTree.

Reimplemented from vtkXMLReader.

void vtkPhyloXMLTreeReader::ReadXMLElement	(	vtkXMLDataElement *	element,
		vtkMutableDirectedGraph *	g,
		vtkIdType	vertex
	)

protected

Read one particular XML element. This method calls the more specific methods (ReadCladeElement, ReadNameElement, etc) based on what type of tag it encounters.

vtkIdType vtkPhyloXMLTreeReader::ReadCladeElement	(	vtkXMLDataElement *	element,
		vtkMutableDirectedGraph *	g,
		vtkIdType	parent
	)

protected

Read a clade element. This method does not parse the subelements of the clade. Instead, this task is handled by other methods of this class. This method returns the vtkIdType of the newly created vertex in our output vtkTree.

void vtkPhyloXMLTreeReader::ReadNameElement	(	vtkXMLDataElement *	element,
		vtkMutableDirectedGraph *	g,
		vtkIdType	vertex
	)

protected

Read a name and assign it to the specified vertex, or the whole tree if vertex is -1.

void vtkPhyloXMLTreeReader::ReadDescriptionElement	(	vtkXMLDataElement *	element,
		vtkMutableDirectedGraph *	g
	)

protected

Read the description for the tree.

void vtkPhyloXMLTreeReader::ReadPropertyElement	(	vtkXMLDataElement *	element,
		vtkMutableDirectedGraph *	g,
		vtkIdType	vertex
	)

protected

Read a property and assign it to our output vtkTree's VertexData for the specified vertex. If this property has not been encountered yet, this method creates a new array and adds it to the VertexData.

void vtkPhyloXMLTreeReader::ReadBranchLengthElement	(	vtkXMLDataElement *	element,
		vtkMutableDirectedGraph *	g,
		vtkIdType	vertex
	)

protected

Read & store the branch length for this clade. Branch length is defined as the edge weight from this vertex to its parent. Note that this value can also be specified as an attribute of the clade element.

void vtkPhyloXMLTreeReader::ReadConfidenceElement	(	vtkXMLDataElement *	element,
		vtkMutableDirectedGraph *	g,
		vtkIdType	vertex
	)

protected

Read confidence value and store it for the specified vertex, or the whole tree is vertex is -1.

void vtkPhyloXMLTreeReader::ReadColorElement	(	vtkXMLDataElement *	element,
		vtkMutableDirectedGraph *	g,
		vtkIdType	vertex
	)

protected

Read RGB color value for this vertex. Note that this color is also applied to all children of this vertex until a new value is specified.

void vtkPhyloXMLTreeReader::PropagateBranchColor ( vtkTree * tree )

protected

Assign the parent's branch color to child vertices where none is otherwise specified.

void vtkPhyloXMLTreeReader::CountNodes ( vtkXMLDataElement * element )

protected

Count the number of vertices in the tree.

std::string vtkPhyloXMLTreeReader::GetTrimmedString ( const char * input )

protected

Return a copy of the input string with all leading & trailing whitespace removed.

std::string vtkPhyloXMLTreeReader::GetStringBeforeColon ( const char * input )

protected

Return the portion of the input string that occurs before the first colon (:).

std::string vtkPhyloXMLTreeReader::GetStringAfterColon ( const char * input )

protected

Return the portion of the input string that occurs after the first colon (:).

virtual int vtkPhyloXMLTreeReader::FillOutputPortInformation	(	int	port,
		vtkInformation *	info
	)

protectedvirtual

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

Reimplemented from vtkAlgorithm.

virtual const char* vtkPhyloXMLTreeReader::GetDataSetName ( )

protectedvirtual

Implements vtkXMLReader.

void vtkPhyloXMLTreeReader::SetOutput ( vtkTree * output )

protected

virtual void vtkPhyloXMLTreeReader::SetupEmptyOutput ( )

protectedvirtual

Implements vtkXMLReader.

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