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
enum	DesiredOutputPrecision { SINGLE_PRECISION, DOUBLE_PRECISION, DEFAULT_PRECISION }
	Values used for setting the desired output precision for various algorithms. More...

typedef vtkObject	Superclass

Public Member Functions
virtual int	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class. More...

vtkPhyloXMLTreeReader *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent)
	Methods invoked by print to print information about the object including superclasses. More...


vtkTree *	GetOutput ()
	Get the output of this reader. More...

vtkTree *	GetOutput (int idx)
	Get the output of this reader. More...

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

void	PrintSelf (ostream &os, vtkIndent indent)
	Methods invoked by print to print information about the object including superclasses. More...

virtual int	CanReadFile (const char *name)
	Test whether the file (type) with the given name can be read by this reader. More...

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

virtual int	GetNumberOfTimeSteps ()

vtkXMLDataParser *	GetXMLParser ()
	Returns the internal XML parser. More...

virtual int	ProcessRequest (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)
	Upstream/Downstream requests form the generalized interface through which executives invoke a algorithm's functionality. More...

virtual void	SetFileName (const char *)
	Get/Set the name of the input file. More...

virtual char *	GetFileName ()
	Get/Set the name of the input file. More...

virtual void	SetReadFromInputString (int)
	Enable reading from an InputString instead of the default, a file. More...

virtual int	GetReadFromInputString ()
	Enable reading from an InputString instead of the default, a file. More...

virtual void	ReadFromInputStringOn ()
	Enable reading from an InputString instead of the default, a file. More...

virtual void	ReadFromInputStringOff ()
	Enable reading from an InputString instead of the default, a file. More...

void	SetInputString (std::string s)
	Enable reading from an InputString instead of the default, a file. More...

vtkDataSet *	GetOutputAsDataSet ()
	Get the output as a vtkDataSet pointer. More...

vtkDataSet *	GetOutputAsDataSet (int index)
	Get the output as a vtkDataSet pointer. More...

virtual vtkDataArraySelection *	GetPointDataArraySelection ()
	Get the data array selection tables used to configure which data arrays are loaded by the reader. More...

virtual vtkDataArraySelection *	GetCellDataArraySelection ()
	Get the data array selection tables used to configure which data arrays are loaded by the reader. More...

int	GetNumberOfPointArrays ()
	Get the number of point or cell arrays available in the input. More...

int	GetNumberOfCellArrays ()
	Get the number of point or cell arrays available in the input. More...

const char *	GetPointArrayName (int index)
	Get the name of the point or cell array with the given index in the input. More...

const char *	GetCellArrayName (int index)
	Get the name of the point or cell array with the given index in the input. More...

int	GetPointArrayStatus (const char *name)
	Get/Set whether the point or cell array with the given name is to be read. More...

int	GetCellArrayStatus (const char *name)
	Get/Set whether the point or cell array with the given name is to be read. More...

void	SetPointArrayStatus (const char *name, int status)
	Get/Set whether the point or cell array with the given name is to be read. More...

void	SetCellArrayStatus (const char *name, int status)
	Get/Set whether the point or cell array with the given name is to be read. More...

virtual void	SetTimeStep (int)
	Which TimeStep to read. More...

virtual int	GetTimeStep ()
	Which TimeStep to read. More...

virtual int *	GetTimeStepRange ()
	Which TimeStepRange to read. More...

virtual void	GetTimeStepRange (int &, int &)
	Which TimeStepRange to read. More...

virtual void	GetTimeStepRange (int[2])
	Which TimeStepRange to read. More...

virtual void	SetTimeStepRange (int, int)
	Which TimeStepRange to read. More...

void	SetTimeStepRange (int[2])
	Which TimeStepRange to read. More...

void	SetReaderErrorObserver (vtkCommand *)
	Set/get the ErrorObserver for the internal reader This is useful for applications that want to catch error messages. More...

virtual vtkCommand *	GetReaderErrorObserver ()
	Set/get the ErrorObserver for the internal reader This is useful for applications that want to catch error messages. More...

void	SetParserErrorObserver (vtkCommand *)
	Set/get the ErrorObserver for the internal xml parser This is useful for applications that want to catch error messages. More...

virtual vtkCommand *	GetParserErrorObserver ()
	Set/get the ErrorObserver for the internal xml parser This is useful for applications that want to catch error messages. More...

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

int	HasExecutive ()
	Check whether this algorithm has an assigned executive. More...

vtkExecutive *	GetExecutive ()
	Get this algorithm's executive. More...

virtual void	SetExecutive (vtkExecutive *executive)
	Set this algorithm's executive. More...

int	ProcessRequest (vtkInformation request, vtkCollection inInfo, vtkInformationVector *outInfo)
	Version of ProcessRequest() that is wrapped. More...

virtual int	ComputePipelineMTime (vtkInformation request, vtkInformationVector inInfoVec, vtkInformationVector outInfoVec, int requestFromOutputPort, vtkMTimeType *mtime)
	A special version of ProcessRequest meant specifically for the pipeline modified time request. More...

virtual int	ModifyRequest (vtkInformation *request, int when)
	This method gives the algorithm a chance to modify the contents of a request before or after (specified in the when argument) it is forwarded. More...

vtkInformation *	GetInputPortInformation (int port)
	Get the information object associated with an input port. More...

vtkInformation *	GetOutputPortInformation (int port)
	Get the information object associated with an output port. More...

int	GetNumberOfInputPorts ()
	Get the number of input ports used by the algorithm. More...

int	GetNumberOfOutputPorts ()
	Get the number of output ports provided by the algorithm. More...

void	UpdateProgress (double amount)
	Update the progress of the process object. More...

virtual void	SetInputArrayToProcess (int idx, int port, int connection, const char fieldAssociation, const char attributeTypeorName)
	String based versions of SetInputArrayToProcess(). More...

vtkInformation *	GetInputArrayInformation (int idx)
	Get the info object for the specified input array to this algorithm. More...

void	RemoveAllInputs ()
	Remove all the input data. More...

vtkDataObject *	GetOutputDataObject (int port)
	Get the data object that will contain the algorithm output for the given port. More...

vtkDataObject *	GetInputDataObject (int port, int connection)
	Get the data object that will contain the algorithm input for the given port and given connection. More...

virtual void	RemoveInputConnection (int port, vtkAlgorithmOutput *input)
	Remove a connection from the given input port index. More...

virtual void	RemoveInputConnection (int port, int idx)
	Remove a connection given by index idx. More...

virtual void	RemoveAllInputConnections (int port)
	Removes all input connections. More...

virtual void	SetInputDataObject (int port, vtkDataObject *data)
	Sets the data-object as an input on the given port index. More...

virtual void	SetInputDataObject (vtkDataObject *data)

virtual void	AddInputDataObject (int port, vtkDataObject *data)
	Add the data-object as an input to this given port. More...

virtual void	AddInputDataObject (vtkDataObject *data)

vtkAlgorithmOutput *	GetOutputPort (int index)
	Get a proxy object corresponding to the given output port of this algorithm. More...

vtkAlgorithmOutput *	GetOutputPort ()

int	GetNumberOfInputConnections (int port)
	Get the number of inputs currently connected to a port. More...

int	GetTotalNumberOfInputConnections ()
	Get the total number of inputs for this algorithm. More...

vtkAlgorithmOutput *	GetInputConnection (int port, int index)
	Get the algorithm output port connected to an input port. More...

vtkAlgorithm *	GetInputAlgorithm (int port, int index, int &algPort)
	Returns the algorithm and the output port index of that algorithm connected to a port-index pair. More...

vtkAlgorithm *	GetInputAlgorithm (int port, int index)
	Returns the algorithm connected to a port-index pair. More...

vtkAlgorithm *	GetInputAlgorithm ()
	Equivalent to GetInputAlgorithm(0, 0). More...

vtkExecutive *	GetInputExecutive (int port, int index)
	Returns the executive associated with a particular input connection. More...

vtkExecutive *	GetInputExecutive ()
	Equivalent to GetInputExecutive(0, 0) More...

vtkInformation *	GetInputInformation (int port, int index)
	Return the information object that is associated with a particular input connection. More...

vtkInformation *	GetInputInformation ()
	Equivalent to GetInputInformation(0, 0) More...

vtkInformation *	GetOutputInformation (int port)
	Return the information object that is associated with a particular output port. More...

virtual int	Update (int port, vtkInformationVector *requests)
	This method enables the passing of data requests to the algorithm to be used during execution (in addition to bringing a particular port up-to-date). More...

virtual int	Update (vtkInformation *requests)
	Convenience method to update an algorithm after passing requests to its first output port. More...

virtual int	UpdatePiece (int piece, int numPieces, int ghostLevels, const int extents[6]=0)
	Convenience method to update an algorithm after passing requests to its first output port. More...

virtual int	UpdateExtent (const int extents[6])
	Convenience method to update an algorithm after passing requests to its first output port. More...

virtual int	UpdateTimeStep (double time, int piece=-1, int numPieces=1, int ghostLevels=0, const int extents[6]=0)
	Convenience method to update an algorithm after passing requests to its first output port. More...

virtual void	UpdateInformation ()
	Bring the algorithm's information up-to-date. More...

virtual void	UpdateDataObject ()
	Create output object(s). More...

virtual void	PropagateUpdateExtent ()
	Propagate meta-data upstream. More...

virtual void	UpdateWholeExtent ()
	Bring this algorithm's outputs up-to-date. More...

void	ConvertTotalInputToPortConnection (int ind, int &port, int &conn)
	Convenience routine to convert from a linear ordering of input connections to a port/connection pair. More...

int	SetUpdateExtentToWholeExtent (int port)
	If the whole output extent is required, this method can be called to set the output update extent to the whole extent. More...

int	SetUpdateExtentToWholeExtent ()
	Convenience function equivalent to SetUpdateExtentToWholeExtent(0) This method assumes that the whole extent is known (that UpdateInformation has been called). More...

void	SetUpdateExtent (int port, int piece, int numPieces, int ghostLevel)
	Set the output update extent in terms of piece and ghost levels. More...

void	SetUpdateExtent (int piece, int numPieces, int ghostLevel)
	Convenience function equivalent to SetUpdateExtent(0, piece, numPieces, ghostLevel) More...

void	SetUpdateExtent (int port, int extent[6])
	Set the output update extent for data objects that use 3D extents. More...

void	SetUpdateExtent (int extent[6])
	Convenience function equivalent to SetUpdateExtent(0, extent) More...

virtual vtkInformation *	GetInformation ()
	Set/Get the information object associated with this algorithm. More...

virtual void	SetInformation (vtkInformation *)
	Set/Get the information object associated with this algorithm. More...

void	Register (vtkObjectBase *o) override
	Participate in garbage collection. More...

void	UnRegister (vtkObjectBase *o) override
	Participate in garbage collection. More...

virtual void	SetAbortExecute (int)
	Set/Get the AbortExecute flag for the process object. More...

virtual int	GetAbortExecute ()
	Set/Get the AbortExecute flag for the process object. More...

virtual void	AbortExecuteOn ()
	Set/Get the AbortExecute flag for the process object. More...

virtual void	AbortExecuteOff ()
	Set/Get the AbortExecute flag for the process object. More...

virtual void	SetProgress (double)
	Set/Get the execution progress of a process object. More...

virtual double	GetProgress ()
	Set/Get the execution progress of a process object. More...

void	SetProgressText (const char *ptext)
	Set the current text message associated with the progress state. More...

virtual char *	GetProgressText ()
	Set the current text message associated with the progress state. More...

virtual unsigned long	GetErrorCode ()
	The error code contains a possible error that occurred while reading or writing the file. More...

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, const char *name)
	Set the input data arrays that this algorithm will process. More...

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, int fieldAttributeType)
	Set the input data arrays that this algorithm will process. More...

virtual void	SetInputArrayToProcess (int idx, vtkInformation *info)
	Set the input data arrays that this algorithm will process. More...

virtual void	SetInputConnection (int port, vtkAlgorithmOutput *input)
	Set the connection for the given input port index. More...

virtual void	SetInputConnection (vtkAlgorithmOutput *input)
	Set the connection for the given input port index. More...

virtual void	AddInputConnection (int port, vtkAlgorithmOutput *input)
	Add a connection to the given input port index. More...

virtual void	AddInputConnection (vtkAlgorithmOutput *input)
	Add a connection to the given input port index. More...

virtual void	Update (int port)
	Bring this algorithm's outputs up-to-date. More...

virtual void	Update ()
	Bring this algorithm's outputs up-to-date. More...

virtual void	SetReleaseDataFlag (int)
	Turn release data flag on or off for all output ports. More...

virtual int	GetReleaseDataFlag ()
	Turn release data flag on or off for all output ports. More...

void	ReleaseDataFlagOn ()
	Turn release data flag on or off for all output ports. More...

void	ReleaseDataFlagOff ()
	Turn release data flag on or off for all output ports. More...

int	UpdateExtentIsEmpty (vtkInformation pinfo, vtkDataObject output)
	This detects when the UpdateExtent will generate no data This condition is satisfied when the UpdateExtent has zero volume (0,-1,...) or the UpdateNumberOfPieces is 0. More...

int	UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)
	This detects when the UpdateExtent will generate no data This condition is satisfied when the UpdateExtent has zero volume (0,-1,...) or the UpdateNumberOfPieces is 0. More...

int *	GetUpdateExtent ()
	These functions return the update extent for output ports that use 3D extents. More...

int *	GetUpdateExtent (int port)
	These functions return the update extent for output ports that use 3D extents. More...

void	GetUpdateExtent (int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)
	These functions return the update extent for output ports that use 3D extents. More...

void	GetUpdateExtent (int port, int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)
	These functions return the update extent for output ports that use 3D extents. More...

void	GetUpdateExtent (int extent[6])
	These functions return the update extent for output ports that use 3D extents. More...

void	GetUpdateExtent (int port, int extent[6])
	These functions return the update extent for output ports that use 3D extents. More...

int	GetUpdatePiece ()
	These functions return the update extent for output ports that use piece extents. More...

int	GetUpdatePiece (int port)
	These functions return the update extent for output ports that use piece extents. More...

int	GetUpdateNumberOfPieces ()
	These functions return the update extent for output ports that use piece extents. More...

int	GetUpdateNumberOfPieces (int port)
	These functions return the update extent for output ports that use piece extents. More...

int	GetUpdateGhostLevel ()
	These functions return the update extent for output ports that use piece extents. More...

int	GetUpdateGhostLevel (int port)
	These functions return the update extent for output ports that use piece extents. More...

void	SetProgressObserver (vtkProgressObserver *)
	If an ProgressObserver is set, the algorithm will report progress through it rather than directly. More...

virtual vtkProgressObserver *	GetProgressObserver ()
	If an ProgressObserver is set, the algorithm will report progress through it rather than directly. More...

Public Member Functions inherited from vtkObject
	vtkBaseTypeMacro (vtkObject, vtkObjectBase)

virtual void	DebugOn ()
	Turn debugging output on. More...

virtual void	DebugOff ()
	Turn debugging output off. More...

bool	GetDebug ()
	Get the value of the debug flag. More...

void	SetDebug (bool debugFlag)
	Set the value of the debug flag. More...

virtual void	Modified ()
	Update the modification time for this object. More...

virtual vtkMTimeType	GetMTime ()
	Return this object's modified time. More...

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)

int	InvokeEvent (unsigned long event)

int	InvokeEvent (const char *event)

unsigned long	AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...

unsigned long	AddObserver (const char event, vtkCommand , float priority=0.0f)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...

vtkCommand *	GetCommand (unsigned long tag)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...

void	RemoveObserver (vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...

void	RemoveObservers (unsigned long event, vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...

void	RemoveObservers (const char event, vtkCommand )
	Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...

int	HasObserver (unsigned long event, vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...

int	HasObserver (const char event, vtkCommand )
	Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::*callback)(), float priority=0.0f)
	Overloads to AddObserver that allow developers to add class member functions as callbacks for events. More...

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)
	Overloads to AddObserver that allow developers to add class member functions as callbacks for events. More...

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, bool(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)
	Allow user to set the AbortFlagOn() with the return value of the callback method. More...

int	InvokeEvent (unsigned long event, void *callData)
	This method invokes an event and return whether the event was aborted or not. More...

int	InvokeEvent (const char event, void callData)
	This method invokes an event and return whether the event was aborted or not. More...

Public Member Functions inherited from vtkObjectBase
const char *	GetClassName () const
	Return the class name as a string. More...

virtual void	Delete ()
	Delete a VTK object. More...

virtual void	FastDelete ()
	Delete a reference to this object. More...

void	InitializeObjectBase ()

void	Print (ostream &os)
	Print an object to an ostream. More...

int	GetReferenceCount ()
	Return the current reference count of this object. More...

void	SetReferenceCount (int)
	Sets the reference count. More...

void	PrintRevisions (ostream &)
	Legacy. More...

virtual void	PrintHeader (ostream &os, vtkIndent indent)
	Methods invoked by print to print information about the object including superclasses. More...

virtual void	PrintTrailer (ostream &os, vtkIndent indent)
	Methods invoked by print to print information about the object including superclasses. More...

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 ()
	Keys used to specify input port requirements. More...

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 ()
	This key tells the executive that a particular output port is capable of producing an arbitrary subextent of the whole extent. More...

static vtkInformationIntegerKey *	CAN_HANDLE_PIECE_REQUEST ()
	Key that tells the pipeline that a particular algorithm can or cannot handle piece request. More...

static void	SetDefaultExecutivePrototype (vtkExecutive *proto)
	If the DefaultExecutivePrototype is set, a copy of it is created in CreateDefaultExecutive() using NewInstance(). More...

Static Public Member Functions inherited from vtkObject
static vtkObject *	New ()
	Create an object with Debug turned off, modified time initialized to zero, and reference counting on. More...

static void	BreakOnError ()
	This method is called when vtkErrorMacro executes. More...

static void	SetGlobalWarningDisplay (int val)
	This is a global flag that controls whether any debug, warning or error messages are displayed. More...

static void	GlobalWarningDisplayOn ()
	This is a global flag that controls whether any debug, warning or error messages are displayed. More...

static void	GlobalWarningDisplayOff ()
	This is a global flag that controls whether any debug, warning or error messages are displayed. More...

static int	GetGlobalWarningDisplay ()
	This is a global flag that controls whether any debug, warning or error messages are displayed. More...

Static Public Member Functions inherited from vtkObjectBase
static vtkTypeBool	IsTypeOf (const char *name)
	Return 1 if this class type is the same type of (or a subclass of) the named class. More...

static vtkObjectBase *	New ()
	Create an object with Debug turned off, modified time initialized to zero, and reference counting on. More...

Protected Member Functions
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkPhyloXMLTreeReader ()

	~vtkPhyloXMLTreeReader ()

virtual void	ReadXMLData ()
	Read the input PhyloXML and populate our output vtkTree. More...

void	ReadXMLElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)
	Read one particular XML element. More...

vtkIdType	ReadCladeElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType parent)
	Read a clade element. More...

void	ReadNameElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)
	Read a name and assign it to the specified vertex, or the whole tree if vertex is -1. More...

void	ReadDescriptionElement (vtkXMLDataElement element, vtkMutableDirectedGraph g)
	Read the description for the tree. More...

void	ReadPropertyElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)
	Read a property and assign it to our output vtkTree's VertexData for the specified vertex. More...

void	ReadBranchLengthElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)
	Read & store the branch length for this clade. More...

void	ReadConfidenceElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)
	Read confidence value and store it for the specified vertex, or the whole tree is vertex is -1. More...

void	ReadColorElement (vtkXMLDataElement element, vtkMutableDirectedGraph g, vtkIdType vertex)
	Read RGB color value for this vertex. More...

void	PropagateBranchColor (vtkTree *tree)
	Assign the parent's branch color to child vertices where none is otherwise specified. More...

void	CountNodes (vtkXMLDataElement *element)
	Count the number of vertices in the tree. More...

std::string	GetTrimmedString (const char *input)
	Return a copy of the input string with all leading & trailing whitespace removed. More...

std::string	GetStringBeforeColon (const char *input)
	Return the portion of the input string that occurs before the first colon (:). More...

std::string	GetStringAfterColon (const char *input)
	Return the portion of the input string that occurs after the first colon (:). More...

virtual int	FillOutputPortInformation (int, vtkInformation *)
	Fill the output port information objects for this algorithm. More...

virtual const char *	GetDataSetName ()

void	SetOutput (vtkTree *output)

virtual void	SetupEmptyOutput ()

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)

bool	ReadInformation (vtkXMLDataElement infoRoot, 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)
	This method is used by CanReadFile() to check if the reader can read an XML with the primary element with the given name. More...

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	SqueezeOutputArrays (vtkDataObject *)

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 () override

virtual int	FillInputPortInformation (int port, vtkInformation *info)
	Fill the input port information objects for this algorithm. More...

virtual void	SetNumberOfInputPorts (int n)
	Set the number of input ports used by the algorithm. More...

virtual void	SetNumberOfOutputPorts (int n)
	Set the number of output ports provided by the algorithm. More...

int	InputPortIndexInRange (int index, const char *action)

int	OutputPortIndexInRange (int index, const char *action)

int	GetInputArrayAssociation (int idx, vtkInformationVector **inputVector)
	Get the assocition of the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass. More...

vtkInformation *	GetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector)
	This method takes in an index (as specified in SetInputArrayToProcess) and a pipeline information vector. More...

virtual vtkExecutive *	CreateDefaultExecutive ()
	Create a default executive. More...

void	ReportReferences (vtkGarbageCollector *) override

virtual void	SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input)
	Replace the Nth connection on the given input port. More...

virtual void	SetNumberOfInputConnections (int port, int n)
	Set the number of input connections on the given input port. More...

void	SetInputDataInternal (int port, vtkDataObject *input)
	These methods are used by subclasses to implement methods to set data objects directly as input. More...

void	AddInputDataInternal (int port, vtkDataObject *input)

int	GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector)
	Filters that have multiple connections on one port can use this signature. More...

int	GetInputArrayAssociation (int idx, vtkDataObject *input)
	Filters that have multiple connections on one port can use this signature. More...

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass. More...

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass. More...

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
	Filters that have multiple connections on one port can use this signature. More...

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
	Filters that have multiple connections on one port can use this signature. More...

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input)
	Filters that have multiple connections on one port can use this signature. More...

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input, int &association)
	Filters that have multiple connections on one port can use this signature. More...

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass. More...

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass. More...

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
	Filters that have multiple connections on one port can use this signature. More...

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
	Filters that have multiple connections on one port can use this signature. More...

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input)
	Filters that have multiple connections on one port can use this signature. More...

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association)
	Filters that have multiple connections on one port can use this signature. More...

virtual void	SetErrorCode (unsigned long)
	The error code contains a possible error that occurred while reading or writing the file. More...

Protected Member Functions inherited from vtkObject
	vtkObject ()

	~vtkObject () override

void	RegisterInternal (vtkObjectBase *, vtkTypeBool check) override

void	UnRegisterInternal (vtkObjectBase *, vtkTypeBool check) override

void	InternalGrabFocus (vtkCommand mouseEvents, vtkCommand keypressEvents=NULL)
	These methods allow a command to exclusively grab all events. More...

void	InternalReleaseFocus ()
	These methods allow a command to exclusively grab all events. More...

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
	The error code contains a possible error that occurred while reading or writing the file. More...

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 50 of file vtkPhyloXMLTreeReader.h.

Member Typedef Documentation

typedef vtkXMLReader vtkPhyloXMLTreeReader::Superclass

Definition at line 54 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:

/home/demarle/Builds/VTK/release/Utilities/Doxygen/dox/IO/Infovis/vtkPhyloXMLTreeReader.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation