write vtkTree data to PhyloXML format. More...

#include <vtkPhyloXMLTreeWriter.h>

Inheritance diagram for vtkPhyloXMLTreeWriter:

Collaboration diagram for vtkPhyloXMLTreeWriter:

Public Types
typedef vtkXMLWriter	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)
Static Public Member Functions
static vtkPhyloXMLTreeWriter *	New ()
static int	IsTypeOf (const char *type)
static vtkPhyloXMLTreeWriter *	SafeDownCast (vtkObjectBase *o)
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 Attributes
vtkInformation *	InputInformation
vtkStdString	EdgeWeightArrayName
vtkStdString	NodeNameArrayName
vtkAbstractArray *	EdgeWeightArray
vtkAbstractArray *	NodeNameArray
vtkSmartPointer< vtkStringArray >	Blacklist

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

Reimplemented from vtkXMLWriter.

Definition at line 41 of file vtkPhyloXMLTreeWriter.h.

Constructor & Destructor Documentation

vtkPhyloXMLTreeWriter::vtkPhyloXMLTreeWriter ( ) [protected]

vtkPhyloXMLTreeWriter::~vtkPhyloXMLTreeWriter ( ) [inline, protected]

Definition at line 78 of file vtkPhyloXMLTreeWriter.h.

Member Function Documentation

static vtkPhyloXMLTreeWriter* vtkPhyloXMLTreeWriter::New ( ) [static]

Create an object with Debug turned off, modified time initialized to zero, and reference counting on.

Reimplemented from vtkAlgorithm.

static int vtkPhyloXMLTreeWriter::IsTypeOf ( const char * name ) [static]

Return 1 if this class type 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.

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]

Reimplemented from vtkXMLWriter.

virtual vtkObjectBase* vtkPhyloXMLTreeWriter::NewInstanceInternal ( ) const [protected, virtual]

Reimplemented from vtkXMLWriter.

vtkPhyloXMLTreeWriter* vtkPhyloXMLTreeWriter::NewInstance ( ) const

Reimplemented from vtkXMLWriter.

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 vtkXMLWriter.

vtkTree* vtkPhyloXMLTreeWriter::GetInput ( )

Get the input to this writer.

Reimplemented from vtkXMLWriter.

vtkTree* vtkPhyloXMLTreeWriter::GetInput ( int port )

Get the input to this writer.

Reimplemented from vtkXMLWriter.

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 ( ) [protected, virtual]

Reimplemented from vtkXMLWriter.

virtual const char* vtkPhyloXMLTreeWriter::GetDataSetName ( ) [protected, virtual]

Implements vtkXMLWriter.

virtual int vtkPhyloXMLTreeWriter::StartFile ( ) [protected, virtual]

Reimplemented from vtkXMLWriter.

virtual int vtkPhyloXMLTreeWriter::EndFile ( ) [protected, virtual]

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
	)		`[protected, virtual]`

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.