35#ifndef vtkPhyloXMLTreeReader_h
36#define vtkPhyloXMLTreeReader_h
38#include "vtkIOInfovisModule.h"
dynamic, self-adjusting array of bits
a simple class to control print indentation
An editable directed graph.
read vtkTree from PhyloXML formatted file
~vtkPhyloXMLTreeReader() override
void ReadBranchLengthElement(vtkXMLDataElement *element, vtkMutableDirectedGraph *g, vtkIdType vertex)
Read & store the branch length for this clade.
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.
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.
vtkIdType ReadCladeElement(vtkXMLDataElement *element, vtkMutableDirectedGraph *g, vtkIdType parent)
Read a clade element.
void ReadColorElement(vtkXMLDataElement *element, vtkMutableDirectedGraph *g, vtkIdType vertex)
Read RGB color value for this vertex.
void SetupEmptyOutput() override
void PropagateBranchColor(vtkTree *tree)
Assign the parent's branch color to child vertices where none is otherwise specified.
void ReadXMLElement(vtkXMLDataElement *element, vtkMutableDirectedGraph *g, vtkIdType vertex)
Read one particular XML element.
std::string GetTrimmedString(const char *input)
Return a copy of the input string with all leading & trailing whitespace removed.
std::string GetStringBeforeColon(const char *input)
Return the portion of the input string that occurs before the first colon (:).
static vtkPhyloXMLTreeReader * New()
vtkTree * GetOutput()
Get the output of this reader.
const char * GetDataSetName() override
void ReadXMLData() override
Read the input PhyloXML and populate our output vtkTree.
void SetOutput(vtkTree *output)
void ReadDescriptionElement(vtkXMLDataElement *element, vtkMutableDirectedGraph *g)
Read the description for the tree.
int FillOutputPortInformation(int, vtkInformation *) override
Fill the output port information objects for this algorithm.
void ReadPropertyElement(vtkXMLDataElement *element, vtkMutableDirectedGraph *g, vtkIdType vertex)
Read a property and assign it to our output vtkTree's VertexData for the specified vertex.
vtkTree * GetOutput(int idx)
Get the output of this reader.
std::string GetStringAfterColon(const char *input)
Return the portion of the input string that occurs after the first colon (:).
void CountNodes(vtkXMLDataElement *element)
Count the number of vertices in the tree.
void PrintSelf(ostream &os, vtkIndent indent) override
Methods invoked by print to print information about the object including superclasses.
Hold a reference to a vtkObjectBase instance.
A rooted tree data structure.
Represents an XML element and those nested inside.
Superclass for VTK's XML format readers.