VTK  9.1.0
vtkPhyloXMLTreeReader.h
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1/*=========================================================================
2
3 Program: Visualization Toolkit
4 Module: vtkPhyloXMLTreeReader.h
5
6 Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
7 All rights reserved.
8 See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
9
10 This software is distributed WITHOUT ANY WARRANTY; without even
11 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
12 PURPOSE. See the above copyright notice for more information.
13
14=========================================================================*/
35#ifndef vtkPhyloXMLTreeReader_h
36#define vtkPhyloXMLTreeReader_h
37
38#include "vtkIOInfovisModule.h" // For export macro
39#include "vtkSmartPointer.h" // For SP ivar
40#include "vtkXMLReader.h"
41
42class vtkBitArray;
44class vtkTree;
46
47class VTKIOINFOVIS_EXPORT vtkPhyloXMLTreeReader : public vtkXMLReader
48{
49public:
52 void PrintSelf(ostream& os, vtkIndent indent) override;
53
55
59 vtkTree* GetOutput(int idx);
61
62protected:
65
69 void ReadXMLData() override;
70
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137
142 std::string GetTrimmedString(const char* input);
143
148 std::string GetStringBeforeColon(const char* input);
149
154 std::string GetStringAfterColon(const char* input);
155
157 const char* GetDataSetName() override;
158 void SetOutput(vtkTree* output);
159 void SetupEmptyOutput() override;
160
161private:
162 vtkIdType NumberOfNodes;
163 bool HasBranchColor;
164 vtkSmartPointer<vtkBitArray> ColoredVertices;
166 void operator=(const vtkPhyloXMLTreeReader&) = delete;
167};
168
169#endif
dynamic, self-adjusting array of bits
Definition: vtkBitArray.h:34
a simple class to control print indentation
Definition: vtkIndent.h:113
Store vtkAlgorithm input/output information.
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.
Definition: vtkTree.h:164
Represents an XML element and those nested inside.
Superclass for VTK's XML format readers.
Definition: vtkXMLReader.h:66
int vtkIdType
Definition: vtkType.h:332