vtkPhyloXMLTreeReader.h

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/*=========================================================================

  Program:   Visualization Toolkit
  Module:    vtkPhyloXMLTreeReader.h

  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
  All rights reserved.
  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
#ifndef vtkPhyloXMLTreeReader_h
#define vtkPhyloXMLTreeReader_h

#include "vtkIOInfovisModule.h" // For export macro
#include "vtkSmartPointer.h"    // For SP ivar
#include "vtkXMLReader.h"

class vtkBitArray;
class vtkMutableDirectedGraph;
class vtkTree;
class vtkXMLDataElement;

class VTKIOINFOVIS_EXPORT vtkPhyloXMLTreeReader : public vtkXMLReader
{
public:
  static vtkPhyloXMLTreeReader *New();
  vtkTypeMacro(vtkPhyloXMLTreeReader,vtkXMLReader);
  void PrintSelf(ostream& os, vtkIndent indent) override;


  vtkTree *GetOutput();
  vtkTree *GetOutput(int idx);

protected:
  vtkPhyloXMLTreeReader();
  ~vtkPhyloXMLTreeReader() override;

  void ReadXMLData() override;

  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);

  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);

  int FillOutputPortInformation(int, vtkInformation*) override;
  const char* GetDataSetName() override;
  void SetOutput(vtkTree *output);
  void SetupEmptyOutput() override;

private:
  vtkIdType NumberOfNodes;
  bool HasBranchColor;
  vtkSmartPointer<vtkBitArray> ColoredVertices;
  vtkPhyloXMLTreeReader(const vtkPhyloXMLTreeReader&) = delete;
  void operator=(const vtkPhyloXMLTreeReader&) = delete;
};

#endif