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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);


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

protected:
  vtkPhyloXMLTreeReader();
  ~vtkPhyloXMLTreeReader();

  virtual void ReadXMLData();


  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);

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

private:
  vtkIdType NumberOfNodes;
  bool HasBranchColor;
  vtkSmartPointer<vtkBitArray> ColoredVertices;
  vtkPhyloXMLTreeReader(const vtkPhyloXMLTreeReader&);  // Not implemented.
  void operator=(const vtkPhyloXMLTreeReader&);  // Not implemented.
};

#endif