DataTable.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1

#ifndef BPP_NUMERIC_DATATABLE_H
#define BPP_NUMERIC_DATATABLE_H


#include "../Clonable.h"
#include "../Text/TextTools.h"
#include "TableExceptions.h"
#include "VectorTools.h"

// From the STL:
#include <string>
#include <vector>
#include <map>

namespace bpp
{
class DataTable :
  public virtual Clonable
{
protected:
  size_t nRow_, nCol_;
  std::vector< std::vector<std::string>> data_;
  std::vector<std::string> rowNames_;
  std::vector<std::string> colNames_;

public:
  DataTable(size_t nRow, size_t nCol);

  DataTable(size_t nRow, const std::vector<std::string>& colNames);

  DataTable(size_t nCol);

  DataTable(const std::vector<std::string>& colNames);

  DataTable(const DataTable& table);

  DataTable& operator=(const DataTable& table);

  DataTable* clone() const { return new DataTable(*this); }

  virtual ~DataTable();

public:
  std::string& operator()(size_t rowIndex, size_t colIndex);

  const std::string& operator()(size_t rowIndex, size_t colIndex) const;

  std::string& operator()(const std::string& rowName, const std::string& colName);

  const std::string& operator()(const std::string& rowName, const std::string& colName) const;

  std::string& operator()(const std::string& rowName, size_t colIndex);

  const std::string& operator()(const std::string& rowName, size_t colIndex) const;

  std::string& operator()(size_t rowIndex, const std::string& colName);

  const std::string& operator()(size_t rowIndex, const std::string& colName) const;

  size_t getNumberOfColumns() const { return nCol_; }

  void setColumnNames(const std::vector<std::string>& colNames);
  std::vector<std::string> getColumnNames() const;
  std::string getColumnName(size_t index) const;

  bool hasColumnNames() const { return colNames_.size() != 0; }

  std::vector<std::string>& getColumn(size_t index);
  const std::vector<std::string>& getColumn(size_t index) const;

  std::vector<std::string>& getColumn(const std::string& colName);
  const std::vector<std::string>& getColumn(const std::string& colName) const;

  bool hasColumn(const std::string& colName) const;

  void deleteColumn(size_t index);

  void deleteColumn(const std::string& colName);

  void addColumn(const std::vector<std::string>& newColumn);
  void addColumn(const std::string& colName, const std::vector<std::string>& newColumn);
  size_t getNumberOfRows() const { return nRow_; }

  void setRowNames(const std::vector<std::string>& rowNames);

  void setRowName(size_t rowIndex, const std::string& rowName);

  std::vector<std::string> getRowNames() const;

  bool hasRow(const std::string& rowName) const;

  std::string getRowName(size_t index) const;

  bool hasRowNames() const { return rowNames_.size() != 0; }

  std::vector<std::string> getRow(size_t index) const;

  std::vector<std::string> getRow(const std::string& rowName) const;

  void deleteRow(size_t index);

  void deleteRow(const std::string& rowName);

  void addRow(const std::vector<std::string>& newRow);

  void addRow(const std::string& rowName, const std::vector<std::string>& newRow);

  void setRow(const size_t rowIndex, const std::vector<std::string>& newRow);


public:
  static std::unique_ptr<DataTable> read(std::istream& in, const std::string& sep = "\t", bool header = true, int rowNames = -1);

  static void write(const DataTable& data, std::ostream& out, const std::string& sep = "\t", bool alignHeaders = false);
  static void write(const DataTable& data, bpp::OutputStream& out, const std::string& sep = "\t", bool alignHeaders = false);
};
} // end of namespace bpp.
#endif // BPP_NUMERIC_DATATABLE_H