DataTable.h

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//
// File: DataTable.h
// Created by: Julien Dutheil
// Created on: Aug 2005
//

/*
   Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)

   This software is a computer program whose purpose is to provide classes
   for numerical calculus.

   This software is governed by the CeCILL  license under French law and
   abiding by the rules of distribution of free software.  You can  use,
   modify and/ or redistribute the software under the terms of the CeCILL
   license as circulated by CEA, CNRS and INRIA at the following URL
   "http://www.cecill.info".

   As a counterpart to the access to the source code and  rights to copy,
   modify and redistribute granted by the license, users are provided only
   with a limited warranty  and the software's author,  the holder of the
   economic rights,  and the successive licensors  have only  limited
   liability.

   In this respect, the user's attention is drawn to the risks associated
   with loading,  using,  modifying and/or developing or reproducing the
   software by the user in light of its specific status of free software,
   that may mean  that it is complicated to manipulate,  and  that  also
   therefore means  that it is reserved for developers  and  experienced
   professionals having in-depth computer knowledge. Users are therefore
   encouraged to load and test the software's suitability as regards their
   requirements in conditions enabling the security of their systems and/or
   data to be ensured and,  more generally, to use and operate it in the
   same conditions as regards security.

   The fact that you are presently reading this means that you have had
   knowledge of the CeCILL license and that you accept its terms.
 */

#ifndef _DataTable_H_
#define _DataTable_H_

#include "VectorTools.h"
#include "DataTableExceptions.h"
#include "../Exceptions.h"
#include "../Text/TextTools.h"
#include "../Clonable.h"

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

namespace bpp
{
class DataTable :
  public 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 nCol);

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

  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) throw (IndexOutOfBoundsException);

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

  std::string& operator()(const std::string& rowName, const std::string& colName)
  throw (NoTableRowNamesException, NoTableColumnNamesException, TableNameNotFoundException);

  const std::string& operator()(const std::string& rowName, const std::string& colName) const
  throw (NoTableRowNamesException, NoTableColumnNamesException, TableNameNotFoundException);

  std::string& operator()(const std::string& rowName, size_t colIndex)
  throw (NoTableRowNamesException, TableNameNotFoundException, IndexOutOfBoundsException);

  const std::string& operator()(const std::string& rowName, size_t colIndex) const
  throw (NoTableRowNamesException, TableNameNotFoundException, IndexOutOfBoundsException);

  std::string& operator()(size_t rowIndex, const std::string& colName)
  throw (IndexOutOfBoundsException, NoTableColumnNamesException, TableNameNotFoundException);

  const std::string& operator()(size_t rowIndex, const std::string& colName) const
  throw (IndexOutOfBoundsException, NoTableColumnNamesException, TableNameNotFoundException);

  size_t getNumberOfColumns() const { return nCol_; }

  void setColumnNames(const std::vector<std::string>& colNames) throw (DimensionException, DuplicatedTableColumnNameException);
  std::vector<std::string> getColumnNames() const throw (NoTableColumnNamesException);
  std::string getColumnName(size_t index) const throw (NoTableColumnNamesException, IndexOutOfBoundsException);

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

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

  std::vector<std::string>& getColumn(const std::string& colName) throw (NoTableColumnNamesException, TableColumnNameNotFoundException);
  const std::vector<std::string>& getColumn(const std::string& colName) const throw (NoTableColumnNamesException, TableColumnNameNotFoundException);

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

  void deleteColumn(size_t index) throw (IndexOutOfBoundsException);

  void deleteColumn(const std::string& colName) throw (NoTableColumnNamesException, TableColumnNameNotFoundException);

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

  void setRowNames(const std::vector<std::string>& rowNames) throw (DimensionException, DuplicatedTableRowNameException);

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

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

  std::string getRowName(size_t index) const throw (NoTableRowNamesException, IndexOutOfBoundsException);

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

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

  std::vector<std::string> getRow(const std::string& rowName) const throw (NoTableRowNamesException, TableRowNameNotFoundException);

  void deleteRow(size_t index) throw (IndexOutOfBoundsException);

  void deleteRow(const std::string& rowName) throw (NoTableRowNamesException, TableRowNameNotFoundException);

  void addRow(const std::vector<std::string>& newRow) throw (DimensionException, TableRowNamesException);
  void addRow(const std::string& rowName, const std::vector<std::string>& newRow) throw (DimensionException, NoTableRowNamesException, DuplicatedTableRowNameException);
public:
  static DataTable* read(std::istream& in, const std::string& sep = "\t", bool header = true, int rowNames = -1)
  throw (DimensionException, IndexOutOfBoundsException, DuplicatedTableRowNameException);

  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 // _DataTable_H_