multipers 2.3.3b6__cp313-cp313-macosx_11_0_arm64.whl

multipers/gudhi/gudhi/Persistence_matrix/Chain_matrix.h

@@ -0,0 +1,1350 @@
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Hannah Schreiber
+ *
+ *    Copyright (C) 2022-24 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+/**
+ * @file Chain_matrix.h
+ * @author Hannah Schreiber
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_matrix class.
+ */
+
+#ifndef PM_CHAIN_MATRIX_H
+#define PM_CHAIN_MATRIX_H
+
+#include <iostream>   //print() only
+#include <set>
+#include <map>
+#include <stdexcept>
+#include <vector>
+#include <utility>    //std::swap, std::move & std::exchange
+#include <algorithm>  //std::sort
+
+#include <gudhi/Persistence_matrix/Id_to_index_overlay.h> //friend
+
+namespace Gudhi {
+namespace persistence_matrix {
+
+/**
+ * @class Chain_matrix Chain_matrix.h gudhi/Persistence_matrix/Chain_matrix.h
+ * @ingroup persistence_matrix
+ *
+ * @brief %Matrix structure storing a compatible base of a filtered chain complex. See @cite zigzag.
+ * The base is constructed from the boundaries of the cells in the complex. Allows the persistent homology to be
+ * computed, as well as representative cycles. Supports vineyards (see @cite vineyards) and the removal 
+ * of maximal cells while maintaining a valid barcode. Provides an access to its columns and rows.
+ * 
+ * @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
+ */
+template <class Master_matrix>
+class Chain_matrix : public Master_matrix::Matrix_dimension_option,
+                     public Master_matrix::Chain_pairing_option,
+                     public Master_matrix::Chain_vine_swap_option,
+                     public Master_matrix::Chain_representative_cycles_option,
+                     public Master_matrix::Matrix_row_access_option 
+{
+ public:
+  /**
+   * @brief Field operators class. Necessary only if @ref PersistenceMatrixOptions::is_z2 is false.
+   */
+  using Field_operators = typename Master_matrix::Field_operators;
+  using Field_element = typename Master_matrix::Element;                    /**< Type of an field element. */
+  using Column = typename Master_matrix::Column;                            /**< Column type. */
+  using Row = typename Master_matrix::Row;                                  /**< Row type, only necessary with row
+                                                                                 access option. */
+  using Entry = typename Master_matrix::Matrix_entry;                       /**< @ref Entry "Matrix entry" type. */
+  using Entry_constructor = typename Master_matrix::Entry_constructor;      /**< Factory of @ref Entry classes. */
+  using Column_settings = typename Master_matrix::Column_settings;          /**< Structure giving access to the columns
+                                                                                 to necessary external classes. */
+  using Boundary = typename Master_matrix::Boundary;                        /**< Type of an input column. */
+  using Entry_representative = typename Master_matrix::Entry_representative;  /**< %Entry content representative. */
+  using Index = typename Master_matrix::Index;                              /**< @ref MatIdx index type. */
+  using ID_index = typename Master_matrix::ID_index;                        /**< @ref IDIdx index type. */
+  using Pos_index = typename Master_matrix::Pos_index;                      /**< @ref PosIdx index type. */
+  using Dimension = typename Master_matrix::Dimension;                      /**< Dimension value type. */
+
+  /**
+   * @brief Constructs an empty matrix. Only available if @ref PersistenceMatrixOptions::has_column_pairings is
+   * true or @ref PersistenceMatrixOptions::has_vine_update is false. Otherwise, birth and death comparators have
+   * to be provided.
+   * 
+   * @param colSettings Pointer to an existing setting structure for the columns. The structure should contain all
+   * the necessary external classes specifically necessary for the choosen column type, such as custom allocators.
+   */
+  Chain_matrix(Column_settings* colSettings);
+  /**
+   * @brief Constructs a new matrix from the given ranges of @ref Matrix::Entry_representative. Each range corresponds
+   * to a column  (the order of the ranges are preserved). The content of the ranges is assumed to be sorted by
+   * increasing IDs. The IDs of the simplices are also assumed to be consecutive, ordered by filtration value, starting
+   * with 0. Only available if @ref PersistenceMatrixOptions::has_column_pairings is true or
+   * @ref PersistenceMatrixOptions::has_vine_update is false. Otherwise, birth and death
+   * comparators have to be provided.
+   * 
+   * @tparam Boundary_range Range type for @ref Matrix::Entry_representative ranges.
+   * Assumed to have a begin(), end() and size() method.
+   * @param orderedBoundaries Range of boundaries: @p orderedBoundaries is interpreted as a boundary matrix of a 
+   * filtered **simplicial** complex, whose boundaries are ordered by filtration order. 
+   * Therefore, `orderedBoundaries[i]` should store the boundary of the \f$ i^{th} \f$ simplex in the filtration,
+   * as an ordered list of indices of its facets (again those indices correspond to their respective position
+   * in the matrix). That is why the indices of the simplices are assumed to be consecutive and starting with 0 
+   * (an empty boundary is interpreted as a vertex boundary and not as a non existing simplex). 
+   * All dimensions up to the maximal dimension of interest have to be present. If only a higher dimension is of 
+   * interest and not everything should be stored, then use the @ref insert_boundary method instead
+   * (after creating the matrix with the
+   * @ref Chain_matrix(unsigned int numberOfColumns, Column_settings* colSettings)
+   * constructor preferably).
+   * @param colSettings Pointer to an existing setting structure for the columns. The structure should contain all
+   * the necessary external classes specifically necessary for the choosen column type, such as custom allocators.
+   */
+  template <class Boundary_range = Boundary>
+  Chain_matrix(const std::vector<Boundary_range>& orderedBoundaries, 
+               Column_settings* colSettings);
+  /**
+   * @brief Constructs a new empty matrix and reserves space for the given number of columns. Only available
+   * if @ref PersistenceMatrixOptions::has_column_pairings is true or @ref PersistenceMatrixOptions::has_vine_update
+   * is false. Otherwise, birth and death comparators have to be provided.
+   * 
+   * @param numberOfColumns Number of columns to reserve space for.
+   * @param colSettings Pointer to an existing setting structure for the columns. The structure should contain all
+   * the necessary external classes specifically necessary for the choosen column type, such as custom allocators.
+   */
+  Chain_matrix(unsigned int numberOfColumns, Column_settings* colSettings);
+  /**
+   * @brief Constructs an empty matrix and stores the given comparators.
+   *
+   * @warning If @ref PersistenceMatrixOptions::has_vine_update is false, the comparators are not used.
+   * And if @ref PersistenceMatrixOptions::has_vine_update is true, but
+   * @ref PersistenceMatrixOptions::has_column_pairings is also true, the comparators are ignored and
+   * the current barcode is used to compare birth and deaths. Therefore it is useless to provide them in those cases.
+   * 
+   * @tparam BirthComparatorFunction Type of the birth comparator: (@ref Pos_index, @ref Pos_index) -> bool
+   * @tparam DeathComparatorFunction Type of the death comparator: (@ref Pos_index, @ref Pos_index) -> bool
+   * @param colSettings Pointer to an existing setting structure for the columns. The structure should contain all
+   * the necessary external classes specifically necessary for the choosen column type, such as custom allocators.
+   * @param birthComparator Method taking two @ref PosIdx indices as input and returning true if and only if
+   * the birth associated to the first position is strictly less than birth associated to
+   * the second one with respect to some self defined order. It is used while swapping two unpaired or
+   * two negative columns.
+   * @param deathComparator Method taking two @ref PosIdx indices as input and returning true if and only if
+   * the death associated to the first position is strictly less than death associated to
+   * the second one with respect to some self defined order. It is used while swapping two positive but paired
+   * columns.
+   */
+  template <typename BirthComparatorFunction, typename DeathComparatorFunction>
+  Chain_matrix(Column_settings* colSettings, 
+               const BirthComparatorFunction& birthComparator,
+               const DeathComparatorFunction& deathComparator);
+  /**
+   * @brief Constructs a new matrix from the given ranges of @ref Matrix::Entry_representative. Each range corresponds
+   * to a column (the order of the ranges are preserved). The content of the ranges is assumed to be sorted by
+   * increasing IDs. The IDs of the simplices are also assumed to be consecutive, ordered by filtration value, starting
+   * with 0.
+   *
+   * @warning If @ref PersistenceMatrixOptions::has_vine_update is false, the comparators are not used.
+   * And if @ref PersistenceMatrixOptions::has_vine_update is true, but
+   * @ref PersistenceMatrixOptions::has_column_pairings is also true, the comparators are ignored and
+   * the current barcode is used to compare birth and deaths. Therefore it is useless to provide them in those cases.
+   * 
+   * @tparam BirthComparatorFunction Type of the birth comparator: (@ref Pos_index, @ref Pos_index) -> bool
+   * @tparam DeathComparatorFunction Type of the death comparator: (@ref Pos_index, @ref Pos_index) -> bool
+   * @tparam Boundary_range  Range type for @ref Matrix::Entry_representative ranges.
+   * Assumed to have a begin(), end() and size() method.
+   * @param orderedBoundaries Range of boundaries: @p orderedBoundaries is interpreted as a boundary matrix of a 
+   * filtered **simplicial** complex, whose boundaries are ordered by filtration order. 
+   * Therefore, `orderedBoundaries[i]` should store the boundary of the \f$ i^{th} \f$ simplex in the filtration,
+   * as an ordered list of indices of its facets (again those indices correspond to their respective position
+   * in the matrix). That is why the indices of the simplices are assumed to be consecutive and starting with 0 
+   * (an empty boundary is interpreted as a vertex boundary and not as a non existing simplex). 
+   * All dimensions up to the maximal dimension of interest have to be present. If only a higher dimension is of 
+   * interest and not everything should be stored, then use the @ref insert_boundary method instead
+   * (after creating the matrix with the @ref Chain_matrix(unsigned int, Column_settings*,
+   * const BirthComparatorFunction&, const DeathComparatorFunction&) constructor preferably).
+   * @param colSettings Pointer to an existing setting structure for the columns. The structure should contain all
+   * the necessary external classes specifically necessary for the choosen column type, such as custom allocators.
+   * @param birthComparator Method taking two @ref PosIdx indices as input and returning true if and only if
+   * the birth associated to the first position is strictly less than birth associated to
+   * the second one with respect to some self defined order. It is used while swapping two unpaired or
+   * two negative columns.
+   * @param deathComparator Method taking two @ref PosIdx indices as input and returning true if and only if
+   * the death associated to the first position is strictly less than death associated to
+   * the second one with respect to some self defined order. It is used while swapping two positive but paired
+   * columns.
+   */
+  template <typename BirthComparatorFunction, typename DeathComparatorFunction, class Boundary_range = Boundary>
+  Chain_matrix(const std::vector<Boundary_range>& orderedBoundaries, 
+               Column_settings* colSettings, 
+               const BirthComparatorFunction& birthComparator,
+               const DeathComparatorFunction& deathComparator);
+  /**
+   * @brief Constructs a new empty matrix and reserves space for the given number of columns.
+   *
+   * @warning If @ref PersistenceMatrixOptions::has_vine_update is false, the comparators are not used.
+   * And if @ref PersistenceMatrixOptions::has_vine_update is true, but
+   * @ref PersistenceMatrixOptions::has_column_pairings is also true, the comparators are ignored and
+   * the current barcode is used to compare birth and deaths. Therefore it is useless to provide them in those cases.
+   * 
+   * @tparam BirthComparatorFunction Type of the birth comparator: (@ref Pos_index, @ref Pos_index) -> bool
+   * @tparam DeathComparatorFunction Type of the death comparator: (@ref Pos_index, @ref Pos_index) -> bool
+   * @param numberOfColumns Number of columns to reserve space for.
+   * @param colSettings Pointer to an existing setting structure for the columns. The structure should contain all
+   * the necessary external classes specifically necessary for the choosen column type, such as custom allocators.
+   * @param birthComparator Method taking two @ref PosIdx indices as input and returning true if and only if
+   * the birth associated to the first position is strictly less than birth associated to
+   * the second one with respect to some self defined order. It is used while swapping two unpaired or
+   * two negative columns.
+   * @param deathComparator Method taking two @ref PosIdx indices as input and returning true if and only if
+   * the death associated to the first position is strictly less than death associated to
+   * the second one with respect to some self defined order. It is used while swapping two positive but paired
+   * columns.
+   */
+  template <typename BirthComparatorFunction, typename DeathComparatorFunction>
+  Chain_matrix(unsigned int numberOfColumns, 
+               Column_settings* colSettings,
+               const BirthComparatorFunction& birthComparator, 
+               const DeathComparatorFunction& deathComparator);
+  /**
+   * @brief Copy constructor. If @p colSettings is not a null pointer, its value is kept
+   * instead of the one in the copied matrix.
+   * 
+   * @param matrixToCopy Matrix to copy.
+   * @param colSettings Either a pointer to an existing setting structure for the columns or a null pointer.
+   * The structure should contain all the necessary external classes specifically necessary for the choosen column type,
+   * such as custom allocators. If null pointer, the pointer stored in @p matrixToCopy is used instead.
+   */
+  Chain_matrix(const Chain_matrix& matrixToCopy, 
+               Column_settings* colSettings = nullptr);
+  /**
+   * @brief Move constructor.
+   * 
+   * @param other Matrix to move.
+   */
+  Chain_matrix(Chain_matrix&& other) noexcept;
+
+  /**
+   * @brief Inserts at the end of the matrix a new ordered column corresponding to the given boundary.
+   * This means that it is assumed that this method is called on boundaries in the order of the filtration.
+   * It also assumes that the cells in the given boundary are identified by their relative position in the filtration,
+   * starting at 0. If it is not the case, use the other
+   * @ref insert_boundary(ID_index cellIndex, const Boundary_range& boundary, Dimension dim) "insert_boundary"
+   * instead by indicating the cell ID used in the boundaries when the cell is inserted.
+   *
+   * Different to the constructor, the boundaries do not have to come from a simplicial complex, but also from
+   * a more general entry complex. This includes cubical complexes or Morse complexes for example.
+   *
+   * When inserted, the given boundary is reduced and from the reduction process, the column is deduced in the form of:
+   * `IDIdx + linear combination of older column IDIdxs`. If the barcode is stored, it will be updated.
+   * 
+   * @tparam Boundary_range Range of @ref Matrix::Entry_representative. Assumed to have a begin(), end() and size()
+   * method.
+   * @param boundary Boundary generating the new column. The content should be ordered by ID.
+   * @param dim Dimension of the cell whose boundary is given. If the complex is simplicial, 
+   * this parameter can be omitted as it can be deduced from the size of the boundary.
+   * @return The @ref MatIdx indices of the unpaired chains used to reduce the boundary.
+   */
+  template <class Boundary_range = Boundary>
+  std::vector<Entry_representative> insert_boundary(const Boundary_range& boundary, Dimension dim = -1);
+  /**
+   * @brief It does the same as the other version, but allows the boundary cells to be identified without restrictions
+   * except that all IDs have to be strictly increasing in the order of filtration. Note that you should avoid then
+   * to use the other insertion method to avoid overwriting IDs.
+   *
+   * As a cell has to be inserted before one of its cofaces in a valid filtration (recall that it is assumed that
+   * the cells are inserted by order of filtration), it is sufficient to indicate the ID of the cell being inserted.
+   * 
+   * @tparam Boundary_range Range of @ref Matrix::Entry_representative. Assumed to have a begin(), end() and size()
+   * method.
+   * @param cellID @ref IDIdx index to use to identify the new cell.
+   * @param boundary Boundary generating the new column. The indices of the boundary have to correspond to the 
+   * @p cellID values of precedent calls of the method for the corresponding cells and should be ordered in 
+   * increasing order.
+   * @param dim Dimension of the cell whose boundary is given. If the complex is simplicial, 
+   * this parameter can be omitted as it can be deduced from the size of the boundary.
+   * @return The @ref MatIdx index of the inserted boundary.
+   */
+  template <class Boundary_range = Boundary>
+  std::vector<Entry_representative> insert_boundary(ID_index cellID,
+                                                    const Boundary_range& boundary,
+                                                    Dimension dim = -1);
+  /**
+   * @brief Returns the column at the given @ref MatIdx index.
+   * The type of the column depends on the choosen options, see @ref PersistenceMatrixOptions::column_type.
+   * 
+   * @param columnIndex @ref MatIdx index of the column to return.
+   * @return Reference to the column.
+   */
+  Column& get_column(Index columnIndex);
+  /**
+   * @brief Returns the column at the given @ref MatIdx index.
+   * The type of the column depends on the choosen options, see @ref PersistenceMatrixOptions::column_type.
+   * 
+   * @param columnIndex @ref MatIdx index of the column to return.
+   * @return Const reference to the column.
+   */
+  const Column& get_column(Index columnIndex) const;
+  /**
+   * @brief Only available if @ref PersistenceMatrixOptions::has_removable_columns and
+   * @ref PersistenceMatrixOptions::has_vine_update are true, as well as,
+   * @ref PersistenceMatrixOptions::has_map_column_container and @ref PersistenceMatrixOptions::has_column_pairings.
+   * Assumes that the cell is maximal in the current complex and removes it such that the matrix remains consistent
+   * (i.e., the matrix is still a compatible bases of the chain complex in the sense of @cite zigzag).
+   * The maximality of the cell is not verified.
+   * Also updates the barcode if it is stored.
+   *
+   * Note that using the other version of the method could perform better depending on how the data is 
+   * maintained on the side of the user, that is, if providing the second parameter is easy.
+   *
+   * See also @ref remove_last.
+   * 
+   * @param cellID @ref IDIdx index of the cell to remove
+   */
+  void remove_maximal_cell(ID_index cellID);
+  /**
+   * @brief Only available if @ref PersistenceMatrixOptions::has_removable_columns,
+   * @ref PersistenceMatrixOptions::has_vine_update and @ref PersistenceMatrixOptions::has_map_column_container
+   * are true.
+   * Assumes that the cell is maximal in the current complex and removes it such that the matrix remains consistent
+   * (i.e., it is still a compatible bases of the chain complex in the sense of @cite zigzag).
+   * The maximality of the cell is not verified.
+   * Also updates the barcode if it is stored.
+   *
+   * To maintain the compatibility, vine swaps are done to move the cell up to the end of the filtration. Once at 
+   * the end, the removal is trivial. But for @ref chainmatrix "chain matrices", swaps do not actually swap the position
+   * of the column every time, so the cells appearing after @p cellID in the filtration have to be searched first within
+   * the matrix. If the user has an easy access to the @ref IDIdx of the cells in the order of filtration, passing them
+   * by argument with @p columnsToSwap allows to skip a linear search process. Typically, if the user knows that the
+   * cell he wants to remove is already the last cell of the filtration, calling
+   * @ref remove_maximal_cell(ID_index cellIndex, const std::vector<ID_index>& columnsToSwap)
+   * "remove_maximal_cell(cellID, {})" will be faster than @ref remove_last().
+   *
+   * See also @ref remove_last.
+   * 
+   * @param cellID @ref IDIdx index of the cell to remove
+   * @param columnsToSwap Vector of @ref IDIdx indices of the cells coming after @p cellID in the filtration.
+   */
+  void remove_maximal_cell(ID_index cellID, const std::vector<ID_index>& columnsToSwap);
+  /**
+   * @brief Only available if @ref PersistenceMatrixOptions::has_removable_columns is true and,
+   * if @ref PersistenceMatrixOptions::has_map_column_container is true or
+   * @ref PersistenceMatrixOptions::has_vine_update is false.
+   * Removes the last cell in the filtration from the matrix and updates the barcode if it is stored.
+   *
+   * See also @ref remove_maximal_cell.
+   *
+   * @warning If @ref PersistenceMatrixOptions::has_vine_update is true, the last cell does not have to
+   * be at the end of the matrix container and therefore has to be searched first. In this case, if the user
+   * already knows the @ref IDIdx of the last cell, calling
+   * @ref remove_maximal_cell(ID_index cellIndex, const std::vector<ID_index>& columnsToSwap)
+   * "remove_maximal_cell(cellID, {})" instead allows to skip the search.
+   */
+  void remove_last();
+
+  /**
+   * @brief Returns the current number of columns in the matrix.
+   * 
+   * @return The number of columns.
+   */
+  Index get_number_of_columns() const;
+
+  /**
+   * @brief Returns the dimension of the given column.
+   * 
+   * @param columnIndex @ref MatIdx index of the column representing the cell.
+   * @return Dimension of the cell.
+   */
+  Dimension get_column_dimension(Index columnIndex) const;
+
+  /**
+   * @brief Adds column at @p sourceColumnIndex onto the column at @p targetColumnIndex in the matrix.
+   *
+   * @warning They will be no verification to ensure that the addition makes sense for the validity of a
+   * @ref chainmatrix "chain matrix". For example, a right-to-left addition could corrupt the computation
+   * of the barcode if done blindly. So should be used with care.
+   * 
+   * @param sourceColumnIndex @ref MatIdx index of the source column.
+   * @param targetColumnIndex @ref MatIdx index of the target column.
+   */
+  void add_to(Index sourceColumnIndex, Index targetColumnIndex);
+  /**
+   * @brief Multiplies the target column with the coefficient and then adds the source column to it.
+   * That is: `targetColumn = (targetColumn * coefficient) + sourceColumn`.
+   *
+   * @warning They will be no verification to ensure that the addition makes sense for the validity of a
+   * @ref chainmatrix "chain matrix". For example, a right-to-left addition could corrupt the computation
+   * of the barcode if done blindly. So should be used with care.
+   * 
+   * @param sourceColumnIndex @ref MatIdx index of the source column.
+   * @param coefficient Value to multiply.
+   * @param targetColumnIndex @ref MatIdx index of the target column.
+   */
+  void multiply_target_and_add_to(Index sourceColumnIndex, 
+                                  const Field_element& coefficient,
+                                  Index targetColumnIndex);
+  /**
+   * @brief Multiplies the source column with the coefficient before adding it to the target column.
+   * That is: `targetColumn += (coefficient * sourceColumn)`. The source column will **not** be modified.
+   *
+   * @warning They will be no verification to ensure that the addition makes sense for the validity of a
+   * @ref chainmatrix "chain matrix". For example, a right-to-left addition could corrupt the computation
+   * of the barcode if done blindly. So should be used with care.
+   * 
+   * @param coefficient Value to multiply.
+   * @param sourceColumnIndex @ref MatIdx index of the source column.
+   * @param targetColumnIndex @ref MatIdx index of the target column.
+   */
+  void multiply_source_and_add_to(const Field_element& coefficient, 
+                                  Index sourceColumnIndex,
+                                  Index targetColumnIndex);
+
+  /**
+   * @brief Indicates if the entry at given coordinates has value zero.
+   * 
+   * @param columnIndex @ref MatIdx index of the column of the entry.
+   * @param rowIndex @ref rowindex "Row index" of the row of the entry.
+   * @return true If the entry has value zero.
+   * @return false Otherwise.
+   */
+  bool is_zero_entry(Index columnIndex, ID_index rowIndex) const;
+  /**
+   * @brief Indicates if the column at given index has value zero. Note that if the matrix is valid, this method
+   * should always return false.
+   * 
+   * @param columnIndex @ref MatIdx index of the column.
+   * @return true If the column has value zero.
+   * @return false Otherwise.
+   */
+  bool is_zero_column(Index columnIndex);
+
+  /**
+   * @brief Returns the column with given @ref rowindex "row index" as pivot. Assumes that the pivot exists.
+   * 
+   * @param cellID @ref rowindex "Row index" of the pivot.
+   * @return @ref MatIdx index of the column with the given pivot.
+   */
+  Index get_column_with_pivot(ID_index cellID) const;
+  /**
+   * @brief Returns the @ref rowindex "row index" of the pivot of the given column.
+   * 
+   * @param columnIndex @ref MatIdx index of the column
+   * @return The @ref rowindex "row index" of the pivot.
+   */
+  ID_index get_pivot(Index columnIndex);
+
+  /**
+   * @brief Resets the matrix to an empty matrix.
+   * 
+   * @param colSettings Pointer to an existing setting structure for the columns. The structure should contain all
+   * the necessary external classes specifically necessary for the choosen column type, such as custom allocators.
+   */
+  void reset(Column_settings* colSettings) {
+    matrix_.clear();
+    pivotToColumnIndex_.clear();
+    nextIndex_ = 0;
+    colSettings_ = colSettings;
+  }
+
+  /**
+   * @brief Assign operator.
+   */
+  Chain_matrix& operator=(const Chain_matrix& other);
+  /**
+   * @brief Swap operator.
+   */
+  friend void swap(Chain_matrix& matrix1, Chain_matrix& matrix2) {
+    swap(static_cast<typename Master_matrix::Matrix_dimension_option&>(matrix1),
+         static_cast<typename Master_matrix::Matrix_dimension_option&>(matrix2));
+    swap(static_cast<typename Master_matrix::Chain_pairing_option&>(matrix1),
+         static_cast<typename Master_matrix::Chain_pairing_option&>(matrix2));
+    swap(static_cast<typename Master_matrix::Chain_vine_swap_option&>(matrix1),
+         static_cast<typename Master_matrix::Chain_vine_swap_option&>(matrix2));
+    swap(static_cast<typename Master_matrix::Chain_representative_cycles_option&>(matrix1),
+         static_cast<typename Master_matrix::Chain_representative_cycles_option&>(matrix2));
+    matrix1.matrix_.swap(matrix2.matrix_);
+    matrix1.pivotToColumnIndex_.swap(matrix2.pivotToColumnIndex_);
+    std::swap(matrix1.nextIndex_, matrix2.nextIndex_);
+    std::swap(matrix1.colSettings_, matrix2.colSettings_);
+
+    if constexpr (Master_matrix::Option_list::has_row_access) {
+      swap(static_cast<typename Master_matrix::Matrix_row_access_option&>(matrix1),
+           static_cast<typename Master_matrix::Matrix_row_access_option&>(matrix2));
+    }
+  }
+
+  void print() const;  // for debug
+
+  friend class Id_to_index_overlay<Chain_matrix<Master_matrix>, Master_matrix>;
+
+ private:
+  using Dim_opt = typename Master_matrix::Matrix_dimension_option;
+  using Swap_opt = typename Master_matrix::Chain_vine_swap_option;
+  using Pair_opt = typename Master_matrix::Chain_pairing_option;
+  using Rep_opt = typename Master_matrix::Chain_representative_cycles_option;
+  using RA_opt = typename Master_matrix::Matrix_row_access_option;
+  using Column_container = typename Master_matrix::Column_container;
+  using Dictionary = typename Master_matrix::template Dictionary<Index>;
+  using Barcode = typename Master_matrix::Barcode;
+  using Bar_dictionary = typename Master_matrix::Bar_dictionary;
+  using Tmp_column = typename std::conditional<Master_matrix::Option_list::is_z2,
+                                               std::set<ID_index>,
+                                               std::map<ID_index, Field_element>
+                                              >::type;
+
+  Column_container matrix_;       /**< Column container. */
+  Dictionary pivotToColumnIndex_; /**< Map from @ref IDIdx to @ref MatIdx index. */
+  Index nextIndex_;               /**< Next unused column index. */
+  Column_settings* colSettings_;  /**< Entry factory. */
+
+  template <class Boundary_range>
+  std::vector<Entry_representative> _reduce_boundary(ID_index cellID, const Boundary_range& boundary, Dimension dim);
+  void _reduce_by_G(Tmp_column& column, std::vector<Entry_representative>& chainsInH, Index currentPivot);
+  void _reduce_by_F(Tmp_column& column, std::vector<Entry_representative>& chainsInF, Index currentPivot);
+  void _build_from_H(ID_index cellID, Tmp_column& column, std::vector<Entry_representative>& chainsInH);
+  void _update_largest_death_in_F(const std::vector<Entry_representative>& chainsInF);
+  void _insert_chain(const Tmp_column& column, Dimension dimension);
+  void _insert_chain(const Tmp_column& column, Dimension dimension, Index pair);
+  void _add_to(const Column& column, Tmp_column& set, unsigned int coef);
+  template <typename F>
+  void _add_to(Column& target, F&& addition);
+  void _remove_last(Index lastIndex);
+  void _update_barcode(Pos_index birth);
+  void _add_bar(Dimension dim);
+  template <class Container>
+  void _container_insert(const Container& column, Index pos, Dimension dim);
+  void _container_insert(const Column& column, [[maybe_unused]] Index pos = 0);
+
+  constexpr Barcode& _barcode();
+  constexpr Bar_dictionary& _indexToBar();
+  constexpr Pos_index& _nextPosition();
+};
+
+template <class Master_matrix>
+inline Chain_matrix<Master_matrix>::Chain_matrix(Column_settings* colSettings)
+    : Dim_opt(-1),
+      Pair_opt(),
+      Swap_opt(),
+      Rep_opt(),
+      RA_opt(),
+      nextIndex_(0),
+      colSettings_(colSettings)
+{}
+
+template <class Master_matrix>
+template <class Boundary_range>
+inline Chain_matrix<Master_matrix>::Chain_matrix(const std::vector<Boundary_range>& orderedBoundaries,
+                                                 Column_settings* colSettings)
+    : Dim_opt(-1),
+      Pair_opt(),
+      Swap_opt(),
+      Rep_opt(),
+      RA_opt(orderedBoundaries.size()),
+      nextIndex_(0),
+      colSettings_(colSettings)
+{
+  matrix_.reserve(orderedBoundaries.size());
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    pivotToColumnIndex_.reserve(orderedBoundaries.size());
+  } else {
+    pivotToColumnIndex_.resize(orderedBoundaries.size(), -1);
+  }
+
+  for (const Boundary_range& b : orderedBoundaries) {
+    insert_boundary(b);
+  }
+}
+
+template <class Master_matrix>
+inline Chain_matrix<Master_matrix>::Chain_matrix(unsigned int numberOfColumns, 
+                                                 Column_settings* colSettings)
+    : Dim_opt(-1),
+      Pair_opt(),
+      Swap_opt(),
+      Rep_opt(),
+      RA_opt(numberOfColumns),
+      nextIndex_(0),
+      colSettings_(colSettings)
+{
+  matrix_.reserve(numberOfColumns);
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    pivotToColumnIndex_.reserve(numberOfColumns);
+  } else {
+    pivotToColumnIndex_.resize(numberOfColumns, -1);
+  }
+}
+
+template <class Master_matrix>
+template <typename BirthComparatorFunction, typename DeathComparatorFunction>
+inline Chain_matrix<Master_matrix>::Chain_matrix(Column_settings* colSettings,
+                                                 const BirthComparatorFunction& birthComparator,
+                                                 const DeathComparatorFunction& deathComparator)
+    : Dim_opt(-1),
+      Pair_opt(),
+      Swap_opt(birthComparator, deathComparator),
+      Rep_opt(),
+      RA_opt(),
+      nextIndex_(0),
+      colSettings_(colSettings)
+{}
+
+template <class Master_matrix>
+template <typename BirthComparatorFunction, typename DeathComparatorFunction, class Boundary_range>
+inline Chain_matrix<Master_matrix>::Chain_matrix(const std::vector<Boundary_range>& orderedBoundaries,
+                                                 Column_settings* colSettings,
+                                                 const BirthComparatorFunction& birthComparator,
+                                                 const DeathComparatorFunction& deathComparator)
+    : Dim_opt(-1),
+      Pair_opt(),
+      Swap_opt(birthComparator, deathComparator),
+      Rep_opt(),
+      RA_opt(orderedBoundaries.size()),
+      nextIndex_(0),
+      colSettings_(colSettings)
+{
+  matrix_.reserve(orderedBoundaries.size());
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    pivotToColumnIndex_.reserve(orderedBoundaries.size());
+  } else {
+    pivotToColumnIndex_.resize(orderedBoundaries.size(), -1);
+  }
+  for (const Boundary_range& b : orderedBoundaries) {
+    insert_boundary(b);
+  }
+}
+
+template <class Master_matrix>
+template <typename BirthComparatorFunction, typename DeathComparatorFunction>
+inline Chain_matrix<Master_matrix>::Chain_matrix(unsigned int numberOfColumns, 
+                                                 Column_settings* colSettings,
+                                                 const BirthComparatorFunction& birthComparator,
+                                                 const DeathComparatorFunction& deathComparator)
+    : Dim_opt(-1),
+      Pair_opt(),
+      Swap_opt(birthComparator, deathComparator),
+      Rep_opt(),
+      RA_opt(numberOfColumns),
+      nextIndex_(0),
+      colSettings_(colSettings)
+{
+  matrix_.reserve(numberOfColumns);
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    pivotToColumnIndex_.reserve(numberOfColumns);
+  } else {
+    pivotToColumnIndex_.resize(numberOfColumns, -1);
+  }
+}
+
+template <class Master_matrix>
+inline Chain_matrix<Master_matrix>::Chain_matrix(const Chain_matrix& matrixToCopy, Column_settings* colSettings)
+    : Dim_opt(static_cast<const Dim_opt&>(matrixToCopy)),
+      Pair_opt(static_cast<const Pair_opt&>(matrixToCopy)),
+      Swap_opt(static_cast<const Swap_opt&>(matrixToCopy)),
+      Rep_opt(static_cast<const Rep_opt&>(matrixToCopy)),
+      RA_opt(static_cast<const RA_opt&>(matrixToCopy)),
+      pivotToColumnIndex_(matrixToCopy.pivotToColumnIndex_),
+      nextIndex_(matrixToCopy.nextIndex_),
+      colSettings_(colSettings == nullptr ? matrixToCopy.colSettings_ : colSettings)
+{
+  matrix_.reserve(matrixToCopy.matrix_.size());
+  for (const auto& cont : matrixToCopy.matrix_){
+    if constexpr (Master_matrix::Option_list::has_map_column_container){
+      _container_insert(cont.second, cont.first);
+    } else {
+      _container_insert(cont);
+    }
+  }
+}
+
+template <class Master_matrix>
+inline Chain_matrix<Master_matrix>::Chain_matrix(Chain_matrix&& other) noexcept
+    : Dim_opt(std::move(static_cast<Dim_opt&>(other))),
+      Pair_opt(std::move(static_cast<Pair_opt&>(other))),
+      Swap_opt(std::move(static_cast<Swap_opt&>(other))),
+      Rep_opt(std::move(static_cast<Rep_opt&>(other))),
+      RA_opt(std::move(static_cast<RA_opt&>(other))),
+      matrix_(std::move(other.matrix_)),
+      pivotToColumnIndex_(std::move(other.pivotToColumnIndex_)),
+      nextIndex_(std::exchange(other.nextIndex_, 0)),
+      colSettings_(std::exchange(other.colSettings_, nullptr)) 
+{}
+
+template <class Master_matrix>
+template <class Boundary_range>
+inline std::vector<typename Master_matrix::Entry_representative> Chain_matrix<Master_matrix>::insert_boundary(
+    const Boundary_range& boundary, Dimension dim) 
+{
+  return insert_boundary(nextIndex_, boundary, dim);
+}
+
+template <class Master_matrix>
+template <class Boundary_range>
+inline std::vector<typename Master_matrix::Entry_representative> Chain_matrix<Master_matrix>::insert_boundary(
+    ID_index cellID, const Boundary_range& boundary, Dimension dim) 
+{
+  if constexpr (!Master_matrix::Option_list::has_map_column_container) {
+    if (pivotToColumnIndex_.size() <= cellID) {
+      pivotToColumnIndex_.resize(cellID * 2 + 1, -1);
+    }
+  }
+
+  if constexpr (Master_matrix::Option_list::has_vine_update && Master_matrix::Option_list::has_column_pairings) {
+    if constexpr (Master_matrix::Option_list::has_map_column_container) {
+      Swap_opt::CP::pivotToPosition_.try_emplace(cellID, _nextPosition());
+    } else {
+      if (Swap_opt::CP::pivotToPosition_.size() <= cellID)
+        Swap_opt::CP::pivotToPosition_.resize(pivotToColumnIndex_.size(), -1);
+      Swap_opt::CP::pivotToPosition_[cellID] = _nextPosition();
+    }
+  }
+
+  if constexpr (Master_matrix::Option_list::has_matrix_maximal_dimension_access) {
+    Dim_opt::update_up(dim == static_cast<Dimension>(-1) ? (boundary.size() == 0 ? 0 : boundary.size() - 1) : dim);
+  }
+
+  return _reduce_boundary(cellID, boundary, dim);
+}
+
+template <class Master_matrix>
+inline typename Chain_matrix<Master_matrix>::Column& Chain_matrix<Master_matrix>::get_column(Index columnIndex) 
+{
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    return matrix_.at(columnIndex);
+  } else {
+    return matrix_[columnIndex];
+  }
+}
+
+template <class Master_matrix>
+inline const typename Chain_matrix<Master_matrix>::Column& Chain_matrix<Master_matrix>::get_column(
+    Index columnIndex) const
+{
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    return matrix_.at(columnIndex);
+  } else {
+    return matrix_[columnIndex];
+  }
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::remove_maximal_cell(ID_index cellID)
+{
+  static_assert(Master_matrix::Option_list::has_removable_columns,
+                "'remove_maximal_cell' is not implemented for the chosen options.");
+  static_assert(Master_matrix::Option_list::has_map_column_container && 
+                    Master_matrix::Option_list::has_vine_update &&
+                    Master_matrix::Option_list::has_column_pairings,
+                "'remove_maximal_cell' is not implemented for the chosen options.");
+
+  // TODO: find simple test to verify that col at columnIndex is maximal even without row access.
+
+  const auto& pivotToPosition = Swap_opt::CP::pivotToPosition_;
+  auto it = pivotToPosition.find(cellID);
+  if (it == pivotToPosition.end()) return;  // cell does not exists. TODO: put an assert instead?
+  Pos_index startPos = it->second;
+  Index startIndex = pivotToColumnIndex_.at(cellID);
+
+  if (startPos != _nextPosition() - 1) {
+    std::vector<Index> colToSwap;
+    colToSwap.reserve(matrix_.size());
+
+    for (auto& p : pivotToPosition) {
+      if (p.second > startPos) colToSwap.push_back(pivotToColumnIndex_.at(p.first));
+    }
+    std::sort(colToSwap.begin(), colToSwap.end(), [&](Index c1, Index c2) {
+      return pivotToPosition.at(get_pivot(c1)) < pivotToPosition.at(get_pivot(c2));
+    });
+
+    for (Index i : colToSwap) {
+      startIndex = Swap_opt::vine_swap(startIndex, i);
+    }
+  }
+
+  _remove_last(startIndex);
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::remove_maximal_cell(ID_index cellID,
+                                                             const std::vector<ID_index>& columnsToSwap)
+{
+  static_assert(Master_matrix::Option_list::has_removable_columns,
+                "'remove_maximal_cell' is not implemented for the chosen options.");
+  static_assert(Master_matrix::Option_list::has_map_column_container && Master_matrix::Option_list::has_vine_update,
+                "'remove_maximal_cell' is not implemented for the chosen options.");
+
+  // TODO: find simple test to verify that col at columnIndex is maximal even without row access.
+
+  Index startIndex = pivotToColumnIndex_.at(cellID);
+
+  for (ID_index i : columnsToSwap) {
+    startIndex = Swap_opt::vine_swap(startIndex, pivotToColumnIndex_.at(i));
+  }
+
+  _remove_last(startIndex);
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::remove_last()
+{
+  static_assert(Master_matrix::Option_list::has_removable_columns,
+                "'remove_last' is not implemented for the chosen options.");
+  static_assert(Master_matrix::Option_list::has_map_column_container || !Master_matrix::Option_list::has_vine_update,
+                "'remove_last' is not implemented for the chosen options.");
+
+  if (nextIndex_ == 0 || matrix_.empty()) return;  // empty matrix
+
+  if constexpr (Master_matrix::Option_list::has_vine_update) {
+    // careful: linear because of the search of the last index. It is better to keep track of the @ref IDIdx index
+    // of the last column while performing swaps (or the @ref MatIdx with the return values of `vine_swap` + get_pivot)
+    // and then call `remove_maximal_cell` with it and an empty `columnsToSwap`.
+
+    ID_index pivot = 0;
+    Index colIndex = 0;
+    for (auto& p : pivotToColumnIndex_) {
+      if (p.first > pivot) {  // pivots have to be strictly increasing in order of filtration
+        pivot = p.first;
+        colIndex = p.second;
+      }
+    }
+    _remove_last(colIndex);
+  } else {
+    _remove_last(nextIndex_ - 1);
+  }
+}
+
+template <class Master_matrix>
+inline typename Chain_matrix<Master_matrix>::Index Chain_matrix<Master_matrix>::get_number_of_columns() const
+{
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    return matrix_.size();
+  } else {
+    return nextIndex_;  // matrix could have been resized much bigger while insert
+  }
+}
+
+template <class Master_matrix>
+inline typename Chain_matrix<Master_matrix>::Dimension Chain_matrix<Master_matrix>::get_column_dimension(
+    Index columnIndex) const 
+{
+  return get_column(columnIndex).get_dimension();
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::add_to(Index sourceColumnIndex, Index targetColumnIndex)
+{
+  auto& col = get_column(targetColumnIndex);
+  _add_to(col, [&]() { col += get_column(sourceColumnIndex); });
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::multiply_target_and_add_to(Index sourceColumnIndex,
+                                                                    const Field_element& coefficient,
+                                                                    Index targetColumnIndex)
+{
+  auto& col = get_column(targetColumnIndex);
+  _add_to(col, [&]() { col.multiply_target_and_add(coefficient, get_column(sourceColumnIndex)); });
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::multiply_source_and_add_to(const Field_element& coefficient,
+                                                                    Index sourceColumnIndex,
+                                                                    Index targetColumnIndex)
+{
+  auto& col = get_column(targetColumnIndex);
+  _add_to(col, [&]() { col.multiply_source_and_add(get_column(sourceColumnIndex), coefficient); });
+}
+
+template <class Master_matrix>
+inline bool Chain_matrix<Master_matrix>::is_zero_entry(Index columnIndex, ID_index rowIndex) const 
+{
+  return !get_column(columnIndex).is_non_zero(rowIndex);
+}
+
+template <class Master_matrix>
+inline bool Chain_matrix<Master_matrix>::is_zero_column(Index columnIndex) 
+{
+  return get_column(columnIndex).is_empty();
+}
+
+template <class Master_matrix>
+inline typename Chain_matrix<Master_matrix>::Index Chain_matrix<Master_matrix>::get_column_with_pivot(
+    ID_index cellID) const
+{
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    return pivotToColumnIndex_.at(cellID);
+  } else {
+    return pivotToColumnIndex_[cellID];
+  }
+}
+
+template <class Master_matrix>
+inline typename Chain_matrix<Master_matrix>::ID_index Chain_matrix<Master_matrix>::get_pivot(Index columnIndex)
+{
+  return get_column(columnIndex).get_pivot();
+}
+
+template <class Master_matrix>
+inline Chain_matrix<Master_matrix>& Chain_matrix<Master_matrix>::operator=(const Chain_matrix& other)
+{
+  Dim_opt::operator=(other);
+  Swap_opt::operator=(other);
+  Pair_opt::operator=(other);
+  Rep_opt::operator=(other);
+  matrix_.clear();
+  pivotToColumnIndex_ = other.pivotToColumnIndex_;
+  nextIndex_ = other.nextIndex_;
+  colSettings_ = other.colSettings_;
+
+  matrix_.reserve(other.matrix_.size());
+  for (const auto& cont : other.matrix_){
+    if constexpr (Master_matrix::Option_list::has_map_column_container){
+      _container_insert(cont.second, cont.first);
+    } else {
+      _container_insert(cont);
+    }
+  }
+
+  return *this;
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::print() const
+{
+  std::cout << "Column Matrix:\n";
+  if constexpr (!Master_matrix::Option_list::has_map_column_container) {
+    for (ID_index i = 0; i < pivotToColumnIndex_.size() && pivotToColumnIndex_[i] != static_cast<Index>(-1); ++i) {
+      Index pos = pivotToColumnIndex_[i];
+      const Column& col = matrix_[pos];
+      for (const auto& entry : col) {
+        std::cout << entry.get_row_index() << " ";
+      }
+      std::cout << "(" << i << ", " << pos << ")\n";
+    }
+    if constexpr (Master_matrix::Option_list::has_row_access) {
+      std::cout << "\n";
+      std::cout << "Row Matrix:\n";
+      for (ID_index i = 0; i < pivotToColumnIndex_.size() && pivotToColumnIndex_[i] != static_cast<Index>(-1); ++i) {
+        Index pos = pivotToColumnIndex_[i];
+        const Row& row = RA_opt::get_row(pos);
+        for (const auto& entry : row) {
+          std::cout << entry.get_column_index() << " ";
+        }
+        std::cout << "(" << i << ", " << pos << ")\n";
+      }
+    }
+  } else {
+    for (const auto& p : pivotToColumnIndex_) {
+      const Column& col = matrix_.at(p.second);
+      for (const auto& entry : col) {
+        std::cout << entry.get_row_index() << " ";
+      }
+      std::cout << "(" << p.first << ", " << p.second << ")\n";
+    }
+    if constexpr (Master_matrix::Option_list::has_row_access) {
+      std::cout << "\n";
+      std::cout << "Row Matrix:\n";
+      for (const auto& p : pivotToColumnIndex_) {
+        const Row& row = RA_opt::get_row(p.first);
+        for (const auto& entry : row) {
+          std::cout << entry.get_column_index() << " ";
+        }
+        std::cout << "(" << p.first << ", " << p.second << ")\n";
+      }
+    }
+  }
+  std::cout << "\n";
+}
+
+template <class Master_matrix>
+template <class Boundary_range>
+inline std::vector<typename Master_matrix::Entry_representative> Chain_matrix<Master_matrix>::_reduce_boundary(
+    ID_index cellID, const Boundary_range& boundary, Dimension dim)
+{
+  Tmp_column column(boundary.begin(), boundary.end());
+  if (dim == static_cast<Dimension>(-1)) dim = boundary.begin() == boundary.end() ? 0 : boundary.size() - 1;
+  std::vector<Entry_representative> chainsInH;  // for corresponding indices in H (paired columns)
+  std::vector<Entry_representative> chainsInF;  // for corresponding indices in F (unpaired, essential columns)
+
+  auto get_last = [&column]() {
+    if constexpr (Master_matrix::Option_list::is_z2)
+      return *(column.rbegin());
+    else
+      return column.rbegin()->first;
+  };
+
+  if (boundary.begin() == boundary.end()) {
+    if constexpr (Master_matrix::Option_list::is_z2)
+      column.insert(cellID);
+    else
+      column.emplace(cellID, 1);
+    _insert_chain(column, dim);
+    return chainsInF;
+  }
+
+  Index currentIndex = get_column_with_pivot(get_last());
+
+  while (get_column(currentIndex).is_paired()) {
+    _reduce_by_G(column, chainsInH, currentIndex);
+
+    if (column.empty()) {
+      // produce the sum of all col_h in chains_in_H
+      _build_from_H(cellID, column, chainsInH);
+      // create a new cycle (in F) sigma - \sum col_h
+      _insert_chain(column, dim);
+      return chainsInF;
+    }
+
+    currentIndex = get_column_with_pivot(get_last());
+  }
+
+  while (!column.empty()) {
+    currentIndex = get_column_with_pivot(get_last());
+
+    if (!get_column(currentIndex).is_paired()) {
+      // only fills currentEssentialCycleIndices if Z2 coefficients, so chainsInF remains empty
+      _reduce_by_F(column, chainsInF, currentIndex);
+    } else {
+      _reduce_by_G(column, chainsInH, currentIndex);
+    }
+  }
+
+  _update_largest_death_in_F(chainsInF);
+
+  // Compute the new column cellID + \sum col_h, for col_h in chains_in_H
+  _build_from_H(cellID, column, chainsInH);
+
+  // Create and insert (\sum col_h) + sigma (in H, paired with chain_fp) in matrix_
+  if constexpr (Master_matrix::Option_list::is_z2)
+    _insert_chain(column, dim, chainsInF[0]);
+  else
+    _insert_chain(column, dim, chainsInF[0].first);
+
+  return chainsInF;
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::_reduce_by_G(Tmp_column& column,
+                                                      std::vector<Entry_representative>& chainsInH,
+                                                      Index currentIndex)
+{
+  Column& col = get_column(currentIndex);
+  if constexpr (Master_matrix::Option_list::is_z2) {
+    _add_to(col, column, 1u);                           // Reduce with the column col_g
+    chainsInH.push_back(col.get_paired_chain_index());  // keep the col_h with which col_g is paired
+  } else {
+    Field_element coef = col.get_pivot_value();
+    auto& operators = colSettings_->operators;
+    coef = operators.get_inverse(coef);
+    operators.multiply_inplace(coef, operators.get_characteristic() - column.rbegin()->second);
+
+    _add_to(col, column, coef);                                       // Reduce with the column col_g
+    chainsInH.emplace_back(col.get_paired_chain_index(), coef); // keep the col_h with which col_g is paired
+  }
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::_reduce_by_F(Tmp_column& column, 
+                                                      std::vector<Entry_representative>& chainsInF,
+                                                      Index currentIndex) 
+{
+  Column& col = get_column(currentIndex);
+  if constexpr (Master_matrix::Option_list::is_z2) {
+    _add_to(col, column, 1u);  // Reduce with the column col_g
+    chainsInF.push_back(currentIndex);
+  } else {
+    Field_element coef = col.get_pivot_value();
+    auto& operators = colSettings_->operators;
+    coef = operators.get_inverse(coef);
+    operators.multiply_inplace(coef, operators.get_characteristic() - column.rbegin()->second);
+
+    _add_to(col, column, coef);  // Reduce with the column col_g
+    chainsInF.emplace_back(currentIndex, operators.get_characteristic() - coef);
+  }
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::_build_from_H(ID_index cellID,
+                                                       Tmp_column& column,
+                                                       std::vector<Entry_representative>& chainsInH)
+{
+  if constexpr (Master_matrix::Option_list::is_z2) {
+    column.insert(cellID);
+    for (Index idx_h : chainsInH) {
+      _add_to(get_column(idx_h), column, 1u);
+    }
+  } else {
+    column.emplace(cellID, 1);
+    for (std::pair<Index, Field_element>& idx_h : chainsInH) {
+      _add_to(get_column(idx_h.first), column, idx_h.second);
+    }
+  }
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::_update_largest_death_in_F(const std::vector<Entry_representative>& chainsInF) 
+{
+  if constexpr (Master_matrix::Option_list::is_z2) {
+    Index toUpdate = chainsInF[0];
+    for (auto other_col_it = chainsInF.begin() + 1; other_col_it != chainsInF.end(); ++other_col_it) {
+      add_to(*other_col_it, toUpdate);
+    }
+  } else {
+    Index toUpdate = chainsInF[0].first;
+    get_column(toUpdate) *= chainsInF[0].second;
+    for (auto other_col_it = chainsInF.begin() + 1; other_col_it != chainsInF.end(); ++other_col_it) {
+      multiply_source_and_add_to(other_col_it->second, other_col_it->first, toUpdate);
+    }
+  }
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::_insert_chain(const Tmp_column& column, Dimension dimension) 
+{
+  _container_insert(column, nextIndex_, dimension);
+  _add_bar(dimension);
+
+  ++nextIndex_;
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::_insert_chain(const Tmp_column& column, Dimension dimension, Index pair)
+{
+  // true when no vine updates and if nextIndex_ is updated in remove_last for special case of no vines
+  // because then @ref PosIdx == @ref MatIdx
+  Pos_index pairPos = pair;
+
+  _container_insert(column, nextIndex_, dimension);
+
+  get_column(nextIndex_).assign_paired_chain(pair);
+  auto& pairCol = get_column(pair);
+  pairCol.assign_paired_chain(nextIndex_);
+
+  if constexpr (Master_matrix::Option_list::has_column_pairings && Master_matrix::Option_list::has_vine_update) {
+    pairPos = Swap_opt::CP::pivotToPosition_[pairCol.get_pivot()];
+  }
+
+  _update_barcode(pairPos);
+
+  ++nextIndex_;
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::_add_to(const Column& column,
+                                                 Tmp_column& set,
+                                                 [[maybe_unused]] unsigned int coef) 
+{
+  if constexpr (Master_matrix::Option_list::is_z2) {
+    std::pair<typename std::set<Index>::iterator, bool> res_insert;
+    for (const Entry& entry : column) {
+      res_insert = set.insert(entry.get_row_index());
+      if (!res_insert.second) {
+        set.erase(res_insert.first);
+      }
+    }
+  } else {
+    auto& operators = colSettings_->operators;
+    for (const Entry& entry : column) {
+      auto res = set.emplace(entry.get_row_index(), entry.get_element());
+      if (res.second){
+        operators.multiply_inplace(res.first->second, coef);
+      } else {
+        operators.multiply_and_add_inplace_back(entry.get_element(), coef, res.first->second);
+        if (res.first->second == Field_operators::get_additive_identity()) {
+          set.erase(res.first);
+        }
+      }
+    }
+  }
+}
+
+template <class Master_matrix>
+template <typename F>
+inline void Chain_matrix<Master_matrix>::_add_to(Column& target, F&& addition)
+{
+  auto pivot = target.get_pivot();
+  addition();
+
+  if (pivot != target.get_pivot()) {
+    if constexpr (Master_matrix::Option_list::has_map_column_container) {
+      std::swap(pivotToColumnIndex_.at(pivot), pivotToColumnIndex_.at(target.get_pivot()));
+    } else {
+      std::swap(pivotToColumnIndex_[pivot], pivotToColumnIndex_[target.get_pivot()]);
+    }
+  }
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::_remove_last(Index lastIndex)
+{
+  static_assert(Master_matrix::Option_list::has_removable_columns,
+                "'_remove_last' is not implemented for the chosen options.");
+  static_assert(Master_matrix::Option_list::has_map_column_container || !Master_matrix::Option_list::has_vine_update,
+                "'_remove_last' is not implemented for the chosen options.");
+
+  ID_index pivot;
+
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    auto itToErase = matrix_.find(lastIndex);
+    Column& colToErase = itToErase->second;
+    pivot = colToErase.get_pivot();
+
+    if constexpr (Master_matrix::Option_list::has_matrix_maximal_dimension_access) {
+      Dim_opt::update_down(colToErase.get_dimension());
+    }
+
+    if (colToErase.is_paired()) matrix_.at(colToErase.get_paired_chain_index()).unassign_paired_chain();
+    pivotToColumnIndex_.erase(pivot);
+    matrix_.erase(itToErase);
+  } else {
+    GUDHI_CHECK(lastIndex == nextIndex_ - 1 && nextIndex_ == matrix_.size(),
+                std::logic_error("Chain_matrix::_remove_last - Indexation problem."));
+
+    Column& colToErase = matrix_[lastIndex];
+    pivot = colToErase.get_pivot();
+
+    if constexpr (Master_matrix::Option_list::has_matrix_maximal_dimension_access) {
+      Dim_opt::update_down(colToErase.get_dimension());
+    }
+
+    if (colToErase.is_paired()) matrix_.at(colToErase.get_paired_chain_index()).unassign_paired_chain();
+    pivotToColumnIndex_[pivot] = -1;
+    matrix_.pop_back();
+    // TODO: resize matrix_ when a lot is removed? Could be not the best strategy if user inserts a lot back afterwards.
+  }
+
+  if constexpr (!Master_matrix::Option_list::has_vine_update) {
+    --nextIndex_;  // should not be updated when there are vine updates, as possibly lastIndex != nextIndex - 1
+  }
+
+  if constexpr (Master_matrix::Option_list::has_column_pairings) {
+    auto it = _indexToBar().find(--_nextPosition());
+    typename Barcode::iterator bar = it->second;
+
+    if (bar->death == static_cast<Pos_index>(-1))
+      _barcode().erase(bar);
+    else
+      bar->death = -1;
+
+    _indexToBar().erase(it);
+    if constexpr (Master_matrix::Option_list::has_vine_update) Swap_opt::CP::pivotToPosition_.erase(pivot);
+  }
+
+  if constexpr (Master_matrix::Option_list::has_row_access) {
+    GUDHI_CHECK(
+        RA_opt::get_row(pivot).size() == 0,
+        std::invalid_argument(
+            "Chain_matrix::_remove_last - Column asked to be removed does not corresponds to a maximal simplex."));
+    if constexpr (Master_matrix::Option_list::has_removable_rows) {
+      RA_opt::erase_empty_row(pivot);
+    }
+  }
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::_update_barcode(Pos_index birth)
+{
+  if constexpr (Master_matrix::Option_list::has_column_pairings) {
+    if constexpr (Master_matrix::Option_list::has_removable_columns) {
+      auto& barIt = _indexToBar().at(birth);
+      barIt->death = _nextPosition();
+      _indexToBar().try_emplace(_nextPosition(), barIt);  // list so iterators are stable
+    } else {
+      _barcode()[_indexToBar()[birth]].death = _nextPosition();
+      _indexToBar().push_back(_indexToBar()[birth]);
+    }
+    ++_nextPosition();
+  }
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::_add_bar(Dimension dim)
+{
+  if constexpr (Master_matrix::Option_list::has_column_pairings) {
+    _barcode().emplace_back(_nextPosition(), -1, dim);
+    if constexpr (Master_matrix::Option_list::has_removable_columns) {
+      _indexToBar().try_emplace(_nextPosition(), --_barcode().end());
+    } else {
+      _indexToBar().push_back(_barcode().size() - 1);
+    }
+    ++_nextPosition();
+  }
+}
+
+template <class Master_matrix>
+template <class Container>
+inline void Chain_matrix<Master_matrix>::_container_insert(const Container& column, Index pos, Dimension dim)
+{
+  ID_index pivot;
+  if constexpr (Master_matrix::Option_list::is_z2) {
+    pivot = *(column.rbegin());
+  } else {
+    pivot = column.rbegin()->first;
+  }
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    pivotToColumnIndex_.try_emplace(pivot, pos);
+    if constexpr (Master_matrix::Option_list::has_row_access) {
+      matrix_.try_emplace(pos, Column(pos, column, dim, RA_opt::rows_, colSettings_));
+    } else {
+      matrix_.try_emplace(pos, Column(column, dim, colSettings_));
+    }
+  } else {
+    if constexpr (Master_matrix::Option_list::has_row_access) {
+      matrix_.emplace_back(pos, column, dim, RA_opt::rows_, colSettings_);
+    } else {
+      matrix_.emplace_back(column, dim, colSettings_);
+    }
+    pivotToColumnIndex_[pivot] = pos;
+  }
+}
+
+template <class Master_matrix>
+inline void Chain_matrix<Master_matrix>::_container_insert(const Column& column, [[maybe_unused]] Index pos)
+{
+  if constexpr (Master_matrix::Option_list::has_map_column_container) {
+    if constexpr (Master_matrix::Option_list::has_row_access) {
+      matrix_.try_emplace(pos, Column(column, column.get_column_index(), RA_opt::rows_, colSettings_));
+    } else {
+      matrix_.try_emplace(pos, Column(column, colSettings_));
+    }
+  } else {
+    if constexpr (Master_matrix::Option_list::has_row_access) {
+      matrix_.emplace_back(column, column.get_column_index(), RA_opt::rows_, colSettings_);
+    } else {
+      matrix_.emplace_back(column, colSettings_);
+    }
+  }
+}
+
+template <class Master_matrix>
+inline constexpr typename Chain_matrix<Master_matrix>::Barcode& Chain_matrix<Master_matrix>::_barcode()
+{
+  if constexpr (Master_matrix::Option_list::has_vine_update)
+    return Swap_opt::template Chain_pairing<Master_matrix>::barcode_;
+  else
+    return Pair_opt::barcode_;
+}
+
+template <class Master_matrix>
+inline constexpr typename Chain_matrix<Master_matrix>::Bar_dictionary&
+Chain_matrix<Master_matrix>::_indexToBar()
+{
+  if constexpr (Master_matrix::Option_list::has_vine_update)
+    return Swap_opt::template Chain_pairing<Master_matrix>::indexToBar_;
+  else
+    return Pair_opt::indexToBar_;
+}
+
+template <class Master_matrix>
+inline constexpr typename Chain_matrix<Master_matrix>::Pos_index& Chain_matrix<Master_matrix>::_nextPosition()
+{
+  if constexpr (Master_matrix::Option_list::has_vine_update)
+    return Swap_opt::template Chain_pairing<Master_matrix>::nextPosition_;
+  else
+    return Pair_opt::nextPosition_;
+}
+
+}  // namespace persistence_matrix
+}  // namespace Gudhi
+
+#endif  // PM_CHAIN_MATRIX_H