#' Vertex connectivity
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `vertex.disjoint.paths()` was renamed to `vertex_disjoint_paths()` to create a more
#' consistent API.
#' @inheritParams vertex_disjoint_paths
#' @keywords internal
#' @export
vertex.disjoint.paths <- function(graph, source = NULL, target = NULL) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "vertex.disjoint.paths()", "vertex_disjoint_paths()")
  vertex_disjoint_paths(graph = graph, source = source, target = target)
} # nocov end

#' Vertex connectivity
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `vertex.connectivity()` was renamed to `vertex_connectivity()` to create a more
#' consistent API.
#' @inheritParams vertex_connectivity
#' @keywords internal
#' @export
vertex.connectivity <- function(graph, source = NULL, target = NULL, checks = TRUE) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "vertex.connectivity()", "vertex_connectivity()")
  vertex_connectivity(graph = graph, source = source, target = target, checks = checks)
} # nocov end

#' List all minimum \((s,t)\)-cuts of a graph
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `stMincuts()` was renamed to `st_min_cuts()` to create a more
#' consistent API.
#' @inheritParams st_min_cuts
#' @keywords internal
#' @export
stMincuts <- function(graph, source, target, capacity = NULL) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "stMincuts()", "st_min_cuts()")
  st_min_cuts(graph = graph, source = source, target = target, capacity = capacity)
} # nocov end

#' List all (s,t)-cuts of a graph
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `stCuts()` was renamed to `st_cuts()` to create a more
#' consistent API.
#' @inheritParams st_cuts
#' @keywords internal
#' @export
stCuts <- function(graph, source, target) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "stCuts()", "st_cuts()")
  st_cuts(graph = graph, source = source, target = target)
} # nocov end

#' Minimum size vertex separators
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `minimum.size.separators()` was renamed to `min_separators()` to create a more
#' consistent API.
#' @inheritParams min_separators
#' @keywords internal
#' @export
minimum.size.separators <- function(graph) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "minimum.size.separators()", "min_separators()")
  min_separators(graph = graph)
} # nocov end

#' Minimum size vertex separators
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `minimal.st.separators()` was renamed to `min_st_separators()` to create a more
#' consistent API.
#' @inheritParams min_st_separators
#' @keywords internal
#' @export
minimal.st.separators <- function(graph) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "minimal.st.separators()", "min_st_separators()")
  min_st_separators(graph = graph)
} # nocov end

#' Vertex separators
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `is.separator()` was renamed to `is_separator()` to create a more
#' consistent API.
#' @inheritParams is_separator
#' @keywords internal
#' @export
is.separator <- function(graph, candidate) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "is.separator()", "is_separator()")
  is_separator(graph = graph, candidate = candidate)
} # nocov end

#' Minimal vertex separators
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `is.minimal.separator()` was renamed to `is_min_separator()` to create a more
#' consistent API.
#' @inheritParams is_min_separator
#' @keywords internal
#' @export
is.minimal.separator <- function(graph, candidate) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "is.minimal.separator()", "is_min_separator()")
  is_min_separator(graph = graph, candidate = candidate)
} # nocov end

#' Minimum cut in a graph
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `graph.mincut()` was renamed to `min_cut()` to create a more
#' consistent API.
#' @inheritParams min_cut
#' @keywords internal
#' @export
graph.mincut <- function(graph, source = NULL, target = NULL, capacity = NULL, value.only = TRUE) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "graph.mincut()", "min_cut()")
  min_cut(graph = graph, source = source, target = target, capacity = capacity, value.only = value.only)
} # nocov end

#' Maximum flow in a graph
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `graph.maxflow()` was renamed to `max_flow()` to create a more
#' consistent API.
#' @inheritParams max_flow
#' @keywords internal
#' @export
graph.maxflow <- function(graph, source, target, capacity = NULL) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "graph.maxflow()", "max_flow()")
  max_flow(graph = graph, source = source, target = target, capacity = capacity)
} # nocov end

#' Edge connectivity
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `graph.adhesion()` was renamed to `adhesion()` to create a more
#' consistent API.
#' @inheritParams adhesion
#' @keywords internal
#' @export
graph.adhesion <- function(graph, checks = TRUE) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "graph.adhesion()", "adhesion()")
  adhesion(graph = graph, checks = checks)
} # nocov end

#' Edge connectivity
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `edge.disjoint.paths()` was renamed to `edge_connectivity()` to create a more
#' consistent API.
#' @inheritParams edge_connectivity
#' @keywords internal
#' @export
edge.disjoint.paths <- function(graph, source = NULL, target = NULL, checks = TRUE) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "edge.disjoint.paths()", "edge_connectivity()")
  edge_connectivity(graph = graph, source = source, target = target, checks = checks)
} # nocov end

#' Edge connectivity
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `edge.connectivity()` was renamed to `edge_connectivity()` to create a more
#' consistent API.
#' @inheritParams edge_connectivity
#' @keywords internal
#' @export
edge.connectivity <- function(graph, source = NULL, target = NULL, checks = TRUE) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "edge.connectivity()", "edge_connectivity()")
  edge_connectivity(graph = graph, source = source, target = target, checks = checks)
} # nocov end

#' Dominator tree
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `dominator.tree()` was renamed to `dominator_tree()` to create a more
#' consistent API.
#' @inheritParams dominator_tree
#' @keywords internal
#' @export
dominator.tree <- function(graph, root, mode = c("out", "in", "all", "total")) { # nocov start
  lifecycle::deprecate_soft("2.0.0", "dominator.tree()", "dominator_tree()")
  dominator_tree(graph = graph, root = root, mode = mode)
} # nocov end
#   IGraph R package
#   Copyright (C) 2006-2012  Gabor Csardi <csardi.gabor@gmail.com>
#   334 Harvard street, Cambridge, MA 02139 USA
#
#   This program is free software; you can redistribute it and/or modify
#   it under the terms of the GNU General Public License as published by
#   the Free Software Foundation; either version 2 of the License, or
#   (at your option) any later version.
#
#   This program is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU General Public License for more details.
#
#   You should have received a copy of the GNU General Public License
#   along with this program; if not, write to the Free Software
#   Foundation, Inc.,  51 Franklin Street, Fifth Floor, Boston, MA
#   02110-1301 USA
#
###################################################################

#' Minimum cut in a graph
#'
#' `min_cut()` calculates the minimum st-cut between two vertices in a graph
#' (if the `source` and `target` arguments are given) or the minimum
#' cut of the graph (if both `source` and `target` are `NULL`).
#'
#' The minimum st-cut between `source` and `target` is the minimum
#' total weight of edges needed to remove to eliminate all paths from
#' `source` to `target`.
#'
#' The minimum cut of a graph is the minimum total weight of the edges needed
#' to remove to separate the graph into (at least) two components. (Which is to
#' make the graph *not* strongly connected in the directed case.)
#'
#' The maximum flow between two vertices in a graph is the same as the minimum
#' st-cut, so `max_flow()` and `min_cut()` essentially calculate the same
#' quantity, the only difference is that `min_cut()` can be invoked without
#' giving the `source` and `target` arguments and then minimum of all
#' possible minimum cuts is calculated.
#'
#' For undirected graphs the Stoer-Wagner algorithm (see reference below) is
#' used to calculate the minimum cut.
#'
#' @param graph The input graph.
#' @param source The id of the source vertex.
#' @param target The id of the target vertex (sometimes also called sink).
#' @param capacity Vector giving the capacity of the edges. If this is
#'   `NULL` (the default) then the `capacity` edge attribute is used.
#' @param value.only Logical scalar, if `TRUE` only the minimum cut value
#'   is returned, if `FALSE` the edges in the cut and a the two (or more)
#'   partitions are also returned.
#' @return For `min_cut()` a nuieric constant, the value of the minimum
#'   cut, except if `value.only = FALSE`. In this case a named list with
#'   components:
#'   \item{value}{Numeric scalar, the cut value.}
#'   \item{cut}{Numeric vector, the edges in the cut.}
#'   \item{partition1}{The vertices in the first partition after the cut
#'     edges are removed. Note that these vertices might be actually in
#'     different components (after the cut edges are removed), as the graph
#'     may fall apart into more than two components.}
#'   \item{partition2}{The vertices in the second partition
#'     after the cut edges are removed. Note that these vertices might be
#'     actually in different components (after the cut edges are removed), as
#'     the graph may fall apart into more than two components.}
#' @references M. Stoer and F. Wagner: A simple min-cut algorithm,
#' *Journal of the ACM*, 44 585-591, 1997.
#' @examples
#' g <- make_ring(100)
#' min_cut(g, capacity = rep(1, vcount(g)))
#' min_cut(g, value.only = FALSE, capacity = rep(1, vcount(g)))
#'
#' g2 <- make_graph(c(1, 2, 2, 3, 3, 4, 1, 6, 6, 5, 5, 4, 4, 1))
#' E(g2)$capacity <- c(3, 1, 2, 10, 1, 3, 2)
#' min_cut(g2, value.only = FALSE)
#' @family flow
#' @export
min_cut <- function(graph, source = NULL, target = NULL, capacity = NULL, value.only = TRUE) {
  ensure_igraph(graph)
  if (is.null(capacity)) {
    if ("capacity" %in% edge_attr_names(graph)) {
      capacity <- E(graph)$capacity
    }
  }
  if (length(source) == 0) {
    source <- NULL
  }
  if (length(target) == 0) {
    target <- NULL
  }
  if (is.null(source) && !is.null(target) ||
    is.null(target) && !is.null(source)) {
    stop("Please give both source and target or neither")
  }
  if (!is.null(capacity)) {
    capacity <- as.numeric(capacity)
  }

  value.only <- as.logical(value.only)
  on.exit(.Call(R_igraph_finalizer))
  if (is.null(target) && is.null(source)) {
    if (value.only) {
      res <- .Call(R_igraph_mincut_value, graph, capacity)
    } else {
      res <- .Call(R_igraph_mincut, graph, capacity)
      res$cut <- res$cut + 1
      res$partition1 <- res$partition1 + 1
      res$partition2 <- res$partition2 + 1

      if (igraph_opt("return.vs.es")) {
        res$cut <- create_es(graph, res$cut)
        res$partition1 <- create_vs(graph, res$partition1)
        res$partition2 <- create_vs(graph, res$partition2)
      }
    }
  } else {
    if (value.only) {
      res <- .Call(
        R_igraph_st_mincut_value, graph,
        as_igraph_vs(graph, source) - 1,
        as_igraph_vs(graph, target) - 1, capacity
      )
    } else {
      res <- .Call(
        R_igraph_st_mincut, graph,
        as_igraph_vs(graph, source) - 1,
        as_igraph_vs(graph, target) - 1, capacity
      )
      # No need to add +1 here; R_igraph_st_mincut() is autogenerated and
      # adds +1 already
      if (igraph_opt("return.vs.es")) {
        res$cut <- create_es(graph, res$cut)
        res$partition1 <- create_vs(graph, res$partition1)
        res$partition2 <- create_vs(graph, res$partition2)
      }
    }
  }

  res
}



#' Vertex connectivity
#'
#' The vertex connectivity of a graph or two vertices, this is recently also
#' called group cohesion.
#'
#' The vertex connectivity of two vertices (`source` and `target`) in
#' a graph is the minimum number of vertices that must be deleted to
#' eliminate all (directed) paths from `source` to `target`.
#' `vertex_connectivity()` calculates this quantity if both the
#' `source` and `target` arguments are given and they're not
#' `NULL`.
#'
#' The vertex connectivity of a pair is the same as the number
#' of different (i.e. node-independent) paths from source to
#' target, assuming no direct edges between them.
#'
#' The vertex connectivity of a graph is the minimum vertex connectivity of all
#' (ordered) pairs of vertices in the graph. In other words this is the minimum
#' number of vertices needed to remove to make the graph not strongly
#' connected. (If the graph is not strongly connected then this is zero.)
#' `vertex_connectivity()` calculates this quantity if neither the
#' `source` nor `target` arguments are given. (I.e. they are both
#' `NULL`.)
#'
#' A set of vertex disjoint directed paths from `source` to `vertex`
#' is a set of directed paths between them whose vertices do not contain common
#' vertices (apart from `source` and `target`). The maximum number of
#' vertex disjoint paths between two vertices is the same as their vertex
#' connectivity in most cases (if the two vertices are not connected by an
#' edge).
#'
#' The cohesion of a graph (as defined by White and Harary, see references), is
#' the vertex connectivity of the graph. This is calculated by
#' `cohesion()`.
#'
#' These three functions essentially calculate the same measure(s), more
#' precisely `vertex_connectivity()` is the most general, the other two are
#' included only for the ease of using more descriptive function names.
#'
#' @aliases cohesion
#' @param graph,x The input graph.
#' @param source The id of the source vertex, for `vertex_connectivity()` it
#'   can be `NULL`, see details below.
#' @param target The id of the target vertex, for `vertex_connectivity()` it
#'   can be `NULL`, see details below.
#' @param checks Logical constant. Whether to check that the graph is connected
#'   and also the degree of the vertices. If the graph is not (strongly)
#'   connected then the connectivity is obviously zero. Otherwise if the minimum
#'   degree is one then the vertex connectivity is also one. It is a good idea to
#'   perform these checks, as they can be done quickly compared to the
#'   connectivity calculation itself.  They were suggested by Peter McMahan,
#'   thanks Peter.
#' @param ... Ignored.
#' @return A scalar real value.
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
#' @references White, Douglas R and Frank Harary 2001. The Cohesiveness of
#' Blocks In Social Networks: Node Connectivity and Conditional Density.
#' *Sociological Methodology* 31 (1) : 305-359.
#' @family flow
#' @export
#' @keywords graphs
#' @examples
#'
#' g <- sample_pa(100, m = 1)
#' g <- delete_edges(g, E(g)[100 %--% 1])
#' g2 <- sample_pa(100, m = 5)
#' g2 <- delete_edges(g2, E(g2)[100 %--% 1])
#' vertex_connectivity(g, 100, 1)
#' vertex_connectivity(g2, 100, 1)
#' vertex_disjoint_paths(g2, 100, 1)
#'
#' g <- sample_gnp(50, 5 / 50)
#' g <- as_directed(g)
#' g <- induced_subgraph(g, subcomponent(g, 1))
#' cohesion(g)
#'
vertex_connectivity <- function(graph, source = NULL, target = NULL, checks = TRUE) {
  ensure_igraph(graph)

  if (length(source) == 0) {
    source <- NULL
  }
  if (length(target) == 0) {
    target <- NULL
  }

  if (is.null(source) && is.null(target)) {
    on.exit(.Call(R_igraph_finalizer))
    .Call(R_igraph_vertex_connectivity, graph, as.logical(checks))
  } else if (!is.null(source) && !is.null(target)) {
    on.exit(.Call(R_igraph_finalizer))
    .Call(
      R_igraph_st_vertex_connectivity, graph, as_igraph_vs(graph, source) - 1,
      as_igraph_vs(graph, target) - 1
    )
  } else {
    stop("either give both source and target or neither")
  }
}



#' Edge connectivity
#'
#' The edge connectivity of a graph or two vertices, this is recently also
#' called group adhesion.
#'
#' @section `edge_connectivity()` Edge connectivity:
#' The edge connectivity of a pair of vertices (`source` and
#' `target`) is the minimum number of edges needed to remove to eliminate
#' all (directed) paths from `source` to `target`.
#' `edge_connectivity()` calculates this quantity if both the `source`
#' and `target` arguments are given (and not `NULL`).
#'
#' The edge connectivity of a graph is the minimum of the edge connectivity of
#' every (ordered) pair of vertices in the graph.  `edge_connectivity()`
#' calculates this quantity if neither the `source` nor the `target`
#' arguments are given (i.e. they are both `NULL`).
#'
#' @section `edge_disjoint_paths()` The maximum number of edge-disjoint paths between two vertices:
#' A set of paths between two vertices is called edge-disjoint if they do not
#' share any edges. The maximum number of edge-disjoint paths are calculated
#' by this function using maximum flow techniques. Directed paths are
#' considered in directed graphs.
#'
#'
#' A set of edge disjoint paths between two vertices is a set of paths between
#' them containing no common edges. The maximum number of edge disjoint paths
#' between two vertices is the same as their edge connectivity.
#'
#' When there are no direct edges between the source and the target, the number
#' of vertex-disjoint paths is the same as the vertex connectivity of
#' the two vertices. When some edges are present, each one of them
#' contributes one extra path.
#'
#' @section `adhesion()` Adhesion of a graph:
#' The adhesion of a graph is the minimum number of edges needed to remove to
#' obtain a graph which is not strongly connected. This is the same as the edge
#' connectivity of the graph.
#'
#' @section All three functions:
#' The three functions documented on this page calculate similar properties,
#' more precisely the most general is `edge_connectivity()`, the others are
#' included only for having more descriptive function names.
#'
#'

#' @param graph The input graph.
#' @param source The id of the source vertex, for `edge_connectivity()` it
#'   can be `NULL`, see details below.
#' @param target The id of the target vertex, for `edge_connectivity()` it
#'   can be `NULL`, see details below.
#' @param checks Logical constant. Whether to check that the graph is connected
#'   and also the degree of the vertices. If the graph is not (strongly)
#'   connected then the connectivity is obviously zero. Otherwise if the minimum
#'   degree is one then the edge connectivity is also one. It is a good idea to
#'   perform these checks, as they can be done quickly compared to the
#'   connectivity calculation itself.  They were suggested by Peter McMahan,
#'   thanks Peter.
#' @return A scalar real value.
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
#' @references Douglas R. White and Frank Harary (2001): The cohesiveness of blocks in
#' social networks: node connectivity and conditional density,
#' Sociological Methodology, vol. 31, 2001, pp. 305–59.
#' @family flow
#' @export
#' @keywords graphs
#' @examples
#'
#' g <- sample_pa(100, m = 1)
#' g2 <- sample_pa(100, m = 5)
#' edge_connectivity(g, 100, 1)
#' edge_connectivity(g2, 100, 1)
#' edge_disjoint_paths(g2, 100, 1)
#'
#' g <- sample_gnp(50, 5 / 50)
#' g <- as_directed(g)
#' g <- induced_subgraph(g, subcomponent(g, 1))
#' adhesion(g)
#'
edge_connectivity <- function(graph, source = NULL, target = NULL, checks = TRUE) {
  ensure_igraph(graph)

  if (length(source) == 0) {
    source <- NULL
  }
  if (length(target) == 0) {
    target <- NULL
  }

  if (is.null(source) && is.null(target)) {
    on.exit(.Call(R_igraph_finalizer))
    .Call(R_igraph_edge_connectivity, graph, as.logical(checks))
  } else if (!is.null(source) && !is.null(target)) {
    on.exit(.Call(R_igraph_finalizer))
    .Call(
      R_igraph_st_edge_connectivity, graph,
      as_igraph_vs(graph, source) - 1, as_igraph_vs(graph, target) - 1
    )
  } else {
    stop("either give both source and target or neither")
  }
}

#' @rdname edge_connectivity
#' @export
edge_disjoint_paths <- function(graph, source, target) {
  ensure_igraph(graph)

  if (length(source) == 0) {
    source <- NULL
  }
  if (length(target) == 0) {
    target <- NULL
  }

  on.exit(.Call(R_igraph_finalizer))
  .Call(
    R_igraph_edge_disjoint_paths, graph,
    as_igraph_vs(graph, source) - 1, as_igraph_vs(graph, target) - 1
  )
}

#' @rdname vertex_connectivity
#' @export
vertex_disjoint_paths <- function(graph, source = NULL, target = NULL) {
  ensure_igraph(graph)

  if (length(source) == 0) {
    source <- NULL
  }
  if (length(target) == 0) {
    target <- NULL
  }

  on.exit(.Call(R_igraph_finalizer))
  .Call(
    R_igraph_vertex_disjoint_paths, graph, as_igraph_vs(graph, source) - 1,
    as_igraph_vs(graph, target) - 1
  )
}

#' @rdname edge_connectivity
#' @export
adhesion <- function(graph, checks = TRUE) {
  ensure_igraph(graph)

  on.exit(.Call(R_igraph_finalizer))
  .Call(R_igraph_adhesion, graph, as.logical(checks))
}

#' @rdname vertex_connectivity
#' @method cohesion igraph
#' @export
cohesion.igraph <- function(x, checks = TRUE, ...) {
  ensure_igraph(x)

  on.exit(.Call(R_igraph_finalizer))
  .Call(R_igraph_cohesion, x, as.logical(checks))
}

#' List all (s,t)-cuts of a graph
#'
#' List all (s,t)-cuts in a directed graph.
#'
#' Given a \eqn{G} directed graph and two, different and non-ajacent vertices,
#' \eqn{s} and \eqn{t}, an \eqn{(s,t)}-cut is a set of edges, such that after
#' removing these edges from \eqn{G} there is no directed path from \eqn{s} to
#' \eqn{t}.
#'
#' @param graph The input graph. It must be directed.
#' @param source The source vertex.
#' @param target The target vertex.
#' @return A list with entries: \item{cuts}{A list of numeric vectors
#'   containing edge ids. Each vector is an \eqn{(s,t)}-cut.}
#'   \item{partition1s}{A list of numeric vectors containing vertex ids, they
#'   correspond to the edge cuts. Each vertex set is a generator of the
#'   corresponding cut, i.e. in the graph \eqn{G=(V,E)}, the vertex set \eqn{X}
#'   and its complementer \eqn{V-X}, generates the cut that contains exactly the
#'   edges that go from \eqn{X} to \eqn{V-X}.}
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
#' @references JS Provan and DR Shier: A Paradigm for listing (s,t)-cuts in
#' graphs, *Algorithmica* 15, 351--372, 1996.
#' @keywords graphs
#' @examples
#'
#' # A very simple graph
#' g <- graph_from_literal(a -+ b -+ c -+ d -+ e)
#' st_cuts(g, source = "a", target = "e")
#'
#' # A somewhat more difficult graph
#' g2 <- graph_from_literal(
#'   s --+ a:b, a:b --+ t,
#'   a --+ 1:2:3, 1:2:3 --+ b
#' )
#' st_cuts(g2, source = "s", target = "t")
#' @family flow
#' @export
#' @cdocs igraph_all_st_cuts
st_cuts <- all_st_cuts_impl


#' List all minimum \eqn{(s,t)}-cuts of a graph
#'
#' Listing all minimum \eqn{(s,t)}-cuts of a directed graph, for given \eqn{s}
#' and \eqn{t}.
#'
#' Given a \eqn{G} directed graph and two, different and non-ajacent vertices,
#' \eqn{s} and \eqn{t}, an \eqn{(s,t)}-cut is a set of edges, such that after
#' removing these edges from \eqn{G} there is no directed path from \eqn{s} to
#' \eqn{t}.
#'
#' The size of an \eqn{(s,t)}-cut is defined as the sum of the capacities (or
#' weights) in the cut. For unweighted (=equally weighted) graphs, this is
#' simply the number of edges.
#'
#' An \eqn{(s,t)}-cut is minimum if it is of the smallest possible size.
#'
#' @param graph The input graph. It must be directed.
#' @param source The id of the source vertex.
#' @param target The id of the target vertex.
#' @param capacity Numeric vector giving the edge capacities. If this is
#'   `NULL` and the graph has a `weight` edge attribute, then this
#'   attribute defines the edge capacities. For forcing unit edge capacities,
#'   even for graphs that have a `weight` edge attribute, supply `NA`
#'   here.
#' @return A list with entries: \item{value}{Numeric scalar, the size of the
#'   minimum cut(s).} \item{cuts}{A list of numeric vectors containing edge ids.
#'   Each vector is a minimum \eqn{(s,t)}-cut.} \item{partition1s}{A list of
#'   numeric vectors containing vertex ids, they correspond to the edge cuts.
#'   Each vertex set is a generator of the corresponding cut, i.e. in the graph
#'   \eqn{G=(V,E)}, the vertex set \eqn{X} and its complementer \eqn{V-X},
#'   generates the cut that contains exactly the edges that go from \eqn{X} to
#'   \eqn{V-X}.}
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
#' @references JS Provan and DR Shier: A Paradigm for listing (s,t)-cuts in
#' graphs, *Algorithmica* 15, 351--372, 1996.
#' @keywords graphs
#' @examples
#'
#' # A difficult graph, from the Provan-Shier paper
#' g <- graph_from_literal(
#'   s --+ a:b, a:b --+ t,
#'   a --+ 1:2:3:4:5, 1:2:3:4:5 --+ b
#' )
#' st_min_cuts(g, source = "s", target = "t")
#' @family flow
#' @export
#' @cdocs igraph_all_st_mincuts
st_min_cuts <- all_st_mincuts_impl


#' Dominator tree
#'
#' Dominator tree of a directed graph.
#'
#' A flowgraph is a directed graph with a distinguished start (or root) vertex
#' \eqn{r}, such that for any vertex \eqn{v}, there is a path from \eqn{r} to
#' \eqn{v}. A vertex \eqn{v} dominates another vertex \eqn{w} (not equal to
#' \eqn{v}), if every path from \eqn{r} to \eqn{w} contains \eqn{v}. Vertex
#' \eqn{v} is the immediate dominator or \eqn{w},
#' \eqn{v=\textrm{idom}(w)}{v=idom(w)}, if \eqn{v} dominates \eqn{w} and every
#' other dominator of \eqn{w} dominates \eqn{v}. The edges
#' \eqn{{(\textrm{idom}(w), w)| w \ne r}}{{(idom(w),w)| w is not r}} form a
#' directed tree, rooted at \eqn{r}, called the dominator tree of the graph.
#' Vertex \eqn{v} dominates vertex \eqn{w} if and only if \eqn{v} is an
#' ancestor of \eqn{w} in the dominator tree.
#'
#' This function implements the Lengauer-Tarjan algorithm to construct the
#' dominator tree of a directed graph. For details see the reference below.
#'
#' @param graph A directed graph. If it is not a flowgraph, and it contains
#'   some vertices not reachable from the root vertex, then these vertices will
#'   be collected and returned as part of the result.
#' @param root The id of the root (or source) vertex, this will be the root of
#'   the tree.
#' @param mode Constant, must be \sQuote{`in`} or \sQuote{`out`}. If
#'   it is \sQuote{`in`}, then all directions are considered as opposite to
#'   the original one in the input graph.
#' @return A list with components: \item{dom}{ A numeric vector giving the
#'   immediate dominators for each vertex. For vertices that are unreachable from
#'   the root, it contains `NaN`. For the root vertex itself it contains
#'   minus one.  } \item{domtree}{ A graph object, the dominator tree. Its vertex
#'   ids are the as the vertex ids of the input graph. Isolate vertices are the
#'   ones that are unreachable from the root.  } \item{leftout}{ A numeric vector
#'   containing the vertex ids that are unreachable from the root.  }
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
#' @references Thomas Lengauer, Robert Endre Tarjan: A fast algorithm for
#' finding dominators in a flowgraph, *ACM Transactions on Programming
#' Languages and Systems (TOPLAS)* I/1, 121--141, 1979.
#' @keywords graphs
#' @examples
#'
#' ## The example from the paper
#' g <- graph_from_literal(
#'   R -+ A:B:C, A -+ D, B -+ A:D:E, C -+ F:G, D -+ L,
#'   E -+ H, F -+ I, G -+ I:J, H -+ E:K, I -+ K, J -+ I,
#'   K -+ I:R, L -+ H
#' )
#' dtree <- dominator_tree(g, root = "R")
#' layout <- layout_as_tree(dtree$domtree, root = "R")
#' layout[, 2] <- -layout[, 2]
#' plot(dtree$domtree, layout = layout, vertex.label = V(dtree$domtree)$name)
#' @family flow
#' @export
dominator_tree <- function(graph, root, mode = c("out", "in", "all", "total")) {
  # Argument checks
 ensure_igraph(graph)
  root <- as_igraph_vs(graph, root)
  if (length(root) == 0) {
    stop("No vertex was specified")
  }
  mode <- switch(igraph.match.arg(mode),
    "out" = 1,
    "in" = 2,
    "all" = 3,
    "total" = 3
  )

  on.exit(.Call(R_igraph_finalizer))
  # Function call
  res <- .Call(R_igraph_dominator_tree, graph, root - 1, mode)
  if (igraph_opt("return.vs.es")) {
    res$leftout <- create_vs(graph, res$leftout)
  }

  # Replace 0 with -1 in `res$dom' to conform with documentation
  res$dom[res$dom == 0] <- -1

  res
}


#' Minimum size vertex separators
#'
#' List all vertex sets that are minimal \eqn{(s,t)} separators for some
#' \eqn{s} and \eqn{t}, in an undirected graph.
#'
#' A \eqn{(s,t)} vertex separator is a set of vertices, such that after their
#' removal from the graph, there is no path between \eqn{s} and \eqn{t} in the
#' graph.
#'
#' A \eqn{(s,t)} vertex separator is minimal if none of its proper subsets is
#' an \eqn{(s,t)} vertex separator for the same \eqn{s} and \eqn{t}.
#'
#' @param graph The input graph. It may be directed, but edge directions are
#'   ignored.
#' @return A list of numeric vectors. Each vector contains a vertex set
#'   (defined by vertex ids), each vector is an (s,t) separator of the input
#'   graph, for some \eqn{s} and \eqn{t}.
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
#' @references Anne Berry, Jean-Paul Bordat and Olivier Cogis: Generating All
#' the Minimal Separators of a Graph, In: Peter Widmayer, Gabriele Neyer and
#' Stephan Eidenbenz (editors): *Graph-theoretic concepts in computer
#' science*, 1665, 167--172, 1999. Springer.
#' @keywords graphs
#' @export
#' @examples
#'
#' ring <- make_ring(4)
#' min_st_separators(ring)
#'
#' chvatal <- make_graph("chvatal")
#' min_st_separators(chvatal)
#' # https://github.com/r-lib/roxygen2/issues/1092
#' @section Note:
#' Note that the code below returns `{1, 3}` despite its subset `{1}` being a
#' separator as well. This is because `{1, 3}` is minimal with respect to
#' separating vertices 2 and 4.
#'
#' ```{r, eval=FALSE}
#' g <- make_graph(~ 0-1-2-3-4-1)
#' min_st_separators(g)
#' ```
#'
#' ```{r, echo=FALSE}
#' local_igraph_options(print.id = FALSE)
#' g <- make_graph(~ 0-1-2-3-4-1)
#' min_st_separators(g)
#' ```
#' @family flow
#' @cdocs igraph_all_minimal_st_separators
min_st_separators <- all_minimal_st_separators_impl


#' Maximum flow in a graph
#'
#' In a graph where each edge has a given flow capacity the maximal flow
#' between two vertices is calculated.
#'
#' `max_flow()` calculates the maximum flow between two vertices in a
#' weighted (i.e. valued) graph. A flow from `source` to `target` is
#' an assignment of non-negative real numbers to the edges of the graph,
#' satisfying two properties: (1) for each edge the flow (i.e. the assigned
#' number) is not more than the capacity of the edge (the `capacity`
#' parameter or edge attribute), (2) for every vertex, except the source and
#' the target the incoming flow is the same as the outgoing flow. The value of
#' the flow is the incoming flow of the `target` vertex. The maximum flow
#' is the flow of maximum value.
#'
#' @param graph The input graph.
#' @param source The id of the source vertex.
#' @param target The id of the target vertex (sometimes also called sink).
#' @param capacity Vector giving the capacity of the edges. If this is
#'   `NULL` (the default) then the `capacity` edge attribute is used.
#'   Note that the `weight` edge attribute is not used by this function.
#' @return A named list with components:
#'   \item{value}{A numeric scalar, the value of the maximum flow.}
#'   \item{flow}{A numeric vector, the flow itself, one entry for each
#'     edge. For undirected graphs this entry is bit trickier, since for
#'     these the flow direction is not predetermined by the edge
#'     direction. For these graphs the elements of the this vector can be
#'     negative, this means that the flow goes from the bigger vertex id to
#'     the smaller one. Positive values mean that the flow goes from
#'     the smaller vertex id to the bigger one.}
#'   \item{cut}{A numeric vector of edge ids, the minimum cut corresponding
#'     to the maximum flow.}
#'   \item{partition1}{A numeric vector of vertex ids, the vertices in the
#'     first partition of the minimum cut corresponding to the maximum
#'     flow.}
#'   \item{partition2}{A numeric vector of vertex ids, the vertices in the
#'     second partition of the minimum cut corresponding to the maximum
#'     flow.}
#'   \item{stats}{A list with some statistics from the push-relabel
#'     algorithm. Five integer values currently: `nopush` is the
#'     number of push operations, `norelabel` the number of
#'     relabelings, `nogap` is the number of times the gap heuristics
#'     was used, `nogapnodes` is the total number of gap nodes omitted
#'     because of the gap heuristics and `nobfs` is the number of
#'     times a global breadth-first-search update was performed to assign
#'     better height (=distance) values to the vertices.}
#' @references A. V. Goldberg and R. E. Tarjan: A New Approach to the Maximum
#' Flow Problem *Journal of the ACM* 35:921-940, 1988.
#' @examples
#'
#' E <- rbind(c(1, 3, 3), c(3, 4, 1), c(4, 2, 2), c(1, 5, 1), c(5, 6, 2), c(6, 2, 10))
#' colnames(E) <- c("from", "to", "capacity")
#' g1 <- graph_from_data_frame(as.data.frame(E))
#' max_flow(g1, source = V(g1)["1"], target = V(g1)["2"])
#' @family flow
#' @export
#' @cdocs igraph_maxflow
max_flow <- maxflow_impl


#' Check whether removing this set of vertices would disconnect the graph.
#'
#' `is_separator()` determines whether the supplied vertex set is a vertex
#' separator:
#' A vertex set \eqn{S} is a separator if there are vertices \eqn{u} and \eqn{v}
#' in the graph such that all paths between \eqn{u} and \eqn{v} pass
#' through some vertices in \eqn{S}.
#'
#' @param graph The input graph. It may be directed, but edge directions are
#'   ignored.
#' @param candidate A numeric vector giving the vertex ids of the candidate
#'   separator.
#' @return A logical scalar, whether the supplied vertex set is a (minimal)
#'   vertex separator or not.
#'   lists all vertex separator of minimum size.
#' @family flow
#' @examples
#' ring <- make_ring(4)
#' min_st_separators(ring)
#' is_separator(ring, 1)
#' is_separator(ring, c(1, 3))
#' is_separator(ring, c(2, 4))
#' is_separator(ring, c(2, 3))
#'
#' @export
#' @cdocs igraph_is_separator
is_separator <- is_separator_impl


#' Minimal vertex separators
#'
#' Check whether a given set of vertices is a minimal vertex separator.
#'
#' `is_min_separator()` decides whether the supplied vertex set is a minimal
#' vertex separator. A minimal vertex separator is a vertex separator, such
#' that none of its proper subsets are a vertex separator.
#'
#' @param graph The input graph. It may be directed, but edge directions are
#'   ignored.
#' @param candidate A numeric vector giving the vertex ids of the candidate
#'   separator.
#' @return A logical scalar, whether the supplied vertex set is a (minimal)
#'   vertex separator or not.
#' @examples
#' # The graph from the Moody-White paper
#' mw <- graph_from_literal(
#'   1 - 2:3:4:5:6, 2 - 3:4:5:7, 3 - 4:6:7, 4 - 5:6:7,
#'   5 - 6:7:21, 6 - 7, 7 - 8:11:14:19, 8 - 9:11:14, 9 - 10,
#'   10 - 12:13, 11 - 12:14, 12 - 16, 13 - 16, 14 - 15, 15 - 16,
#'   17 - 18:19:20, 18 - 20:21, 19 - 20:22:23, 20 - 21,
#'   21 - 22:23, 22 - 23
#' )
#'
#' # Cohesive subgraphs
#' mw1 <- induced_subgraph(mw, as.character(c(1:7, 17:23)))
#' mw2 <- induced_subgraph(mw, as.character(7:16))
#' mw3 <- induced_subgraph(mw, as.character(17:23))
#' mw4 <- induced_subgraph(mw, as.character(c(7, 8, 11, 14)))
#' mw5 <- induced_subgraph(mw, as.character(1:7))
#'
#' check.sep <- function(G) {
#'   sep <- min_separators(G)
#'   sapply(sep, is_min_separator, graph = G)
#' }
#'
#' check.sep(mw)
#' check.sep(mw1)
#' check.sep(mw2)
#' check.sep(mw3)
#' check.sep(mw4)
#' check.sep(mw5)
#'
#' @family flow
#' @export
#' @cdocs igraph_is_minimal_separator
is_min_separator <- is_minimal_separator_impl


#' Minimum size vertex separators
#'
#' Find all vertex sets of minimal size whose removal separates the graph into
#' more components
#'
#' This function implements the Kanevsky algorithm for finding all minimal-size
#' vertex separators in an undirected graph. See the reference below for the
#' details.
#'
#' In the special case of a fully connected input graph with \eqn{n} vertices,
#' all subsets of size \eqn{n-1} are listed as the result.
#'
#' @param graph The input graph. It may be directed, but edge directions are
#'   ignored.
#' @return A list of numeric vectors. Each numeric vector is a vertex
#'   separator.
#' @references Arkady Kanevsky: Finding all minimum-size separating vertex sets
#' in a graph. *Networks* 23 533--541, 1993.
#'
#' JS Provan and DR Shier: A Paradigm for listing (s,t)-cuts in graphs,
#' *Algorithmica* 15, 351--372, 1996.
#'
#' J. Moody and D. R. White. Structural cohesion and embeddedness: A
#' hierarchical concept of social groups. *American Sociological Review*,
#' 68 103--127, Feb 2003.
#' @family flow
#' @export
#' @examples
#' # The graph from the Moody-White paper
#' mw <- graph_from_literal(
#'   1 - 2:3:4:5:6, 2 - 3:4:5:7, 3 - 4:6:7, 4 - 5:6:7,
#'   5 - 6:7:21, 6 - 7, 7 - 8:11:14:19, 8 - 9:11:14, 9 - 10,
#'   10 - 12:13, 11 - 12:14, 12 - 16, 13 - 16, 14 - 15, 15 - 16,
#'   17 - 18:19:20, 18 - 20:21, 19 - 20:22:23, 20 - 21,
#'   21 - 22:23, 22 - 23
#' )
#'
#' # Cohesive subgraphs
#' mw1 <- induced_subgraph(mw, as.character(c(1:7, 17:23)))
#' mw2 <- induced_subgraph(mw, as.character(7:16))
#' mw3 <- induced_subgraph(mw, as.character(17:23))
#' mw4 <- induced_subgraph(mw, as.character(c(7, 8, 11, 14)))
#' mw5 <- induced_subgraph(mw, as.character(1:7))
#'
#' min_separators(mw)
#' min_separators(mw1)
#' min_separators(mw2)
#' min_separators(mw3)
#' min_separators(mw4)
#' min_separators(mw5)
#'
#' # Another example, the science camp network
#' camp <- graph_from_literal(
#'   Harry:Steve:Don:Bert - Harry:Steve:Don:Bert,
#'   Pam:Brazey:Carol:Pat - Pam:Brazey:Carol:Pat,
#'   Holly - Carol:Pat:Pam:Jennie:Bill,
#'   Bill - Pauline:Michael:Lee:Holly,
#'   Pauline - Bill:Jennie:Ann,
#'   Jennie - Holly:Michael:Lee:Ann:Pauline,
#'   Michael - Bill:Jennie:Ann:Lee:John,
#'   Ann - Michael:Jennie:Pauline,
#'   Lee - Michael:Bill:Jennie,
#'   Gery - Pat:Steve:Russ:John,
#'   Russ - Steve:Bert:Gery:John,
#'   John - Gery:Russ:Michael
#' )
#' min_separators(camp)
#' @cdocs igraph_minimum_size_separators
min_separators <- minimum_size_separators_impl