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Full Discussion: Matrix parsing help !
Top Forums Programming Matrix parsing help ! Post 302587085 by mchimich on Wednesday 4th of January 2012 10:04:54 AM
Old 01-04-2012
OK sir !! thanks very much i will have a look and I will keep you informed

---------- Post updated at 04:04 PM ---------- Previous update was at 11:04 AM ----------

the TreeSoft software is adapted for coding sequences (Amino acid) and not nucleotides sequence (i'm working with non coding sequence). I begin to despair... Smilie
Anyway thanks a lot for your help
 

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Graph::TransitiveClosure::Matrix(3pm)			User Contributed Perl Documentation		     Graph::TransitiveClosure::Matrix(3pm)

NAME
Graph::TransitiveClosure::Matrix - create and query transitive closure of graph SYNOPSIS
use Graph::TransitiveClosure::Matrix; use Graph::Directed; # or Undirected my $g = Graph::Directed->new; $g->add_...(); # build $g # Compute the transitive closure matrix. my $tcm = Graph::TransitiveClosure::Matrix->new($g); # Being reflexive is the default, # meaning that null transitions are included. my $tcm = Graph::TransitiveClosure::Matrix->new($g, reflexive => 1); $tcm->is_reachable($u, $v) # is_reachable(u, v) is always reflexive. $tcm->is_reachable($u, $v) # The reflexivity of is_transitive(u, v) depends of the reflexivity # of the transitive closure. $tcg->is_transitive($u, $v) my $tcm = Graph::TransitiveClosure::Matrix->new($g, path_length => 1); my $n = $tcm->path_length($u, $v) my $tcm = Graph::TransitiveClosure::Matrix->new($g, path_vertices => 1); my @v = $tcm->path_vertices($u, $v) my $tcm = Graph::TransitiveClosure::Matrix->new($g, attribute_name => 'length'); my $n = $tcm->path_length($u, $v) my @v = $tcm->vertices DESCRIPTION
You can use "Graph::TransitiveClosure::Matrix" to compute the transitive closure matrix of a graph and optionally also the minimum paths (lengths and vertices) between vertices, and after that query the transitiveness between vertices by using the "is_reachable()" and "is_transitive()" methods, and the paths by using the "path_length()" and "path_vertices()" methods. If you modify the graph after computing its transitive closure, the transitive closure and minimum paths may become invalid. Methods Class Methods new($g) Construct the transitive closure matrix of the graph $g. new($g, options) Construct the transitive closure matrix of the graph $g with options as a hash. The known options are "attribute_name" => attribute_name By default the edge attribute used for distance is "w". You can change that by giving another attribute name with the "attribute_name" attribute to the new() constructor. reflexive => boolean By default the transitive closure matrix is not reflexive: that is, the adjacency matrix has zeroes on the diagonal. To have ones on the diagonal, use true for the "reflexive" option. NOTE: this behaviour has changed from Graph 0.2xxx: transitive closure graphs were by default reflexive. path_length => boolean By default the path lengths are not computed, only the boolean transitivity. By using true for "path_length" also the path lengths will be computed, they can be retrieved using the path_length() method. path_vertices => boolean By default the paths are not computed, only the boolean transitivity. By using true for "path_vertices" also the paths will be computed, they can be retrieved using the path_vertices() method. Object Methods is_reachable($u, $v) Return true if the vertex $v is reachable from the vertex $u, or false if not. path_length($u, $v) Return the minimum path length from the vertex $u to the vertex $v, or undef if there is no such path. path_vertices($u, $v) Return the minimum path (as a list of vertices) from the vertex $u to the vertex $v, or an empty list if there is no such path, OR also return an empty list if $u equals $v. has_vertices($u, $v, ...) Return true if the transitive closure matrix has all the listed vertices, false if not. is_transitive($u, $v) Return true if the vertex $v is transitively reachable from the vertex $u, false if not. vertices Return the list of vertices in the transitive closure matrix. path_predecessor Return the predecessor of vertex $v in the transitive closure path going back to vertex $u. RETURN VALUES
For path_length() the return value will be the sum of the appropriate attributes on the edges of the path, "weight" by default. If no attribute has been set, one(1) will be assumed. If you try to ask about vertices not in the graph, undefs and empty lists will be returned. ALGORITHM
The transitive closure algorithm used is Warshall and Floyd-Warshall for the minimum paths, which is O(V**3) in time, and the returned matrices are O(V**2) in space. SEE ALSO
Graph::AdjacencyMatrix AUTHOR AND COPYRIGHT
Jarkko Hietaniemi jhi@iki.fi LICENSE
This module is licensed under the same terms as Perl itself. perl v5.10.0 2009-01-17 Graph::TransitiveClosure::Matrix(3pm)
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