Tristan Colombo >
BioGraph >
BioGraph::FileAccess

Module Version: 1.0.1
BioGraph::FileAccess

use BioGraph::FileAccess;

Package for manipulate graphs represented as well as adjacent matrix or adjacent list. Library for read and write different types of graph.

This is the list of the differents functions implemented in this library.

**read_graph**-
Use this function to read graph from file

- SYNOPSIS %G=read_graph(file, representation, symetrisation)
- PARAMETERS
*file*-
the name of the graph file to read ; the recognized formats of graphs are

*dot*(extension '.dot') Graph format used by the**dot**program of the package graphviz from AT&T (http://www.graphviz.org)*graph*(extension '.gr') In this graph format, the first line is the number of edges and the other lines are the edges in the form : edge1 tabulate edge2*biolayout*(extension '.biolayout') Graph format used by the**biolayout**program (http://www.biolayout.org)*pajek*(extension '.net') Graph format used by the**pajek**program

Note that the format of the graph is detected by checking the name file, so ensure that your file has the correct extension.

*representation*-
the type of representation choosen : 1 = adjacent matrix, and 2 = adjacent list

*symetrisation*-
enable (or not) the symetrisation of the edges of the graph : 0 = disable, 1 = enable

- OUTPUT The hash table of the graph read
*adjacent matrix*-
$G{$s1}{$s2} exists if (and only if) the edge ($s1, $s2) exists

*adjacent list*-
$G{$s1} contains the list of all the vertices connected to $s1

**read_association**-
Associate a comment to vertices (ex: associate a function to a protein, ...)

- SYNOPSIS %C=read_association(file, representation, graph)
- PARAMETERS
*file*-
the name of the associations file (format : vertex tabulate comment)

*representation*-
the type of representation choosen : 1 = adjacent matrix, and 2 = adjacent list

*graph*-
the hash table of the graph

- OUTPUT The hash table of the associations : vertex <=> comment

**write_graph**-
Use this function to write graph to disk in the required format

- SYNOPSIS write_graph(representation, file_name, format, graph)
- PARAMETERS
*representation*-
the type of representation choosen : 1 = adjacent matrix, and 2 = adjacent list

*file_name*-
the basename of the output file (ex: graph => graph.dot)

*format*-
one type of format in : dot, gr, biolayout, net

*graph*-
the hash table of the graph

- OUTPUT Nothing else the file written to disk

**write_valuated_graph**-
Use this function to write valuated graph to disk in the required format

- SYNOPSIS write_graph(representation, file_name, format, ref_distance, graph)
- PARAMETERS
*representation*-
the type of representation choosen : 1 = adjacent matrix, and 2 = adjacent list

*file_name*-
the basename of the output file (ex: graph => graph.dot)

*format*-
one type of format in : dot, gr, biolayout, net

*ref_distance*-
the reference to the table of distances

*graph*-
the hash table of the graph

- OUTPUT Nothing else the file written to disk

**write_graph_clusters**-
Use this function to write graph with clusters to disk in the required format

- SYNOPSIS write_graph_clusters(representation, file_name, format, cluster_nb, ref_cluster, graph)
- PARAMETERS
*representation*-
the type of representation choosen : 1 = adjacent matrix, and 2 = adjacent list

*file_name*-
the basename of the output file (ex: graph => graph.dot)

*format*-
one type of format in : dot, gr, biolayout, net

*cluster_nb*-
the number of clusters

*ref_cluster*-
the table of clusters's elements

*graph*-
the hash table of the graph

- OUTPUT Nothing else the file written to disk

**write_treedyn_clusters**-
Use this function to write clusters to disk in the treedyn format

- SYNOPSIS write_treedyn_clusters(file_name, cluster_nb, ref_cluster)
- PARAMETERS
*file_name*-
the basename of the output file (ex: graph => graph.dot)

*cluster_nb*-
the number of clusters

*ref_cluster*-
the table of clusters's elements

- OUTPUT Nothing else the file written to disk

BioGraph::FileAccess is Copyright (C) 2004, Tristan Colombo CNRS - LCB, 31 chemin Joseph Aiguier 13009 Marseille France Email: tristan.colombo@ibsm.cnrs-mrs.fr All rights reserved. You may distribute this package under the terms of the GNU General Public License.

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