# NAME

BioGraph::FileAccess

# SYNOPSIS

use BioGraph::FileAccess;

# DESCRIPTION

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

# AVAILABLE FUNCTIONS

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

# AUTHOR AND COPYRIGHT

```
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.
```