Tristan Colombo > BioGraph > BioGraph::FileAccess

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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

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.
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