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README

NAME
    String::Cluster::Hobohm - Cluster strings using the Hobohm algorithm

VERSION
    version 0.112890

SYNOPSIS
        use String::Cluster::Hobohm;

        my @strings = qw(foo foa bar);

        my $clusterer = String::Clusterer::Hobohm->new( similarity => 0.62 );

        my $groups = $clusterer->cluster( \@strings );

        # [ [ \'foo', \'foa' ], [ \'bar' ] ];

        my @reduced = map { ${ $_->[0] } } @$groups;

        # [ 'foo', 'bar' ];

DESCRIPTION
    String::Clusterer::Hobohm implements the Hobohm clustering algorithm
    [1], originally devised to reduce redundancy of biological sequence data
    sets.

    As a clustering algorithm, it takes a set of sequences, and returns them
    grouped by similarity. The latter is computed using the Levenshtein
    distance, as implemented by the "Text::LevenshteinXS" module.

ATTRIBUTES
  similarity
    The similarity threshold that defines whether two strings are
    sufficiently alike to be part of the same cluster. Should be a number
    between 0 and 1. Defaults to 0.62.

METHODS
  cluster
        my $grouped = $hobohm->cluster( \@strings );

    Takes an array reference with the sequences to cluster as argument, and
    returns an array reference of clusters. Each cluster is depicted as a
    list of references to the strings that define it.

    For example, given the following array of strings, and a similarity of
    0.62:

        [ 'foo', 'foa', 'bar' ];

    The data structure returned after clustering would be:

        [ [ \'foo', \'foa' ], [ \'bar' ] ];

    The reason to use references instead of the actual strings is to avoid
    copying potentially large strings and taking up too much memory
    (remember that the algorithm was designed with biological sequences in
    mind).

REFERENCES
    [1] Uwe Hobohm, Michael Scharf, Reinhard Schneider and Chris Sander.
    Selection of representative protein data sets. Protein Science (1992),
    409-417. Cambridge University Press.

AUTHOR
    Bruno Vecchi <vecchi.b gmail.com>

COPYRIGHT AND LICENSE
    This software is copyright (c) 2011 by Bruno Vecchi.

    This is free software; you can redistribute it and/or modify it under
    the same terms as the Perl 5 programming language system itself.

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