Bio::Search::GenericDatabase - Generic implementation of Bio::Search::DatabaseI

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Search::GenericDatabase - Generic implementation of Bio::Search::DatabaseI

SYNOPSIS

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    use Bio::Search::GenericDatabase;

    $db = Bio::Search::GenericDatabase->new( -name => 'my Blast db',
					     -date => '2001-03-13',
					     -length => 2352511,
					     -entries => 250000 );

    $name = $db->name();
    $date = $db->date();
    $num_letters = $db->letters();
    $num_entries = $db->entries();

DESCRIPTION

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This module provides a basic implementation of Bio::Search::DatabaseI. See documentation in that module for more information.

FEEDBACK

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Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR

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Steve Chervitz <sac@bioperl.org>

See the FEEDBACK section (FEEDBACK) for where to send bug reports and comments.

COPYRIGHT

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Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

DISCLAIMER

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This software is provided "as is" without warranty of any kind.

APPENDIX

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The rest of the documentation details each of the object methods.

name

See Bio::Search::DatabaseI::name() for documentation

This implementation is a combined set/get accessor.

date

See Bio::Search::DatabaseI::date() for documentation

This implementation is a combined set/get accessor.

letters

See Bio::Search::DatabaseI::letters() for documentation

This implementation is a combined set/get accessor.

entries

See Bio::Search::DatabaseI::entries() for documentation

This implementation is a combined set/get accessor.

BioPerl documentation Contained in the BioPerl distribution. 
#-----------------------------------------------------------------
#
# BioPerl module Bio::Search::GenericDatabase
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Steve Chervitz <sac@bioperl.org>
#
# You may distribute this module under the same terms as perl itself
#-----------------------------------------------------------------

# POD documentation - main docs before the code


# Let the code begin...

package Bio::Search::GenericDatabase;

use strict;

use base qw(Bio::Root::Root Bio::Search::DatabaseI);

sub new {
    my ($class, @args) = @_; 
    my $self = $class->SUPER::new(@args);
    my ($name, $date, $length, $ents) = 
        $self->_rearrange( [qw(NAME DATE LENGTH ENTRIES)], @args);

    $name    && $self->name($name);
    $date    && $self->date($date);
    $length  && $self->letters($length);
    $ents    && $self->entries($ents);

    return $self;
}


#---------------
sub name {
#---------------
    my $self = shift;
    if(@_) { 
        my $name = shift;
        $name =~ s/(^\s+|\s+$)//g;
        $self->{'_db'} = $name;
    }
    $self->{'_db'};
}


#-----------------------
sub date {
#-----------------------
    my $self = shift;
    if(@_) { $self->{'_dbDate'} = shift; }
    $self->{'_dbDate'};
}



#----------------------
sub letters {
#----------------------
    my $self = shift;
    if(@_) { $self->{'_dbLetters'} = shift; }
    $self->{'_dbLetters'};
}



#------------------
sub entries {
#------------------
    my $self = shift;
    if(@_) { $self->{'_dbEntries'} = shift; }
    $self->{'_dbEntries'};
}

1;