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package Bio::Tools::Run::SCLBlast::Hit;
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
# OVERVIEW
# PSORT-B is described in Gardy, J.L. et al (2003). PSORT-B:
# improving protein subcellular localization prediction for
# Gram-negative bacteria. Nuc Acids Res 31(13):3613-17. Please
# cite this publication if you use PSORT-B in your research.
# The standalone version of PSORT-B is distributed under the GNU
# General Public Licence (Gnu GPL) (see the LICENSE file included
# in the download) by the Brinkman Laboratory, Simon Fraser
# University, Burnaby, B.C., Canada.
# This standalone version of PSORT-B has initially been developed
# for the Linux environment.
# This document describes the installation of the PSORT-B version
# 1.1.4 command line program and the PSORT-B server packages. For
# most purposes, following the installation instructions for the
# command line version will be sufficient.
# For further information, please contact psort-mail@sfu.ca.
use Bio::Search::Hit::GenericHit;
use Bio::Root::Root;
use strict;
our @ISA = qw(Bio::Search::Hit::GenericHit);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($loc, $secloc, $desc) = $self->_rearrange([qw(LOCALIZATION SECONDLOC DESCRIPTION)], @args);
$loc = [$loc] if(ref($loc) ne "ARRAY");
$secloc = [$secloc] if(ref($secloc) ne "ARRAY");
$self->{_locs} = $loc || $self->throw("Must provide a localization site.");
$self->{_seclocs} = $secloc || '';
$self->{_desc} = $desc || '';
return $self;
}
sub num_locs {
my $self = shift;
return scalar(@{$self->{_locs}});
}
sub num_seclocs {
my $self = shift;
return (@_) ? scalar(@{$self->{_seclocs}}) : 0;
}
sub description {
my $self = shift;
return (@_) ? $self->{_desc} = shift : $self->{_desc};
}
sub localization {
my $self = shift;
if(@_) {
my $loc = shift;
$self->{_locs} = (ref($loc) eq "ARRAY") ? $loc : [$loc];
} else {
use Data::Dumper;
return (wantarray) ? @{$self->{_locs}} : $self->{_locs}->[0];
}
}
sub secondarylocalization {
my $self = shift;
if (@_) {
my $secondloc = shift;
$self->{_seclocs} = (ref($secondloc) eq "ARRAY") ? $secondloc : [$secondloc];
}
else {
use Data::Dumper;
return (wantarray) ? @{$self->{_seclocs}} : $self->{_seclocs}->[0];
}
}
1;
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