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package Sanger::CGP::Vagrent::Data::AbstractGenomicPosition; |
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##########LICENCE########## |
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# Copyright (c) 2014 Genome Research Ltd. |
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# |
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# Author: Cancer Genome Project cgpit@sanger.ac.uk |
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# |
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# This file is part of VAGrENT. |
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# |
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# VAGrENT is free software: you can redistribute it and/or modify it under |
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# the terms of the GNU Affero General Public License as published by the Free |
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# Software Foundation; either version 3 of the License, or (at your option) any |
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# later version. |
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# |
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# This program is distributed in the hope that it will be useful, but WITHOUT |
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS |
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# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more |
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# details. |
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# |
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# You should have received a copy of the GNU Affero General Public License |
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# along with this program. If not, see <http://www.gnu.org/licenses/>. |
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##########LICENCE########## |
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use strict; |
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use Carp; |
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use Attribute::Abstract; |
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use Sanger::CGP::Vagrent qw($VERSION); |
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use base qw(Sanger::CGP::Vagrent); |
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1; |
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sub new { |
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my $proto = shift; |
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my $class = ref($proto) || $proto; |
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my $self = {}; |
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bless($self, $class); |
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$self->_localInit(@_); |
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$self->_init(@_); |
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return $self; |
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} |
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sub _localInit { |
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my $self = shift; |
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my %vars = @_; |
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foreach my $k(keys(%vars)){ |
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if($k eq 'species'){ |
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$self->{_species} = $vars{species}; |
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} elsif($k eq 'genomeVersion'){ |
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$self->{_genomeVersion} = $vars{genomeVersion}; |
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} elsif($k eq 'chr'){ |
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$self->{_chr} = $vars{'chr'}; |
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} elsif($k eq 'minpos'){ |
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$self->{_minpos} = $vars{minpos}; |
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} elsif($k eq 'maxpos'){ |
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$self->{_maxpos} = $vars{maxpos}; |
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} elsif($k eq 'id'){ |
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$self->{_id} = $vars{id}; |
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} |
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} |
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croak('must specify a species') unless(exists($self->{_species}) && defined($self->{_species})); |
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croak('must specify a genomeVersion') unless(exists($self->{_genomeVersion}) && defined($self->{_genomeVersion})); |
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croak('must specify a chr') unless(exists($self->{_chr}) && defined($self->{_chr})); |
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croak('must specify a minpos') unless(exists($self->{_minpos}) && defined($self->{_minpos})); |
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croak('must specify a maxpos') unless(exists($self->{_maxpos}) && defined($self->{_maxpos})); |
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} |
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sub _init: Abstract; |
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sub getSpecies { |
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return shift->{_species}; |
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} |
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sub getGenomeVersion { |
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return shift->{_genomeVersion}; |
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} |
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sub getChr { |
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return shift->{_chr}; |
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} |
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sub getMinPos { |
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return shift->{_minpos}; |
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} |
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sub setMinPos { |
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my ($self,$pos) = @_; |
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if(defined $pos){ |
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$self->{_minpos} = $pos; |
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} |
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} |
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sub getMaxPos { |
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return shift->{_maxpos}; |
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} |
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sub setMaxPos { |
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my ($self,$pos) = @_; |
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if(defined $pos){ |
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$self->{_maxpos} = $pos; |
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} |
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} |
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sub getId { |
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return shift->{_id}; |
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} |
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sub getLength { |
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my $self = shift; |
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return (($self->{_maxpos} - $self->{_minpos}) + 1); |
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} |
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__END__ |
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=head1 NAME |
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Sanger::CGP::Vagrent::Data::AbstractGenomicPosition - Abstract Data object representing |
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Genomic position |
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=head1 DESCRIPTION |
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This is an abstract data class designed to be extended, it provides basic functionality for holding |
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genomic position. Child classes must implement an _init method to handle parameter values handed to |
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the object when the constructor is called. |
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=head1 METHODS |
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=head2 Constructor |
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=head3 new |
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=over |
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=item Usage : |
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my $gp = Sanger::CGP::Vagrent::Data::AbstractGenomicPositionSubClass->new(%params); |
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=item Function : |
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Builds a new Sanger::CGP::Vagrent::Data::AbstractGenomicPosition inheriting object |
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=item Returns : |
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L<Sanger::CGP::Vagrent::Data::AbstractGenomicPosition|Sanger::CGP::Vagrent::Data::AbstractGenomicPosition> sub class object initialized with parameter values |
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=item Params : |
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species => Species string (eg Human) |
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genomeVersion => Genome version String (eg GRCh37) |
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chr => Chromosome/contig name |
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minpos => Lowest coordinate of the feature |
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maxpos => Highest coordinate of the feature |
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id => Identifier (Optional) |
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=back |
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=head3 _init |
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=over |
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=item Usage : |
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Abstract internal initialisation method, must be implemented in subclasses. All parameters are passed through from the constructor. |
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=back |
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=head2 Attributes |
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=head3 getId |
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=over |
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=item Usage : |
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my $id = $gp->getId; |
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=item Function : |
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Returns the value of Id |
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=item Returns : |
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String |
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=back |
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=head3 getSpecies |
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=over |
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=item Usage : |
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my $species = $gp->getSpecies; |
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=item Function : |
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Returns the species name |
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=item Returns : |
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String |
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=back |
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=head3 getGenomeVersion |
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=over |
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=item Usage : |
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my $gVers = $gp->getGenomeVersion; |
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=item Function : |
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Returns the genome version string |
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=item Returns : |
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String |
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=back |
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=head3 getChr |
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=over |
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=item Usage : |
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my $chr = $gp->getChr; |
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=item Function : |
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Returns the chromosome/contig name |
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=item Returns : |
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String |
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=back |
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=head3 getMinPos |
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=over |
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=item Usage : |
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my $min = $gp->getMinPos; |
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=item Function : |
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Returns the lowest coordinate of the feature on the sequence |
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=item Returns : |
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Integer |
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=back |
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=head3 setMinPos |
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=over |
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=item Usage : |
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$gp->setMinPos($newPos); |
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=item Function : |
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Sets the lowest coordinate of the feature on the sequence |
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=item Params |
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Integer, new position |
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=item Returns : |
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None |
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=back |
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=head3 getMaxPos |
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=over |
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=item Usage : |
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my $max = $gp->getMaxPos; |
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=item Function : |
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Returns the highest coordinate of the feature on the sequence |
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=item Returns : |
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Integer |
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=back |
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=head3 setMaxPos |
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=over |
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=item Usage : |
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$gp->setMaxPos($newPos); |
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=item Function : |
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Sets the highest coordinate of the feature on the sequence |
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=item Params |
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Integer, new position |
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=item Returns : |
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None |
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=back |