Bio::EnsEMBL::IdMapping::StableIdGenerator AedesAegypti
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Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric
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Methods
increment_stable_id
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is_valid
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Methods code
increment_stable_iddescriptionprevnextTop
sub increment_stable_id {
  # This method will increment a stable ID.  For Anopheles, it will
# pick out the numerical part of the stable ID (no matter what type of
# stable ID it is) and increment it by one. It will then replace the
# numerical part by the incremented value and return the new stable
# ID. The parsing of the stable ID is very naive.
my ( $self, $stable_id ) = @_; if ( !$self->is_valid($stable_id) ) { throw("Unknown or missing stable ID: $stable_id."); } $stable_id =~ /^(\D*)(\d+)(\D*)/; my $number_as_string = "$2"; my $number = $2 + 1; $stable_id = sprintf( "%s" . sprintf( "%%0%dd", length($number_as_string) ) . "%s", $1, $number, $3 ); return $stable_id;
}
is_validdescriptionprevnextTop
sub is_valid {
  # A stable ID is a valid Anopheles stable ID if it begins with the
# character string "AGAP" or (for exons) just "E"
# explicitly make the exon one E+digits to exclude old-style ENSANG ids
# otherwise ENSANGnnn found as higher then AGAPnnn
# when initial_stable_id method checks archive tables
my ( $self, $stable_id ) = @_; if ( !( defined($stable_id) && ( $stable_id =~ /^AGAP/ || $stable_id =~ /^E\d+$/ ) ) ) { return 0; } return 1; } 1;
}
General documentation
LICENSETop
  Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license. For license details, please see /info/about/code_licence.html
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  Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>.