/ 
Bio-EnsEMBL-112.0_55
River stage zero No dependents
/ Bio::EnsEMBL::IdentityXref

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::IdentityXref

SYNOPSIS

my $xref = Bio::EnsEMBL::IdentityXref->new(
  -XREF_IDENTITY    => 80.4,
  -ENSEMBL_IDENTITY => 90.1,
  -SCORE            => 90,
  -EVALUE           => 12,
  -CIGAR_LINE       => '23MD3M2I40M',
  -XREF_START       => 1,
  -XREF_END         => 68,
  -ENSEMBL_START    => 10,
  -ENSEMBL_END      => 77,
  -ADAPTOR          => $adaptor,
  -PRIMARY_ID       => $primary_id,
  -DBNAME           => 'SwissProt'
);

METHODS

new

Arg [...]  : XREF_IDENTITY ENSEMBL_IDENTITY SCORE EVALUE CIGAR_LINE
           : XREF_START XREF_END ENSEMBL_START ENSEMBL_END
           : ANALYSIS pairs
Example    : see synopsis 
Description: Create a new Bio::EnsEMBL::IdentityXref object
Returntype : Bio::EnsEMBL::IdentityXref
Exceptions : none
Caller     : general
Status     : Stable

xref_identity

Arg [1]    : (optional) string $value
Example    : $xref_identity = $id_xref->xref_identity;
Description: Getter/Setter for xref identity
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

ensembl_identity

Arg [1]    : (optional) string $value
Example    : $ensembl_identity = $id_xref->ensembl_identity;
Description: Getter/Setter for ensembl identity
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

cigar_line

Arg [1]    : string $cigar_line
Example    : none
Description: get/set for attribute cigar_line
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

ensembl_start

Arg [1]    : string $ensembl_start
Example    : none
Description: get/set for attribute ensembl_start
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

ensembl_end

Arg [1]    : string $ensembl_end
Example    : none
Description: get/set for attribute ensembl_end
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

xref_start

Arg [1]    : string $xref_start
Example    : none
Description: get/set for attribute xref_start
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

xref_end

Arg [1]    : string $xref_end
Example    : none
Description: get/set for attribute xref_end
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

score

Arg [1]    : string $score
Example    : none
Description: get/set for attribute score
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

evalue

Arg [1]    : string $evalue
Example    : none
Description: get/set for attribute evalue
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

get_mapper

Args       : none
Example    : none
Description: produces a mapper object that takes coordinates from one side 
             of the alignment to the other side. "ensembl" and "external" 
             are the two coordinate systems contained.
Returntype : Bio::EnsEMBL::Mapper
Exceptions : none
Caller     : general, ProteinDAS subsystem
Status     : Stable

transform_feature

Arg [1]    : a feature type with start and end $feature
             This doesnt need to be a Bio::EnsEMBL::Feature as it doesnt
             need an attached slice. We may have to introduce an appropriate
             object type.
Example    : my $ens_prot_feature_list = 
                  $ident_xref->transform_feature( $swiss_prot_feature );
Description: a list of potential partial features which represent all 
             mappable places
             of the original feature in ensembl translation coordinates.
Returntype : listref of whatever was put in
Exceptions : none
Caller     : general, ProteinDAS subsystem
Status     : Stable

map_feature

Arg [1]    : a start,end capable feature object
Example    : none
Description: 
Returntype : list of Coordinates/Gaps which represents the mapping
Exceptions : none
Caller     : another way of doing ProteinDAS
Status     : Stable