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

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL