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

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NAME

Bio::EnsEMBL::ProteinFeature

SYNOPSIS

  my $feature = Bio::EnsEMBL::ProteinFeature->new(
    -start    => $start,
    -end      => $end,
    -hstart   => $hit_start,
    -hend     => $hit_end,
    -hseqname => $hit_name
  );

DESCRIPTION

ProteinFeature objects represent domains or other features of interest on a peptide sequence.

METHODS

new

  Arg [IDESC]           : (optional) string An interpro description
  Arg [INTERPRO_AC]     : (optional) string An interpro accession
  Arg [TRANSLATION_ID]  : (optional) integer A translation dbID
  Arg [...]             : named arguments to FeaturePair superclass
  Example    :

    $pf =
      Bio::EnsEMBL::ProteinFeature->new( -IDESC       => $idesc,
                                         -INTERPRO_AC => $iac,
                                         @fp_args );

  Description: Instantiates a Bio::EnsEMBL::ProteinFeature
  Returntype : Bio::EnsEMBL::FeaturePair
  Exceptions : none
  Caller     : general
  Status     : Stable

strand

  Arg [1]    : Ignored
  Description: Overwrites Bio::EnsEMBL::Feature->strand to not allow
             : the strand to be set.
  Returntype : int
  Status     : Stable

idesc

  Arg [1]    : (optional) string The interpro description
  Example    : print $protein_feature->idesc();
  Description: Getter/Setter for the interpro description of this protein
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

ilabel

  Arg [1]    : (optional) string The interpro label
  Example    : print $protein_feature->ilabel();
  Description: Getter/Setter for the interpro label of this protein
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

interpro_ac

  Arg [1]    : (optional) string The interpro accession
  Example    : print $protein_feature->interpro_ac();
  Description: Getter/Setter for the interpro accession of this protein
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

translation_id

  Arg [1]    : (optional) integer The dbID of the translation
  Example    : print $protein_feature->translation_id();
  Description: Getter/Setter for the translation dbID of this protein
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

summary_as_hash

  Example       : $protein_feature_summary = $protein_feature->summary_as_hash();
  Description   : Retrieves a textual summary of this Protein feature.
                  Not inherited from Feature.
  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use

alignment_strings

  Arg [1]    : list of string $flags
  Example    : $pf->alignment_strings
  Description: Allows to rebuild the alignment string of both the query and target sequence
               using the sequence from translation object and
               MD Z String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)* (Refer:  SAM/BAM specification)
               eg: MD:Z:96^RHKTDSFVGLMGKRALNS0V14
  Returntype : array reference containing 2 strings
               the first corresponds to seq
               the second corresponds to hseq
  Exceptions : none
  Caller     : general
  Status     : Stable

_hit_unit

  Arg [1]    : none
  Description: PRIVATE implementation of abstract superclass method.  Returns
               1 as the 'unit' used for the hit sequence.
  Returntype : int
  Exceptions : none
  Caller     : Bio::EnsEMBL::BaseAlignFeature
  Status     : Stable

_query_unit

  Arg [1]    : none
  Description: PRIVATE implementation of abstract superclass method.  Returns
               3 as the 'unit' used for the query sequence.
  Returntype : int
  Exceptions : none
  Caller     : Bio::EnsEMBL::BaseAlignFeature
  Status     : Stable

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL