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::DBSQL::PredictionExonAdaptor - Performs database interaction for PredictionExons.

SYNOPSIS

  $pea   = $database_adaptor->get_PredictionExonAdaptor();
  $pexon = $pea->fetch_by_dbID();

  my $slice =
    $database_adaptor->get_SliceAdaptor->fetch_by_region( 'X', 1, 1e6 );

  my @pexons = @{ $pea->fetch_all_by_Slice($slice) };

METHODS

fetch_all_by_PredictionTranscript

  Arg [1]    : Bio::EnsEMBL::PredcitionTranscript $transcript
  Example    : none
  Description: Retrieves all Exons for the Transcript in 5-3 order
  Returntype : listref Bio::EnsEMBL::Exon on Transcript slice 
  Exceptions : throws if transcript does not have a slice
  Caller     : Transcript->get_all_Exons()
  Status     : Stable

store

  Arg [1]    : Bio::EnsEMBL::PredictionExon $exon
               The exon to store in this database
  Arg [2]    : int $prediction_transcript_id
               The internal identifier of the prediction exon that that this
               exon is associated with.
  Arg [3]    : int $rank
               The rank of the exon in the transcript (starting at 1)
  Example    : $pexon_adaptor->store($pexon, 1211, 2);
  Description: Stores a PredictionExon in the database
  Returntype : none
  Exceptions : thrown if exon does not have a slice attached
               or if $exon->start, $exon->end, $exon->strand, or $exon->phase 
               are not defined or if $exon is not a Bio::EnsEMBL::PredictionExon 
  Caller     : general
  Status     : Stable

remove

  Arg [1]    : Bio::EnsEMBL::PredictionExon $exon
               the exon to remove from the database 
  Example    : $exon_adaptor->remove($exon);
  Description: Removes an exon from the database
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable

list_dbIDs

  Arg [1]    : none
  Example    : @exon_ids = @{$exon_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all exons in the current db
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable