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::PredictionTranscriptAdaptor - Performs database interaction related to PredictionTranscripts

SYNOPSIS

  # get a prediction transcript adaptor from the database
  $pta = $database_adaptor->get_PredictionTranscriptAdaptor();

  # get a slice on a region of chromosome 1
  $sa = $database_adaptor->get_SliceAdaptor();

  $slice = $sa->fetch_by_region( 'chromosome', 'x', 100000, 200000 );

  # get all the prediction transcripts from the slice region
  $prediction_transcripts = @{ $pta->fetch_all_by_Slice($slice) };

METHODS

fetch_by_stable_id

  Arg [1]    : string $stable_id
               The stable id of the transcript to retrieve
  Example    : $trans = $trans_adptr->fetch_by_stable_id('GENSCAN00000001234');
  Description: Retrieves a prediction transcript via its display_label.
               This method is called fetch_by_stable_id for polymorphism with
               the TranscriptAdaptor.  Prediction transcript display_labels are
               not necessarily stable in that the same identifier may be reused
               for a completely different prediction transcript in a subsequent
               database release.
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Caller     : general
  Status     : Stable

fetch_all_by_Slice

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice to fetch transcripts on.
  Arg [3]    : (optional) boolean $load_exons
               if true, exons will be loaded immediately rather than
               lazy loaded later.
  Example    : $transcripts = $
  Description: Overrides superclass method to optionally load exons
               immediately rather than lazy-loading them later.  This
               is more efficient when there are a lot of transcripts whose
               exons are going to be used.
  Returntype : reference to list of transcripts
  Exceptions : thrown if exon cannot be placed on transcript slice
  Caller     : Slice::get_all_Transcripts
  Status     : Stable

fetch_by_prediction_exon_id

  Arg [1]    : Int $prediction_exon_id
               Unique database identifier for the prediction exon
               whose prediction transcript should be retrieved.
  Example    : $prediction_transcript = $prediction_transcript_adaptor->fetch_by_exon_id(1241);
  Description: Retrieves a prediction transcript from the database via the database identifier
               of one of its exons.
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

_objs_from_sth

  Arg [1]    : DBI:st $sth 
               An executed DBI statement handle
  Arg [2]    : (optional) Bio::EnsEMBL::Mapper $mapper 
               An mapper to be used to convert contig coordinates
               to assembly coordinates.
  Arg [3]    : (optional) Bio::EnsEMBL::Slice $slice
               A slice to map the prediction transcript to.   
  Example    : $p_transcripts = $self->_objs_from_sth($sth);
  Description: Creates a list of Prediction transcripts from an executed DBI
               statement handle.  The columns retrieved via the statement 
               handle must be in the same order as the columns defined by the
               _columns method.  If the slice argument is provided then the
               the prediction transcripts will be in returned in the coordinate
               system of the $slice argument.  Otherwise the prediction 
               transcripts will be returned in the RawContig coordinate system.
  Returntype : reference to a list of Bio::EnsEMBL::PredictionTranscripts
  Exceptions : none
  Caller     : superclass generic_fetch
  Status     : Stable

store

  Arg [1]    : list of Bio::EnsEMBL::PredictionTranscript @pre_transcripts 
  Example    : $prediction_transcript_adaptor->store(@pre_transcripts);
  Description: Stores a list of given prediction transcripts in database. 
               Puts dbID and Adaptor into each object stored object.
  Returntype : none
  Exceptions : on wrong argument type 
  Caller     : general 
  Status     : Stable

remove

  Arg [1]    : Bio::EnsEMBL::PredictionTranscript $pt 
  Example    : $prediction_transcript_adaptor->remove($pt);
  Description: removes given prediction transcript $pt from database. 
  Returntype : none
  Exceptions : throws if argument not a  Bio::EnsEMBL::PredictionTranscript
  Caller     : general
  Status     : Stable

list_dbIDs

  Arg [1]    : none
  Example    : @feature_ids = @{$prediction_transcript_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all prediction transcript
               features 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