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::IntronSupportingEvidenceAdaptor

SYNOPSIS

  my $isea = $dba->get_IntronSupportingEvidenceAdaptor();
  my $ise = $isea->fetch_by_dbID(1);
  my $ise_array = $dfa->fetch_all();

METHODS

list_linked_transcript_ids

  Arg[1]      : Bio::EnsEMBL::IntronSupportingEvidence Evidence to search with
  Example     : my $transcript_ids = @{$isea->list_linked_transcript_ids($ise)};
  Description : Uses the given IntronSupportingEvidence to find all linked
                transcript ids 
  Returntype  : ArrayRef[Integer] of transcript_id
  Exceptions  : Thrown if arguments are not as stated and for DB errors 

fetch_all_by_Transcript

  Arg[1]      : Bio::EnsEMBL::Transcript Transcript to search with
  Example     : my $ises = $isea->fetch_all_by_Transcript($transcript);
  Description : Uses the given Transcript to search for all instances of
                IntronSupportingEvidence linked to the transcript in the 
                database 
  Returntype  : ArrayRef of IntronSupportingEvidence objects
  Exceptions  : Thrown if arguments are not as stated and for DB errors 

fetch_flanking_exon_ids

  Arg[1]      : Bio::EnsEMBL::IntronSupportingEvidence Evidence to search with
  Arg[2]      : Bio::EnsEMBL::Transcript Transcript to search with
  Example     : my ($prev_id, $next_id) = @{$isea->fetch_flanking_exon_ids($ise, $transcript)};
  Description : Uses the given IntronSupportingEvidence and Transcript to search
                for the recorded previous and next exon database ids 
  Returntype  : ArrayRef 1 row long but with 2 columns representing previous 
                and next IDs respectivly
  Exceptions  : Thrown if arguments are not as stated and for DB errors 

store

  Arg[1]      : Bio::EnsEMBL::IntronSupportingEvidence Evidence to store
  Example     : $isea->store($ise);
  Description : Stores the IntronSupportingEvidence in the database. Duplicates
                are ignored.
  Returntype  : Integer The assigned database identifier
  Exceptions  : Thrown if the given object is not a IntronSupportingEvidence, 
                and for any DB exception. 

store_transcript_linkage

  Arg[1]      : Bio::EnsEMBL::IntronSupportingEvidence Evidence to link
  Arg[2]      : Bio::EnsEMBL::Transcript Transcript to link
  Arg[3]      : Integer an optional ID to give if the Transcript's own ID is possibly incorrect
  Example     : $isea->store_transcript_linkage($ise, $transcript);
                $isea->store_transcript_linkage($ise, $transcript, $tid);
  Description : Links a Transcript to a portion of Intron evidence
  Returntype  : None
  Exceptions  : Thrown if the given object is not a Transcript, if the 
                transcript is not stored, if the supporting evidence is not
                stored and for any DB exception. 

update

  Arg[1]      : Bio::EnsEMBL::IntronSupportingEvidence Evidence to update
  Example     : $isea->update($ise);
  Description : Updates all attributes of an evidence object
  Returntype  : None
  Exceptions  : Thrown if the given object is not a IntronSupportingEvidence,
                if the object is not stored and for normal DB errors

remove

  Arg[1]      : Bio::EnsEMBL::IntronSupportingEvidence
  Example                       : $isea->remove($ise);
  Description   : Deletes the given IntronSupportingEvidence from the database. 
                This can only occur if the object has no linked transcripts
  Returntype    : None
  Exceptions    : Thrown if the IntronSupportingEvidence is not stored, if
                the object has linked transcripts and in the event of any
                database error

remove_all_transcript_linkages

  Arg[1]      : Bio::EnsEMBL::IntronSupportingEvidence
  Example     : $isea->remove_all_transcript_linkages($ise);
  Description : Deletes the transcript links to the given IntronSupportingEvidence
  Returntype  : None
  Exceptions  : See remove_transcript_linkage

remove_transcript_linkage

  Arg[1]      : Bio::EnsEMBL::IntronSupportingEvidence Evidence to unlink
  Arg[2]      : Bio::EnsEMBL::Transcript Transcript to unlink
  Example     : $isea->remove_transcript_linkages($ise, $transcript);
  Description : Deletes a transcript's link to the given IntronSupportingEvidence
  Returntype  : None
  Exceptions  : Thrown if the given object is not a Transcript, if the 
                transcript is not stored, if the supporting evidence is not
                stored and for any DB exception.