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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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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.