15 Apr 2011 19:35:57 UTC
- Distribution: BioPerl-DB
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- License: perl_5
- Perl: v5.6.1
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- Latest versionCJFIELDS Christopher Fieldsand 1 contributors
- BioPerl Team
- AUTHOR - Yves Bastide
Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver - DESCRIPTION of Object
Give standard usage here
Describe the object here
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Email ybastide at irisa.fr
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : insert_object Usage : Function: We override this here in order to omit the insert if there are no values. This is because this entity basically represents a derived class, and we may simply be dealing with the base class. Example : Returns : The primary key of the newly inserted record. Args : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object (basically, it needs to implement dbh(), sth($key, $sth), dbcontext(), and get_persistent_slots()). The object to be inserted. A reference to an array of foreign key objects; if any of those foreign key values is NULL (some foreign keys may be nullable), then give the class name.
Title : update_object Usage : Function: See parent class. We need to override this here because there is no Biosequence object separate from PrimarySeq that would hold a primary key. Hence, store()s cannot recognize when the Biosequence for a Bioentry already exists and needs to be updated, or when it needs to be created. The way the code is currently wired, the presence of the primary key (stemming from the bioentry) will always trigger an update. So, what we need to do here is check whether the entry already exists and if not delegate to insert_object(). Example : Returns : The number of updated rows Args : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object (basically, it needs to implement dbh(), sth($key, $sth), dbcontext(), and get_persistent_slots()). The object to be updated. A reference to an array of foreign key objects; if any of those foreign key values is NULL (some foreign keys may be nullable), then give the class name.
Title : get_biosequence Usage : Function: Returns the actual sequence for a bioentry, or a substring of it. Example : Returns : A string (the sequence or subsequence) Args : The calling persistence adaptor. The primary key of the bioentry for which to obtain the sequence. Optionally, start and end position if only a subsequence is to be returned (for long sequences, obtaining the subsequence from the database may be much faster than obtaining it from the complete in-memory string, because the latter has to be retrieved first).
Module Install Instructions
To install Bio::BioEntry, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell install Bio::BioEntry
For more information on module installation, please visit the detailed CPAN module installation guide.