=head1 NAME cdnadb module - part of the Wise2 package =head1 SYNOPSIS This module contains the following objects =over =item cDNADB =back =head1 DESCRIPTION =head2 Object cDNADB =over =item is_single_seq Type [boolean] Scalar No documentation =item done_forward Type [boolean] Scalar No documentation =item forward_only Type [boolean] Scalar No documentation =item forw Type [ComplexSequence *] Scalar No documentation =item rev Type [ComplexSequence *] Scalar No documentation =item sdb Type [SequenceDB *] Scalar No documentation =item current Type [Sequence *] Scalar No documentation =item cses Type [ComplexSequenceEvalSet *] Scalar No documentation =item error_handling Type [CdnaDBErrorType] Scalar No documentation =item error_tol Type [double] Scalar No documentation =back This object hold a database of cDNA sequences. You will probably use it in one of two ways 1 A sequence formatted database, which is provided by a /SequenceDB object is used to provide the raw sequences 2 A single cDNA sequence is used. In each case this database provides both the forward and reverse strands into the system. Notice that what is exported are /ComplexSequence objects, not cDNA dna, as this is what is generally needed. These are things with splice sites calculated etc. This is why for initialisation this needs a /ComplexSequenceEvalSet of the correct type. =head2 Member functions of cDNADB =over =item get_entry &Wise2::cDNADB::get_entry(cdnadb,de) Gets cDNA sequence out from the cDNADB using the information stored in dataentry Argument cdnadb [READ ] cDNA database [cDNADB *] Argument de [READ ] DataEntry information [DataEntry *] Return [UNKN ] Undocumented return value [cDNA *] =item hard_link_cDNADB &Wise2::cDNADB::hard_link_cDNADB(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [cDNADB *] Return [UNKN ] Undocumented return value [cDNADB *] =item alloc &Wise2::cDNADB::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [cDNADB *] =item set_is_single_seq &Wise2::cDNADB::set_is_single_seq(obj,is_single_seq) Replace member variable is_single_seq For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Argument is_single_seq [OWNER] New value of the variable [boolean] Return [SOFT ] member variable is_single_seq [boolean] =item is_single_seq &Wise2::cDNADB::is_single_seq(obj) Access member variable is_single_seq For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Return [SOFT ] member variable is_single_seq [boolean] =item set_done_forward &Wise2::cDNADB::set_done_forward(obj,done_forward) Replace member variable done_forward For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Argument done_forward [OWNER] New value of the variable [boolean] Return [SOFT ] member variable done_forward [boolean] =item done_forward &Wise2::cDNADB::done_forward(obj) Access member variable done_forward For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Return [SOFT ] member variable done_forward [boolean] =item set_forward_only &Wise2::cDNADB::set_forward_only(obj,forward_only) Replace member variable forward_only For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Argument forward_only [OWNER] New value of the variable [boolean] Return [SOFT ] member variable forward_only [boolean] =item forward_only &Wise2::cDNADB::forward_only(obj) Access member variable forward_only For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Return [SOFT ] member variable forward_only [boolean] =item set_forw &Wise2::cDNADB::set_forw(obj,forw) Replace member variable forw For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Argument forw [OWNER] New value of the variable [ComplexSequence *] Return [SOFT ] member variable forw [boolean] =item forw &Wise2::cDNADB::forw(obj) Access member variable forw For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Return [SOFT ] member variable forw [ComplexSequence *] =item set_rev &Wise2::cDNADB::set_rev(obj,rev) Replace member variable rev For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Argument rev [OWNER] New value of the variable [ComplexSequence *] Return [SOFT ] member variable rev [boolean] =item rev &Wise2::cDNADB::rev(obj) Access member variable rev For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Return [SOFT ] member variable rev [ComplexSequence *] =item set_sdb &Wise2::cDNADB::set_sdb(obj,sdb) Replace member variable sdb For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Argument sdb [OWNER] New value of the variable [SequenceDB *] Return [SOFT ] member variable sdb [boolean] =item sdb &Wise2::cDNADB::sdb(obj) Access member variable sdb For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Return [SOFT ] member variable sdb [SequenceDB *] =item set_current &Wise2::cDNADB::set_current(obj,current) Replace member variable current For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Argument current [OWNER] New value of the variable [Sequence *] Return [SOFT ] member variable current [boolean] =item current &Wise2::cDNADB::current(obj) Access member variable current For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Return [SOFT ] member variable current [Sequence *] =item set_cses &Wise2::cDNADB::set_cses(obj,cses) Replace member variable cses For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Argument cses [OWNER] New value of the variable [ComplexSequenceEvalSet *] Return [SOFT ] member variable cses [boolean] =item cses &Wise2::cDNADB::cses(obj) Access member variable cses For use principly by API functions Argument obj [UNKN ] Object holding the variable [cDNADB *] Return [SOFT ] member variable cses [ComplexSequenceEvalSet *] =back =over =item new_cDNADB_from_single_seq &Wise2::new_cDNADB_from_single_seq(seq) To make a new cDNA database from a single cDNA Sequence with a eval system Argument seq [UNKN ] sequence which as placed into cDNADB structure. [cDNA *] Return [UNKN ] Undocumented return value [cDNADB *] =item new_cDNADB &Wise2::new_cDNADB(seqdb) To make a new cDNA database Argument seqdb [READ ] sequence database [SequenceDB *] Return [UNKN ] Undocumented return value [cDNADB *] =back