=head1 NAME genomicdb module - part of the Wise2 package =head1 SYNOPSIS This module contains the following objects =over =item GenomicDB =back =head1 DESCRIPTION =head2 Object GenomicDB =over =item is_single_seq Type [boolean] Scalar No documentation =item done_forward 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 [Genomic *] Scalar No documentation =item cses Type [ComplexSequenceEvalSet *] Scalar No documentation =item error_handling Type [GenDBErrorType] Scalar No documentation =item single Type [Genomic *] Scalar for single sequence cases, so we can 'index' on it =item revsingle Type [Genomic *] Scalar No documentation =item length_of_N Type [int] Scalar No documentation =item repeat_in_cds_score Type [int] Scalar No documentation =back This object hold a database of genomic 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 Genomic 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 genomic 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 GenomicDB =over =item get_Genomic_from_GenomicDB &Wise2::GenomicDB::get_Genomic_from_GenomicDB(gendb,de) Gets Genomic sequence out from the GenomicDB using the information stored in dataentry Argument gendb [UNKN ] Undocumented argument [GenomicDB *] Argument de [UNKN ] Undocumented argument [DataEntry *] Return [UNKN ] Undocumented return value [Genomic *] =item hard_link_GenomicDB &Wise2::GenomicDB::hard_link_GenomicDB(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [GenomicDB *] Return [UNKN ] Undocumented return value [GenomicDB *] =item alloc &Wise2::GenomicDB::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [GenomicDB *] =item set_is_single_seq &Wise2::GenomicDB::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 [GenomicDB *] Argument is_single_seq [OWNER] New value of the variable [boolean] Return [SOFT ] member variable is_single_seq [boolean] =item is_single_seq &Wise2::GenomicDB::is_single_seq(obj) Access member variable is_single_seq For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Return [SOFT ] member variable is_single_seq [boolean] =item set_done_forward &Wise2::GenomicDB::set_done_forward(obj,done_forward) Replace member variable done_forward For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Argument done_forward [OWNER] New value of the variable [boolean] Return [SOFT ] member variable done_forward [boolean] =item done_forward &Wise2::GenomicDB::done_forward(obj) Access member variable done_forward For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Return [SOFT ] member variable done_forward [boolean] =item set_forw &Wise2::GenomicDB::set_forw(obj,forw) Replace member variable forw For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Argument forw [OWNER] New value of the variable [ComplexSequence *] Return [SOFT ] member variable forw [boolean] =item forw &Wise2::GenomicDB::forw(obj) Access member variable forw For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Return [SOFT ] member variable forw [ComplexSequence *] =item set_rev &Wise2::GenomicDB::set_rev(obj,rev) Replace member variable rev For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Argument rev [OWNER] New value of the variable [ComplexSequence *] Return [SOFT ] member variable rev [boolean] =item rev &Wise2::GenomicDB::rev(obj) Access member variable rev For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Return [SOFT ] member variable rev [ComplexSequence *] =item set_sdb &Wise2::GenomicDB::set_sdb(obj,sdb) Replace member variable sdb For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Argument sdb [OWNER] New value of the variable [SequenceDB *] Return [SOFT ] member variable sdb [boolean] =item sdb &Wise2::GenomicDB::sdb(obj) Access member variable sdb For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Return [SOFT ] member variable sdb [SequenceDB *] =item set_current &Wise2::GenomicDB::set_current(obj,current) Replace member variable current For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Argument current [OWNER] New value of the variable [Genomic *] Return [SOFT ] member variable current [boolean] =item current &Wise2::GenomicDB::current(obj) Access member variable current For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Return [SOFT ] member variable current [Genomic *] =item set_cses &Wise2::GenomicDB::set_cses(obj,cses) Replace member variable cses For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Argument cses [OWNER] New value of the variable [ComplexSequenceEvalSet *] Return [SOFT ] member variable cses [boolean] =item cses &Wise2::GenomicDB::cses(obj) Access member variable cses For use principly by API functions Argument obj [UNKN ] Object holding the variable [GenomicDB *] Return [SOFT ] member variable cses [ComplexSequenceEvalSet *] =back =over =item new_GenomicDB_from_single_seq &Wise2::new_GenomicDB_from_single_seq(gen,cses,score_in_repeat_coding) To make a new genomic database from a single Genomic Sequence with a eval system Argument gen [UNKN ] sequence which as placed into GenomicDB structure. [Genomic *] Argument cses [UNKN ] Undocumented argument [ComplexSequenceEvalSet *] Argument score_in_repeat_coding [UNKN ] Undocumented argument [int] Return [UNKN ] Undocumented return value [GenomicDB *] =item new_GenomicDB &Wise2::new_GenomicDB(seqdb,cses,length_of_N,repeat_in_cds_score) To make a new genomic database Argument seqdb [UNKN ] sequence database [SequenceDB *] Argument cses [UNKN ] protein evaluation set [ComplexSequenceEvalSet *] Argument length_of_N [UNKN ] Undocumented argument [int] Argument repeat_in_cds_score [UNKN ] Undocumented argument [int] Return [UNKN ] Undocumented return value [GenomicDB *] =back