=head1 NAME proteindb module - part of the Wise2 package =head1 SYNOPSIS This module contains the following objects =over =item ProteinDB =back =head1 DESCRIPTION =head2 Object ProteinDB =over =item is_single_seq Type [boolean] Scalar No documentation =item is_random_db Type [boolean] Scalar No documentation =item single Type [ComplexSequence *] Scalar No documentation =item sdb Type [SequenceDB *] Scalar No documentation =item cses Type [ComplexSequenceEvalSet *] Scalar No documentation =item rnd Type [RandomProteinDB *] Scalar No documentation =item test_dna Type [boolean] Scalar No documentation =back A database of proteins. This takes either a single sequence or a sequence database and allows a method expecting protein complexsequences to loop over it. It also provides generic database indexing for this Horrible physical dependency in this generated by the random protein db requiring histogram and randommodel stuff. Yuk! =head2 Member functions of ProteinDB =over =item hard_link_ProteinDB &Wise2::ProteinDB::hard_link_ProteinDB(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [ProteinDB *] Return [UNKN ] Undocumented return value [ProteinDB *] =item alloc &Wise2::ProteinDB::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [ProteinDB *] =item set_is_single_seq &Wise2::ProteinDB::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 [ProteinDB *] Argument is_single_seq [OWNER] New value of the variable [boolean] Return [SOFT ] member variable is_single_seq [boolean] =item is_single_seq &Wise2::ProteinDB::is_single_seq(obj) Access member variable is_single_seq For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Return [SOFT ] member variable is_single_seq [boolean] =item set_is_random_db &Wise2::ProteinDB::set_is_random_db(obj,is_random_db) Replace member variable is_random_db For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Argument is_random_db [OWNER] New value of the variable [boolean] Return [SOFT ] member variable is_random_db [boolean] =item is_random_db &Wise2::ProteinDB::is_random_db(obj) Access member variable is_random_db For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Return [SOFT ] member variable is_random_db [boolean] =item set_single &Wise2::ProteinDB::set_single(obj,single) Replace member variable single For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Argument single [OWNER] New value of the variable [ComplexSequence *] Return [SOFT ] member variable single [boolean] =item single &Wise2::ProteinDB::single(obj) Access member variable single For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Return [SOFT ] member variable single [ComplexSequence *] =item set_sdb &Wise2::ProteinDB::set_sdb(obj,sdb) Replace member variable sdb For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Argument sdb [OWNER] New value of the variable [SequenceDB *] Return [SOFT ] member variable sdb [boolean] =item sdb &Wise2::ProteinDB::sdb(obj) Access member variable sdb For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Return [SOFT ] member variable sdb [SequenceDB *] =item set_cses &Wise2::ProteinDB::set_cses(obj,cses) Replace member variable cses For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Argument cses [OWNER] New value of the variable [ComplexSequenceEvalSet *] Return [SOFT ] member variable cses [boolean] =item cses &Wise2::ProteinDB::cses(obj) Access member variable cses For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Return [SOFT ] member variable cses [ComplexSequenceEvalSet *] =item set_rnd &Wise2::ProteinDB::set_rnd(obj,rnd) Replace member variable rnd For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Argument rnd [OWNER] New value of the variable [RandomProteinDB *] Return [SOFT ] member variable rnd [boolean] =item rnd &Wise2::ProteinDB::rnd(obj) Access member variable rnd For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Return [SOFT ] member variable rnd [RandomProteinDB *] =item set_test_dna &Wise2::ProteinDB::set_test_dna(obj,test_dna) Replace member variable test_dna For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Argument test_dna [OWNER] New value of the variable [boolean] Return [SOFT ] member variable test_dna [boolean] =item test_dna &Wise2::ProteinDB::test_dna(obj) Access member variable test_dna For use principly by API functions Argument obj [UNKN ] Object holding the variable [ProteinDB *] Return [SOFT ] member variable test_dna [boolean] =back =over =item new_ProteinDB_from_single_seq &Wise2::new_ProteinDB_from_single_seq(seq) To make a new protein database from a single Sequence with default amino acid mapping Argument seq [UNKN ] sequence which as placed into ProteinDB structure. [Sequence *] Return [UNKN ] Undocumented return value [ProteinDB *] =item single_fasta_ProteinDB &Wise2::single_fasta_ProteinDB(filename) pre-packed single fasta protein database Argument filename [UNKN ] name of fasta file [char *] Return [UNKN ] Undocumented return value [ProteinDB *] =item new_ProteinDB &Wise2::new_ProteinDB(seqdb,cses) To make a new protein database Argument seqdb [UNKN ] sequence database [SequenceDB *] Argument cses [UNKN ] protein evaluation set [ComplexSequenceEvalSet *] Return [UNKN ] Undocumented return value [ProteinDB *] =back