=head1 NAME genefrequency module - part of the Wise2 package =head1 SYNOPSIS This module contains the following objects =over =item GeneFrequency21 =item GeneConsensus =item GeneSingleCons =back =head1 DESCRIPTION =head2 Object GeneFrequency21 =over =item ss5 Type [GeneConsensus *] Scalar No documentation =item ss3 Type [GeneConsensus *] Scalar No documentation =item codon[64] Type [double] Scalar No documentation =item central[4] Type [double] Scalar No documentation =item py[4] Type [double] Scalar No documentation =item spacer[4] Type [double] Scalar No documentation =item transition[GENEFREQUENCY21_TRANSITION_LEN] Type [double] Scalar No documentation =item cds_triplet[64] Type [double] Scalar phase 0 =back No documentation for GeneFrequency21 =head2 Member functions of GeneFrequency21 =over =item hard_link_GeneFrequency21 &Wise2::GeneFrequency21::hard_link_GeneFrequency21(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [GeneFrequency21 *] Return [UNKN ] Undocumented return value [GeneFrequency21 *] =item alloc &Wise2::GeneFrequency21::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [GeneFrequency21 *] =item set_ss5 &Wise2::GeneFrequency21::set_ss5(obj,ss5) Replace member variable ss5 For use principly by API functions Argument obj [UNKN ] Object holding the variable [GeneFrequency21 *] Argument ss5 [OWNER] New value of the variable [GeneConsensus *] Return [SOFT ] member variable ss5 [boolean] =item ss5 &Wise2::GeneFrequency21::ss5(obj) Access member variable ss5 For use principly by API functions Argument obj [UNKN ] Object holding the variable [GeneFrequency21 *] Return [SOFT ] member variable ss5 [GeneConsensus *] =item set_ss3 &Wise2::GeneFrequency21::set_ss3(obj,ss3) Replace member variable ss3 For use principly by API functions Argument obj [UNKN ] Object holding the variable [GeneFrequency21 *] Argument ss3 [OWNER] New value of the variable [GeneConsensus *] Return [SOFT ] member variable ss3 [boolean] =item ss3 &Wise2::GeneFrequency21::ss3(obj) Access member variable ss3 For use principly by API functions Argument obj [UNKN ] Object holding the variable [GeneFrequency21 *] Return [SOFT ] member variable ss3 [GeneConsensus *] =back =head2 Object GeneConsensus =over =item center Type [int] Scalar No documentation =item gsc Type [GeneSingleCons **] List No documentation =back No documentation for GeneConsensus =head2 Member functions of GeneConsensus =over =item hard_link_GeneConsensus &Wise2::GeneConsensus::hard_link_GeneConsensus(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [GeneConsensus *] Return [UNKN ] Undocumented return value [GeneConsensus *] =item GeneConsensus_alloc_std &Wise2::GeneConsensus::GeneConsensus_alloc_std(void) Equivalent to GeneConsensus_alloc_len(GeneConsensusLISTLENGTH) Return [UNKN ] Undocumented return value [GeneConsensus *] =item set_center &Wise2::GeneConsensus::set_center(obj,center) Replace member variable center For use principly by API functions Argument obj [UNKN ] Object holding the variable [GeneConsensus *] Argument center [OWNER] New value of the variable [int] Return [SOFT ] member variable center [boolean] =item center &Wise2::GeneConsensus::center(obj) Access member variable center For use principly by API functions Argument obj [UNKN ] Object holding the variable [GeneConsensus *] Return [SOFT ] member variable center [int] =item gsc &Wise2::GeneConsensus::gsc(obj,i) Access members stored in the gsc list For use principly by API functions Argument obj [UNKN ] Object holding the list [GeneConsensus *] Argument i [UNKN ] Position in the list [int] Return [SOFT ] Element of the list [GeneSingleCons *] =item length_gsc &Wise2::GeneConsensus::length_gsc(obj) discover the length of the list For use principly by API functions Argument obj [UNKN ] Object holding the list [GeneConsensus *] Return [UNKN ] length of the list [int] =item flush_gsc &Wise2::GeneConsensus::flush_gsc(obj) Frees the list elements, sets length to 0 If you want to save some elements, use hard_link_xxx to protect them from being actually destroyed in the free Argument obj [UNKN ] Object which contains the list [GeneConsensus *] Return [UNKN ] Undocumented return value [int] =item add_gsc &Wise2::GeneConsensus::add_gsc(obj,add) Adds another object to the list. It will expand the list if necessary Argument obj [UNKN ] Object which contains the list [GeneConsensus *] Argument add [OWNER] Object to add to the list [GeneSingleCons *] Return [UNKN ] Undocumented return value [boolean] =back =head2 Object GeneSingleCons =over =item string Type [char *] Scalar No documentation =item number Type [double] Scalar No documentation =back No documentation for GeneSingleCons =head2 Member functions of GeneSingleCons =over =item hard_link_GeneSingleCons &Wise2::GeneSingleCons::hard_link_GeneSingleCons(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [GeneSingleCons *] Return [UNKN ] Undocumented return value [GeneSingleCons *] =item alloc &Wise2::GeneSingleCons::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [GeneSingleCons *] =item set_string &Wise2::GeneSingleCons::set_string(obj,string) Replace member variable string For use principly by API functions Argument obj [UNKN ] Object holding the variable [GeneSingleCons *] Argument string [OWNER] New value of the variable [char *] Return [SOFT ] member variable string [boolean] =item string &Wise2::GeneSingleCons::string(obj) Access member variable string For use principly by API functions Argument obj [UNKN ] Object holding the variable [GeneSingleCons *] Return [SOFT ] member variable string [char *] =item set_number &Wise2::GeneSingleCons::set_number(obj,number) Replace member variable number For use principly by API functions Argument obj [UNKN ] Object holding the variable [GeneSingleCons *] Argument number [OWNER] New value of the variable [double] Return [SOFT ] member variable number [boolean] =item number &Wise2::GeneSingleCons::number(obj) Access member variable number For use principly by API functions Argument obj [UNKN ] Object holding the variable [GeneSingleCons *] Return [SOFT ] member variable number [double] =back =over =item read_GeneFrequency21_file &Wise2::read_GeneFrequency21_file(filename) Opens the file with /openfile Reads in a GeneFrequency (Mor-Ewan style) Argument filename [UNKN ] will open from WISECONFIGDIR etc via openfile [char *] Return [UNKN ] a newly allocated structure [GeneFrequency21 *] =item read_GeneFrequency21 &Wise2::read_GeneFrequency21(ifp) Reads in a GeneFrequency (Mor-Ewan style) file from ifp Argument ifp [UNKN ] file pointer [FILE *] Return [UNKN ] a newly allocated structure [GeneFrequency21 *] =back