ARB
Classes | Typedefs | Functions | Variables
rns.h File Reference
#include "base.h"
#include "simcfg.h"
#include "frand.h"
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Classes

struct  S_RNS
 

Typedefs

typedef double SingleProb [BASETYPES]
 
typedef double DoubleProb [BASETYPES][BASETYPES]
 
typedef struct S_RNSRNS
 

Functions

RNS createOriginRNS ()
 
void freeRNS (RNS rns)
 
void splitRNS (int no_of_father, RNS origin, double age, int steps, int depth)
 
void dumpDepths ()
 

Variables

int orgLen
 
double orgHelixPart
 
int timeSteps
 
Frand mrpb_Init
 
Frand l2hrpb_Init
 
Frand pairPart
 
Frand mutationRate
 
Frand splitRate
 
Frand helixGcDruck
 
Frand helixGcRate
 
Frand helixAtRate
 
Frand loopGcDruck
 
Frand loopGcRate
 
Frand loopAtRate
 
double transitionRate
 
double transversionRate
 
FILE * topo
 
FILE * seq
 

Typedef Documentation

typedef double SingleProb[BASETYPES]

Definition at line 14 of file rns.h.

typedef double DoubleProb[BASETYPES][BASETYPES]

Definition at line 15 of file rns.h.

typedef struct S_RNS * RNS

Function Documentation

RNS createOriginRNS ( )
void freeRNS ( RNS  rns)

Definition at line 278 of file rns.c.

References S_RNS::base.

Referenced by splitRNS().

void splitRNS ( int  no_of_father,
RNS  origin,
double  age,
int  steps,
int  depth 
)
void dumpDepths ( )

Definition at line 55 of file rns.c.

References maxDepth.

Referenced by ARB_main().

Variable Documentation

int orgLen

Definition at line 12 of file rns.c.

Referenced by createOriginRNS(), GBS_shorten_repeated_data(), and readSimCfg().

double orgHelixPart

Definition at line 13 of file rns.c.

Referenced by createOriginRNS().

int timeSteps

Definition at line 19 of file rns.c.

Referenced by ARB_main(), and readSimCfg().

Frand mrpb_Init

Definition at line 20 of file rns.c.

Referenced by readSimCfg().

Frand l2hrpb_Init

Definition at line 20 of file rns.c.

Referenced by readSimCfg().

Frand pairPart

Definition at line 20 of file rns.c.

Referenced by readSimCfg().

Frand mutationRate

Definition at line 20 of file rns.c.

Referenced by readSimCfg().

Frand splitRate

Definition at line 20 of file rns.c.

Referenced by readSimCfg().

Frand helixGcDruck

Definition at line 20 of file rns.c.

Referenced by readSimCfg().

Frand helixGcRate

Definition at line 20 of file rns.c.

Referenced by readSimCfg().

Frand helixAtRate

Definition at line 20 of file rns.c.

Referenced by readSimCfg().

Frand loopGcDruck

Definition at line 20 of file rns.c.

Referenced by readSimCfg().

Frand loopGcRate

Definition at line 20 of file rns.c.

Referenced by readSimCfg().

Frand loopAtRate

Definition at line 20 of file rns.c.

Referenced by readSimCfg().

double transitionRate

Definition at line 31 of file rns.c.

Referenced by calcMutationMatrix().

double transversionRate

Definition at line 31 of file rns.c.

Referenced by calcMutationMatrix().

FILE* topo

Definition at line 46 of file rns.c.

Referenced by ARB_main(), and splitRNS().

FILE * seq

Definition at line 46 of file rns.c.

Referenced by add_area_for_gde(), ali_family_member::ali_family_member(), ARB_main(), calculate_clusters(), ALI_PROFILE::cheapest_sequence(), ED4_manager::check_in_bases(), ED4_manager::check_out_bases(), compress_sequence_tree(), compressSeq(), convert(), LowDataCheck::count(), ImportTestData::countSpeciesAndData(), create_probe_design_variables(), export_sequence_data::detectVerticalGaps(), AP_sequence::do_lazy_load(), ED4_set_iupac(), embl_to_gcg(), enter_stage_1_build_tree(), FastSearchSequence::FastSearchSequence(), find_family(), findLeftmostProbe(), g_b_Consensus_add(), g_b_Consensus_get_sequence(), gbl_export_sequence(), gbl_read_seq_sai_or_species(), gbl_sequence(), genbank_to_gcg(), DesignTargets::generate(), MismatchWeights::get(), export_sequence_data::get_export_sequence(), get_match_hinfo_formatted(), get_match_overlay(), ST_ML::get_ml_vectors(), SequenceBuffer::getSequence(), ALI_MAP::insert_marker(), InsertDatainGDE(), macke_to_gcg(), main(), modsai_cb(), MP_new_sequence(), NT_count_different_chars(), case_op::operate(), unalign_op::operate(), perform_block_operation_on_part_of_sequence(), perform_block_operation_on_whole_sequence(), PT_prepare_species_sequence(), PT_start_design(), read_alignment(), readCompactedSequence(), reverseComplement(), ED4_SearchResults::search(), selected_probe_changed_cb(), seqFileFormatFp(), ALI_MAP::sequence(), ALI_MAP::sequence_without_inserts(), splitRNS(), to_macke(), to_paup(), to_printable(), trackAlignmentChanges(), XML_recursive(), export_sequence_data::~export_sequence_data(), and SequenceBuffer::~SequenceBuffer().