ARB
Functions | Variables
rns.c File Reference
#include <limits.h>
#include <stdlib.h>
#include <memory.h>
#include "rns.h"
#include "spreadin.h"
Include dependency graph for rns.c:

Go to the source code of this file.

Functions

void dumpDepths ()
 
static void dumpRNS (RNS rns)
 
static void initBaseSpecificProbs (int bases)
 
static RNS allocRNS (int len)
 
RNS createOriginRNS ()
 
void freeRNS (RNS rns)
 
static RNS dupRNS (RNS rns)
 
static void calcMutationMatrix (DoubleProb mutationMatrix, double gcDruck, double gcRate, double atRate, double *pairProb)
 
static int calcPairTrials (double pairProb, double actPairPart)
 
static void mutateRNS (int no_of_father, RNS rns, int steps, int depth)
 
void splitRNS (int no_of_father, RNS origin, double age, int steps, int depth)
 

Variables

int orgLen
 
double orgHelixPart
 
static int rnsCreated
 
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
 
static double * mutationRatePerBase
 
static double * loop2helixRatePerBase
 
static int mrpb_anz
 
static int mrpb_allocated
 
static int l2hrpb_anz
 
static int l2hrpb_allocated
 
static DoubleProb helixMutationMatrix
 
static DoubleProb loopMutationMatrix
 
FILE * topo
 
FILE * seq
 
static int minDepth = INT_MAX
 
static int maxDepth = INT_MIN
 

Function Documentation

void dumpDepths ( )

Definition at line 55 of file rns.c.

References maxDepth.

Referenced by ARB_main().

static void dumpRNS ( RNS  rns)
static

Definition at line 59 of file rns.c.

References S_RNS::base, BASE_A, BASE_C, BASE_G, BASE_T, S_RNS::bases, BASETYPES, char2BaseType, and isHelical.

Referenced by splitRNS().

static void initBaseSpecificProbs ( int  bases)
static

Definition at line 127 of file rns.c.

References getFrand(), loop2helixRatePerBase, mutationRatePerBase, and outOfMemory.

Referenced by createOriginRNS().

static RNS allocRNS ( int  len)
static

Definition at line 145 of file rns.c.

References S_RNS::base, S_RNS::bases, and outOfMemory.

Referenced by createOriginRNS().

RNS createOriginRNS ( )
void freeRNS ( RNS  rns)

Definition at line 278 of file rns.c.

References S_RNS::base.

Referenced by splitRNS().

static RNS dupRNS ( RNS  rns)
static

Definition at line 282 of file rns.c.

References S_RNS::base, S_RNS::bases, S_RNS::laufNr, and outOfMemory.

Referenced by splitRNS().

static void calcMutationMatrix ( DoubleProb  mutationMatrix,
double  gcDruck,
double  gcRate,
double  atRate,
double *  pairProb 
)
static

Definition at line 296 of file rns.c.

References BASE_A, BASE_C, BASE_G, BASE_T, BASETYPES, transitionRate, and transversionRate.

Referenced by mutateRNS().

static int calcPairTrials ( double  pairProb,
double  actPairPart 
)
static

Definition at line 352 of file rns.c.

Referenced by mutateRNS().

static void mutateRNS ( int  no_of_father,
RNS  rns,
int  steps,
int  depth 
)
static
void splitRNS ( int  no_of_father,
RNS  origin,
double  age,
int  steps,
int  depth 
)

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 rnsCreated
static

Definition at line 14 of file rns.c.

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().

double* mutationRatePerBase
static

Definition at line 34 of file rns.c.

Referenced by initBaseSpecificProbs(), and mutateRNS().

double * loop2helixRatePerBase
static

Definition at line 34 of file rns.c.

Referenced by initBaseSpecificProbs().

int mrpb_anz
static

Definition at line 36 of file rns.c.

int mrpb_allocated
static

Definition at line 36 of file rns.c.

int l2hrpb_anz
static

Definition at line 36 of file rns.c.

int l2hrpb_allocated
static

Definition at line 36 of file rns.c.

DoubleProb helixMutationMatrix
static

Definition at line 40 of file rns.c.

Referenced by mutateRNS().

DoubleProb loopMutationMatrix
static

Definition at line 40 of file rns.c.

Referenced by mutateRNS().

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().

int minDepth = INT_MAX
static

Definition at line 52 of file rns.c.

int maxDepth = INT_MIN
static

Definition at line 53 of file rns.c.

Referenced by dumpDepths(), and splitRNS().