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_RNS *	RNS

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

(

)

Definition at line 157 of file rns.c.

References allocRNS(), assert, S_RNS::base, BASE_A, BASE_C, BASE_G, BASE_T, BASEQUAD, BASETYPES, freeSpreading(), getFrand(), S_RNS::helix, helixBaseChar, initBaseSpecificProbs(), isPairing, S_RNS::laufNr, loopBaseChar, newSpreading(), orgHelixPart, orgLen, S_RNS::pairing, s, and spreadRand().

Referenced by ARB_main().

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
	)

Definition at line 493 of file rns.c.

References S_RNS::base, S_RNS::bases, dumpRNS(), dupRNS(), fputc(), fputs(), freeRNS(), S_RNS::laufNr, maxDepth, mutateRNS(), seq, topo, and S_Frand::val.

Referenced by ARB_main(), and mutateRNS().

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(), split_data_into_parts(), splitRNS(), to_macke(), to_paup(), to_printable(), trackAlignmentChanges(), XML_recursive(), export_sequence_data::~export_sequence_data(), and SequenceBuffer::~SequenceBuffer().