#include <limits.h>
#include <stdlib.h>
#include <memory.h>
#include "rns.h"
#include "spreadin.h"

Include dependency graph for rns.c:

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 ( )

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().

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

Definition at line 369 of file rns.c.

References assert, S_RNS::base, S_RNS::bases, BASETYPES, calcMutationMatrix(), calcPairTrials(), char2BaseType, freeSpreading(), getFrand(), helixBaseChar, helixMutationMatrix, isDeleted, isHelical, isPairing, loopBaseChar, loopMutationMatrix, mutationRatePerBase, newSpreading(), S_RNS::pairing, randProb(), s, splitRNS(), and spreadRand().

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().

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