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model.h
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model.h
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#ifndef __MODEL_H__
#define __MODEL_H__
int AreDoublesEqual (MrBFlt x, MrBFlt y, MrBFlt tol);
int ChangeNumRuns (int from, int to);
int ChangeNumChains (int from, int to);
int CheckModel (void);
int DoesTreeSatisfyConstraints (Tree *t);
int DoLink (void);
int DoLinkParm (char *parmName, char *tkn);
int DoLset (void);
int DoLsetParm (char *parmName, char *tkn);
int DoPlot (void);
int DoPlotParm (char *parmName, char *tkn);
int DoPropset (void);
int DoPropsetParm (char *parmName, char *tkn);
int DoPrset (void);
int DoPrsetParm (char *parmName, char *tkn);
int DoQuit (void);
int DoReport (void);
int DoReportParm (char *parmName, char *tkn);
int DoShowMcmcTrees (void);
int DoShowModel (void);
int DoShowMoves (void);
int DoShowmovesParm (char *parmName, char *tkn);
int DoShowParams (void);
int DoStartvals (void);
int DoStartvalsParm (char *parmName, char *tkn);
int DoUnlink (void);
int FillNormalParams (RandLong *seed, int fromChain, int toChain);
int FillRelPartsString (Param *p, char **relPartString);
void FillStdStateFreqs (int chfrom, int chto, RandLong *seed);
int FillTopologySubParams (Param *param, int chn, int state, RandLong *seed);
int FillTreeParams (RandLong *seed, int fromChain, int toChain);
int FreeModel (void);
int GetEmpiricalFreqs (int *relParts, int nRelParts);
int GetNumDivisionChars (void);
int *GetParamIntVals (Param *parm, int chain, int state);
MrBFlt *GetParamStdStateFreqs (Param *parm, int chain, int state);
MrBFlt *GetParamSubVals (Param *parm, int chain, int state);
MrBFlt *GetParamVals (Param *parm, int chain, int state);
Tree *GetTree (Param *parm, int chain, int state);
Tree *GetTreeFromIndex (int index, int chain, int state);
int InitializeLinks (void);
int InitializeTreeCalibrations (Tree *t);
int Link (void);
int SetAARates (void);
int SetLocalTaxa (void);
int SetModelDefaults (void);
int SetMoves (void);
int SetUpAnalysis (RandLong *seed);
void SetUpMoveTypes (void);
int ShowModel (void);
int Unlink (void);
int UpdateClockRate (MrBFlt clockRate, int chain);
int UpdateCppEvolLengths (Param *param, TreeNode *p, int chain);
int UpdateTK02EvolLengths (Param *param, Tree *t, int chain);
int UpdateIgrBrachLengths (Param *param, Tree *t, int chain);
#endif /* __MODEL_H__ */