4 int AreDoublesEqual (MrBFlt x, MrBFlt y, MrBFlt tol);
5 int ChangeNumRuns (int from, int to);
6 int ChangeNumChains (int from, int to);
8 int DoesTreeSatisfyConstraints (Tree *t);
10 int DoLinkParm (char *parmName, char *tkn);
12 int DoLsetParm (char *parmName, char *tkn);
14 int DoPlotParm (char *parmName, char *tkn);
16 int DoPropsetParm (char *parmName, char *tkn);
18 int DoPrsetParm (char *parmName, char *tkn);
21 int DoReportParm (char *parmName, char *tkn);
22 int DoShowMcmcTrees (void);
23 int DoShowModel (void);
24 int DoShowMoves (void);
25 int DoShowmovesParm (char *parmName, char *tkn);
26 int DoShowParams (void);
27 int DoStartvals (void);
28 int DoStartvalsParm (char *parmName, char *tkn);
30 int FillNormalParams (RandLong *seed, int fromChain, int toChain);
31 int FillRelPartsString (Param *p, char **relPartString);
32 void FillStdStateFreqs (int chfrom, int chto, RandLong *seed);
33 int FillTopologySubParams (Param *param, int chn, int state, RandLong *seed);
34 int FillTreeParams (RandLong *seed, int fromChain, int toChain);
36 int GetEmpiricalFreqs (int *relParts, int nRelParts);
37 int GetNumDivisionChars (void);
38 int *GetParamIntVals (Param *parm, int chain, int state);
39 MrBFlt *GetParamStdStateFreqs (Param *parm, int chain, int state);
40 MrBFlt *GetParamSubVals (Param *parm, int chain, int state);
41 MrBFlt *GetParamVals (Param *parm, int chain, int state);
42 Tree *GetTree (Param *parm, int chain, int state);
43 Tree *GetTreeFromIndex (int index, int chain, int state);
44 int InitializeLinks (void);
45 int InitializeTreeCalibrations (Tree *t);
47 int SetAARates (void);
48 int SetLocalTaxa (void);
49 int SetModelDefaults (void);
51 int SetUpAnalysis (RandLong *seed);
52 void SetUpMoveTypes (void);
55 int UpdateClockRate (MrBFlt clockRate, int chain);
56 int UpdateCppEvolLengths (Param *param, TreeNode *p, int chain);
57 int UpdateTK02EvolLengths (Param *param, Tree *t, int chain);
58 int UpdateIgrBrachLengths (Param *param, Tree *t, int chain);
60 #endif /* __MODEL_H__ */