| 1 | int AreDoublesEqual (MrBFlt x, MrBFlt y, MrBFlt tol); |
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| 2 | int ChangeNumRuns (int from, int to); |
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| 3 | int ChangeNumChains (int from, int to); |
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| 4 | int CheckModel (void); |
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| 5 | int DoesTreeSatisfyConstraints(Tree *t); |
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| 6 | int DoLink (void); |
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| 7 | int DoLinkParm (char *parmName, char *tkn); |
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| 8 | int DoLset (void); |
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| 9 | int DoLsetParm (char *parmName, char *tkn); |
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| 10 | int DoPropset (void); |
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| 11 | int DoPropsetParm (char *parmName, char *tkn); |
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| 12 | int DoPrset (void); |
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| 13 | int DoPrsetParm (char *parmName, char *tkn); |
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| 14 | int DoReport (void); |
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| 15 | int DoReportParm (char *parmName, char *tkn); |
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| 16 | int DoShowMcmcTrees (void); |
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| 17 | int DoShowModel (void); |
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| 18 | int DoShowMoves (void); |
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| 19 | int DoShowmovesParm (char *parmName, char *tkn); |
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| 20 | int DoShowParams (void); |
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| 21 | int DoStartvals (void); |
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| 22 | int DoStartvalsParm (char *parmName, char *tkn); |
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| 23 | int DoUnlink (void); |
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| 24 | int FillNormalParams (SafeLong *seed, int fromChain, int toChain); |
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| 25 | int FillRelPartsString (Param *p, char **relPartString); |
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| 26 | void FillStdStateFreqs(int chfrom, int chto, SafeLong *seed); |
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| 27 | int FillTopologySubParams (Param *param, int chn, int state, SafeLong *seed); |
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| 28 | int FillTreeParams (SafeLong *seed, int fromChain, int toChain); |
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| 29 | int FreeModel (void); |
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| 30 | int GetEmpiricalFreqs (int *relParts, int nRelParts); |
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| 31 | int GetNumDivisionChars (void); |
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| 32 | int *GetParamIntVals (Param *parm, int chain, int state); |
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| 33 | MrBFlt *GetParamStdStateFreqs (Param *parm, int chain, int state); |
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| 34 | MrBFlt *GetParamSubVals (Param *parm, int chain, int state); |
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| 35 | MrBFlt *GetParamVals (Param *parm, int chain, int state); |
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| 36 | Tree *GetTree (Param *parm, int chain, int state); |
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| 37 | Tree *GetTreeFromIndex (int index, int chain, int state); |
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| 38 | int InitializeLinks (void); |
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| 39 | int InitializeTreeCalibrations (Tree *t); |
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| 40 | int Link (void); |
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| 41 | int SetAARates (void); |
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| 42 | int SetLocalTaxa (void); |
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| 43 | int SetModelDefaults (void); |
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| 44 | int SetMoves (void); |
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| 45 | int SetUpAnalysis (SafeLong *seed); |
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| 46 | void SetUpMoveTypes (void); |
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| 47 | int ShowModel (void); |
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| 48 | int Unlink (void); |
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| 49 | int UpdateTK02EvolLengths (Param *param, Tree *t, int chain); |
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| 50 | int UpdateClockRate(MrBFlt clockRate, int chain); |
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| 51 | int UpdateCppEvolLengths (Param *param, TreeNode *p, int chain); |
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| 52 | int UpdateIgrBranchRates (Param *param, Tree *t, int chain); |
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| 53 | |
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