diff -ur mrbayes-3.1.2.new/Makefile mrbayes-3.1.2/Makefile --- mrbayes-3.1.2.new/Makefile 2006-08-08 16:26:36.000000000 +0200 +++ mrbayes-3.1.2/Makefile 2005-12-22 17:13:06.000000000 +0100 @@ -6,7 +6,6 @@ # Set MPI=yes for the parallel version MPI ?= no -_64BIT ?= no # Set DEBUG=yes for a debug version of mrbayes, otherwise set OPTFLAGS # to the desired optimization level (e.g. -O2 -fomit-frame-pointer for # less aggressive optimization than the default -O3) @@ -64,10 +63,6 @@ CFLAGS += $(OPTFLAGS) endif -ifeq ($(strip $(_64BIT)), yes) - CFLAGS += -D_64BIT -endif - CFLAGS += -Wall LIBS += -lm diff -ur mrbayes-3.1.2.new/bayes.c mrbayes-3.1.2/bayes.c --- mrbayes-3.1.2.new/bayes.c 2006-08-08 16:01:52.000000000 +0200 +++ mrbayes-3.1.2/bayes.c 2005-12-23 17:26:28.000000000 +0100 @@ -81,11 +81,11 @@ int defPairs; /* flag for whether pairs are read */ Doublet doublet[16]; /* holds information on states for doublets */ int fileNameChanged; /* has file name been changed ? */ -safeLong globalSeed; /* seed that is initialized at start up */ -int nBitsInALong; /* number of bits in a safeLong */ +long int globalSeed; /* seed that is initialized at start up */ +int nBitsInALong; /* number of bits in a long */ int readWord; /* should we read word next ? */ -safeLong runIDSeed; /* seed used only for determining run ID [stamp] */ -safeLong swapSeed; /* seed used only for determining which to swap */ +long int runIDSeed; /* seed used only for determining run ID [stamp] */ +long int swapSeed; /* seed used only for determining which to swap */ int userLevel; /* user level */ # if defined (MPI_ENABLED) @@ -143,7 +143,7 @@ # endif /*mtrace();*/ /* calculate the size of a long - used by bit manipulation functions */ - nBitsInALong = sizeof(safeLong) * 8; + nBitsInALong = sizeof(long) * 8; if (nBitsInALong > 32) /* Do not use more than 32 bits until we */ nBitsInALong = 32; /* understand how 64-bit longs are handled. */ @@ -401,7 +401,7 @@ if (proc_id == 0) { curTime = time(NULL); - globalSeed = (safeLong)curTime; + globalSeed = (long int)curTime; if (globalSeed < 0) globalSeed = -globalSeed; } @@ -414,7 +414,7 @@ if (proc_id == 0) { curTime = time(NULL); - swapSeed = (safeLong)curTime; + swapSeed = (long int)curTime; if (swapSeed < 0) swapSeed = -swapSeed; } @@ -427,7 +427,7 @@ if (proc_id == 0) { curTime = time(NULL); - runIDSeed = (safeLong)curTime; + runIDSeed = (long int)curTime; if (runIDSeed < 0) runIDSeed = -runIDSeed; } @@ -439,17 +439,17 @@ # else curTime = time(NULL); - globalSeed = (safeLong)curTime; + globalSeed = (long int)curTime; if (globalSeed < 0) globalSeed = -globalSeed; curTime = time(NULL); - swapSeed = (safeLong)curTime; + swapSeed = (long int)curTime; if (swapSeed < 0) swapSeed = -swapSeed; curTime = time(NULL); - runIDSeed = (safeLong)curTime; + runIDSeed = (long int)curTime; if (runIDSeed < 0) runIDSeed = -globalSeed; @@ -473,7 +473,7 @@ readWord = NO; /* should we read a word next ? */ fileNameChanged = NO; /* has the file name been changed ? */ echoMB = YES; /* flag used by Manual to control printing */ - longIntegerSize = sizeof(safeLong); /* size of an safeLong */ + longIntegerSize = sizeof(long int); /* size of an long integer */ # if defined (MPI_ENABLED) sprintf(manFileName, "commref_mb%sp.txt", VERSION_NUMBER); /* name of command reference file */ diff -ur mrbayes-3.1.2.new/command.c mrbayes-3.1.2/command.c --- mrbayes-3.1.2.new/command.c 2006-08-08 16:03:50.000000000 +0200 +++ mrbayes-3.1.2/command.c 2005-12-23 17:53:30.000000000 +0100 @@ -142,7 +142,7 @@ int StateCode_AA (int n); int StateCode_NUC4 (int n); int StateCode_Std (int n); -void WhatVariableExp (unignedSafeLong exp, char *st); +void WhatVariableExp (unsigned long int exp, char *st); char WhichAA (int x); MrBFlt WhichCont (int x); char WhichRes (int x); @@ -161,7 +161,7 @@ char *constraintNames; /* holds names of constraints */ int dataType; /* type of data */ int echoMB; /* flag used by Manual to prevent echoing */ -unignedSafeLong expecting; /* variable denoting expected token type */ +unsigned long int expecting; /* variable denoting expected token type */ int foundNewLine; /* whether a new line has been found */ int inComment; /* flag for whether input stream is commented */ int inferAncStates; /* should ancestral states be inferred (y/n) */ @@ -7348,13 +7348,13 @@ -unignedSafeLong Expecting (int y) +unsigned long int Expecting (int y) { - unignedSafeLong x; + unsigned long int x; - x = (unignedSafeLong)pow(2.0, (MrBFlt)y); + x = (unsigned long int)pow(2.0, (MrBFlt)y); return (x); @@ -12200,7 +12200,7 @@ -void WhatVariableExp (unignedSafeLong exp, char *st) +void WhatVariableExp (unsigned long int exp, char *st) { diff -ur mrbayes-3.1.2.new/command.h mrbayes-3.1.2/command.h --- mrbayes-3.1.2.new/command.h 2006-08-08 16:03:50.000000000 +0200 +++ mrbayes-3.1.2/command.h 2005-03-09 04:01:30.000000000 +0100 @@ -1,7 +1,7 @@ extern int AddToString (char *s1, char *s2, int *x); -extern unignedSafeLong Expecting (int y); +extern unsigned long int Expecting (int y); extern int CheckString (char *s1, char *s2, int *x); extern int CheckStringValidity (char *s); extern int DerootUserTree (TreeNode *p); diff -ur mrbayes-3.1.2.new/globals.h mrbayes-3.1.2/globals.h --- mrbayes-3.1.2.new/globals.h 2006-08-08 16:03:51.000000000 +0200 +++ mrbayes-3.1.2/globals.h 2005-12-22 22:34:40.000000000 +0100 @@ -17,11 +17,11 @@ extern int defTaxa; /* flag for whether number of taxa is known */ extern Doublet doublet[16]; /* holds information on states for doublets */ extern int echoMB; /* flag used by Manual to prevent echoing */ -extern unignedSafeLong expecting; /* variable denoting expected token type */ +extern long unsigned int expecting; /* variable denoting expected token type */ extern int fileNameChanged; /* has file name been changed? */ extern int foundNewLine; /* whether a new line has been found */ extern char gapId; /* gap character Id */ -extern safeLong globalSeed; /* seed that is initialized at start up */ +extern long int globalSeed; /* seed that is initialized at start up */ extern char *headerNames; /* string to hold headers in sump and plot */ extern int inComment; /* flag for whether input stream is commented */ extern int inferAncStates; /* should ancestral states be inferred (y/n) */ @@ -75,9 +75,9 @@ extern ReassembleInfo reassembleParams; /* holds parameters for reassemble command */ extern MrBFlt relConstraintProbs[30]; /* relative probs. of trees with constraint */ extern int replaceLogFile; /* should logfile be replace/appended to */ -extern safeLong runIDSeed; /* seed used only for generating run ID [stamp] */ +extern long int runIDSeed; /* seed used only for generating run ID [stamp] */ extern char spacer[10]; /* holds blanks for printing indentations */ -extern safeLong swapSeed; /* seed used only for determining which to swap */ +extern long int swapSeed; /* seed used only for determining which to swap */ extern Sump sumpParams; /* holds parameters for sump command */ extern Sumt sumtParams; /* holds parameters for sumt command */ extern char stamp[11]; /* holds a unique identifier for each analysis */ @@ -88,7 +88,7 @@ extern int theAmbigChar; /* int containing ambiguous character */ extern char *transFrom; /* translation block information */ extern char *transTo; /* translation block information */ -extern int longIntegerSize; /* size of an safeLong */ +extern int longIntegerSize; /* size of an long integer */ extern int userBrlensDef; /* are the branch lengths on user tree defined */ extern int userLevel; /* the level of the user */ extern Tree *userTree; /* user tree */ diff -ur mrbayes-3.1.2.new/mb.h mrbayes-3.1.2/mb.h --- mrbayes-3.1.2.new/mb.h 2006-08-08 16:03:51.000000000 +0200 +++ mrbayes-3.1.2/mb.h 2005-12-23 17:26:28.000000000 +0100 @@ -6,22 +6,6 @@ #endif #endif -/* found out that mrbayes crashes on 64 bit platform - especially in sumt function. If every long is substituted with - an int, it works. I'm going to define a safeLong and a unsigned - safeLong for 64 bit platforms... - Davide Cittaro - daweonline(at)gmail.com -*/ - -#ifdef _64BIT -typedef int safeLong; -typedef unsigned int unignedSafeLong; -#else -typedef long safeLong; -typedef long unsigned int unignedSafeLong; -#endif - - /* definition of UNIX_VERSION, WIN_VERSION or MAC_VERSION is now set in the Makefile file; for compilers not using a project file or Makefile, use the #defines above to select version */ @@ -370,8 +354,8 @@ struct node *left, *right, *anc; int memoryIndex, index, upDateCl, upDateTi, marked, x, y, scalerNode, isLocked, lockID, uL, dL, mL, isDated; - safeLong scalersSet[MAX_NUM_DIV_LONGS], clSpace[MAX_NUM_DIV_LONGS], tiSpace[MAX_NUM_DIV_LONGS]; - safeLong *partition; + long int scalersSet[MAX_NUM_DIV_LONGS], clSpace[MAX_NUM_DIV_LONGS], tiSpace[MAX_NUM_DIV_LONGS]; + long int *partition; char label[100]; MrBFlt length, nodeDepth, d, age; Calibration *calibration; @@ -405,7 +389,7 @@ int x, y, mark, index, memoryIndex, isLocked, lockID, isDated; MrBFlt length, support, f, age; char label[100]; - safeLong *partition; + long int *partition; Calibration *calibration; } PolyNode; @@ -561,7 +545,7 @@ #define OMEGA_10FFF 108 /* typedef for a MoveFxn */ -typedef int (MoveFxn)(Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +typedef int (MoveFxn)(Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); /* struct holding info on each move type that the program handles */ typedef struct @@ -788,7 +772,7 @@ int numStartPerts; /* number of perturbations to starting tree */ char chainStartTree[100]; /* starting tree for chain (random/user) */ int saveBrlens; /* should branch lengths be saved */ - safeLong chainSeed; /* random seed for chain */ + long int chainSeed; /* random seed for chain */ MrBFlt weightScheme[3]; /* percent chars to increase/decrease in weight */ int calcPbf; /* should we calculate the pseudo Bayes factor */ int pbfInitBurnin; /* initial burnin when calculating pseudo BF */ @@ -963,12 +947,12 @@ typedef struct doublet { - safeLong first, second; + long int first, second; } Doublet; typedef struct matrix { - safeLong *origin; + long *origin; int rowSize; int nRows; int column; diff -ur mrbayes-3.1.2.new/mbmath.c mrbayes-3.1.2/mbmath.c --- mrbayes-3.1.2.new/mbmath.c 2006-08-08 16:01:53.000000000 +0200 +++ mrbayes-3.1.2/mbmath.c 2005-12-23 17:26:28.000000000 +0100 @@ -90,7 +90,7 @@ void Exchange (int j, int k, int l, int m, int n, MrBFlt **a, MrBFlt *scale); MrBFlt Factorial (int x); void ForwardSubstitutionRow (int dim, MrBFlt **L, MrBFlt *b); -MrBFlt GammaRandomVariable (MrBFlt a, MrBFlt b, safeLong *seed); +MrBFlt GammaRandomVariable (MrBFlt a, MrBFlt b, long int *seed); void GaussianElimination (int dim, MrBFlt **a, MrBFlt **bMat, MrBFlt **xMat); int Hqr2 (int dim, int low, int high, MrBFlt **h, MrBFlt *wr, MrBFlt *wi, MrBFlt **z); MrBFlt IncompleteBetaFunction (MrBFlt alpha, MrBFlt beta, MrBFlt x); @@ -108,9 +108,9 @@ void PrintSquareDoubleMatrix (int dim, MrBFlt **matrix); void PrintSquareIntegerMatrix (int dim, int **matrix); complex ProductOfRealAndComplex (MrBFlt a, complex b); -MrBFlt RndGamma (MrBFlt s, safeLong *seed); -MrBFlt RndGamma1 (MrBFlt s, safeLong *seed); -MrBFlt RndGamma2 (MrBFlt s, safeLong *seed); +MrBFlt RndGamma (MrBFlt s, long int *seed); +MrBFlt RndGamma1 (MrBFlt s, long int *seed); +MrBFlt RndGamma2 (MrBFlt s, long int *seed); int SetQvalue (MrBFlt tol); void SetToIdentity (int dim, MrBFlt **matrix); MrBFlt Tha (MrBFlt h1, MrBFlt h2, MrBFlt a1, MrBFlt a2); @@ -1910,7 +1910,7 @@ | in the vector z. | ---------------------------------------------------------------------------------*/ -void DirichletRandomVariable (MrBFlt *alp, MrBFlt *z, int n, safeLong *seed) +void DirichletRandomVariable (MrBFlt *alp, MrBFlt *z, int n, long int *seed) { @@ -2578,7 +2578,7 @@ | a and b. The mean is E(X) = a / b and the variance is Var(X) = a / b^2. | ---------------------------------------------------------------------------------*/ -MrBFlt GammaRandomVariable (MrBFlt a, MrBFlt b, safeLong *seed) +MrBFlt GammaRandomVariable (MrBFlt a, MrBFlt b, long int *seed) { @@ -4746,11 +4746,11 @@ | ones are hard to find. Communications of the ACM, 31(10):1192-1201. | ---------------------------------------------------------------------------------*/ -MrBFlt RandomNumber (safeLong *seed) +MrBFlt RandomNumber (long int *seed) { - safeLong lo, hi, test; + long int lo, hi, test; hi = (*seed) / 127773; lo = (*seed) % 127773; @@ -4772,7 +4772,7 @@ | RndGamma | ---------------------------------------------------------------------------------*/ -MrBFlt RndGamma (MrBFlt s, safeLong *seed) +MrBFlt RndGamma (MrBFlt s, long int *seed) { @@ -4800,7 +4800,7 @@ | RndGamma1 | ---------------------------------------------------------------------------------*/ -MrBFlt RndGamma1 (MrBFlt s, safeLong *seed) +MrBFlt RndGamma1 (MrBFlt s, long int *seed) { @@ -4844,7 +4844,7 @@ | RndGamma2 | ---------------------------------------------------------------------------------*/ -MrBFlt RndGamma2 (MrBFlt s, safeLong *seed) +MrBFlt RndGamma2 (MrBFlt s, long int *seed) { diff -ur mrbayes-3.1.2.new/mbmath.h mrbayes-3.1.2/mbmath.h --- mrbayes-3.1.2.new/mbmath.h 2006-08-08 16:01:53.000000000 +0200 +++ mrbayes-3.1.2/mbmath.h 2005-03-09 04:01:30.000000000 +0100 @@ -15,7 +15,7 @@ void CalcCijk (int dim, MrBFlt *c_ijk, MrBFlt **u, MrBFlt **v); void CopyComplexMatrices (int dim, complex **from, complex **to); void CopyDoubleMatrices (int dim, MrBFlt **from, MrBFlt **to); -void DirichletRandomVariable (MrBFlt *alp, MrBFlt *z, int n, safeLong *seed); +void DirichletRandomVariable (MrBFlt *alp, MrBFlt *z, int n, long int *seed); int DiscreteGamma (MrBFlt *rK, MrBFlt alfa, MrBFlt beta, int K, int median); void FreeSquareComplexMatrix (complex **m); void FreeSquareDoubleMatrix (MrBFlt **m); @@ -25,4 +25,4 @@ void MultiplyMatrices (int dim, MrBFlt **a, MrBFlt **b, MrBFlt **result); int MultiplyMatrixNTimes (int dim, MrBFlt **Mat, int power, MrBFlt **Result); MrBFlt QuantileGamma (MrBFlt x, MrBFlt alfa, MrBFlt beta); -MrBFlt RandomNumber (safeLong *seed); +MrBFlt RandomNumber (long int *seed); diff -ur mrbayes-3.1.2.new/mcmc.c mrbayes-3.1.2/mcmc.c --- mrbayes-3.1.2.new/mcmc.c 2006-08-08 16:01:53.000000000 +0200 +++ mrbayes-3.1.2/mcmc.c 2005-12-23 17:26:28.000000000 +0100 @@ -139,21 +139,21 @@ struct pfnode *left; struct pfnode *right; int *count; - safeLong *partition; + long *partition; } PFNODE; /* local prototypes */ int AddDummyChars (void); int AddTreeSamples (int from, int to); -PFNODE *AddPartition (PFNODE *r, safeLong *p, int runId); +PFNODE *AddPartition (PFNODE *r, long *p, int runId); int AddToPrintString (char *tempStr); int AddTreeToPartitionCounters (Tree *tree, int treeId, int runId); Tree *AllocateTree (int numTaxa, int isTreeRooted); -int AttemptSwap (int swapA, int swapB, safeLong *seed); -int Bit (int n, safeLong *p); +int AttemptSwap (int swapA, int swapB, long int *seed); +int Bit (int n, long *p); int BuildConstraintTree (Tree *t, PolyTree *pt); void BuildExhaustiveSearchTree (Tree *t, int chain, int nTaxInTree, TreeInfo *tInfo); -int BuildStartTree (Tree *t, safeLong *seed); +int BuildStartTree (Tree *t, long int *seed); int CalcLike_Adgamma (int d, Param *param, int chain, MrBFlt *lnL); void CalcPartFreqStats (PFNODE *p, STATS *stat); void CalculateTopConvDiagn (int numSamples); @@ -214,12 +214,12 @@ # endif int ExhaustiveParsimonySearch (Tree *t, int chain, TreeInfo *tInfo); int ExtendChainQuery (); -int FillNormalParams (safeLong *seed); +int FillNormalParams (long int *seed); int FillNumSitesOfPat (void); int FillRelPartsString (Param *p, char relPartString[100]); -int FillTreeParams (safeLong *seed); +int FillTreeParams (long int *seed); int Flip01 (int x); -void FlipOneBit (int n, safeLong *p); +void FlipOneBit (int n, long *p); void FreeChainMemory (void); void FreeTree (Tree *t); void GetChainIds (void); @@ -237,7 +237,7 @@ void GetPossibleAAs (int aaCode, int aa[]); void GetPossibleNucs (int nucCode, int nuc[]); void GetPossibleRestrictionSites (int resSiteCode, int *sites); -int GetRandomEmbeddedSubtree (Tree *t, int nTerminals, safeLong *seed, int *nEmbeddedTrees); +int GetRandomEmbeddedSubtree (Tree *t, int nTerminals, long *seed, int *nEmbeddedTrees); MrBFlt GetRate (int division, int chain); void GetSprParsimonyLengths (int chain, int nNodes1, int nNodes2, TreeNode **subTree1DP, TreeNode **subTree2DP, TreeNode *root2, MrBFlt *pLengths); void GetStamp (void); @@ -253,13 +253,13 @@ int InitSprParsSets (void); int InitTermCondLikes (void); void InitTreeNode (TreeNode *p); -int IsBitSet (int i, safeLong *bits); +int IsBitSet (int i, long *bits); int IsClockSatisfied (Tree *t, MrBFlt tol); int IsCalibratedClockSatisfied (Tree *t, MrBFlt tol); int IsPFNodeEmpty (PFNODE *p); void JukesCantor (MrBFlt *tiP, MrBFlt length); PFNODE *LargestNonemptyPFNode (PFNODE *p, int *i, int j); -safeLong LastBlock (FILE *fp, char *lineBuf, int longestLine); +long LastBlock (FILE *fp, char *lineBuf, int longestLine); int Likelihood_Adgamma (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats); int Likelihood_Gen (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats); int Likelihood_NUC4 (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats); @@ -279,62 +279,62 @@ void MarkClsBelow (TreeNode *p); MrBFlt MaximumValue (MrBFlt x, MrBFlt y); MrBFlt MinimumValue (MrBFlt x, MrBFlt y); -int Move_Aamodel (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Adgamma (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Beta (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Beta_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_BiasedSpr (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_BrLen (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Extinction (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Extinction_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_ExtSPR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_ExtSPR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_ExtSPRClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_ExtSS (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_ExtTBR (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_ExtTBR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_ExtTBR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_ExtTBR3 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_ExtTBR4 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_GammaShape_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Growth (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Local (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_LocalClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_NNI (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_NNI_Hetero (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_NodeSlider (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_NodeSliderClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Omega (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Omega_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_OmegaBeta_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_OmegaCat (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_OmegaGamma_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_OmegaNeu (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_OmegaPos (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_OmegaPur (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_ParsEraser1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Pinvar (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_RanSPR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_RanSPR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_RanSPR3 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_RanSPR4 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_RateMult_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Revmat_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Speciation (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Speciation_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_SPRClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Statefreqs (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_StatefreqsSymDirMultistate (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_SwitchRate (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_SwitchRate_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Theta (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_Tratio_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_TreeHeight (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -int Move_UnrootedSlider (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Aamodel (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Adgamma (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Beta (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Beta_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_BiasedSpr (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_BrLen (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Extinction (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Extinction_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_ExtSPR1 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_ExtSPR2 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_ExtSPRClock (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_ExtSS (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_ExtTBR (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_ExtTBR1 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_ExtTBR2 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_ExtTBR3 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_ExtTBR4 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_GammaShape_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Growth (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Local (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_LocalClock (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_NNI (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_NNI_Hetero (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_NodeSlider (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_NodeSliderClock (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Omega (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Omega_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_OmegaBeta_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_OmegaCat (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_OmegaGamma_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_OmegaNeu (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_OmegaPos (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_OmegaPur (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_ParsEraser1 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Pinvar (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_RanSPR1 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_RanSPR2 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_RanSPR3 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_RanSPR4 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_RateMult_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Revmat_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Speciation (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Speciation_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_SPRClock (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Statefreqs (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_StatefreqsSymDirMultistate (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_SwitchRate (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_SwitchRate_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Theta (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_Tratio_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_TreeHeight (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); +int Move_UnrootedSlider (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); void NodeToNodeDistances (Tree *t, TreeNode *fromNode); int NumNonExcludedChar (void); int NumNonExcludedTaxa (void); -int PickProposal (safeLong *seed); +int PickProposal (long int *seed); int PosSelProbs (TreeNode *p, int division, int chain); int PreparePrintFiles (void); int PrintAncStates_Bin (TreeNode *p, int division, int chain); @@ -361,19 +361,19 @@ int PrintTree (int curGen, Tree *tree); int ProcessStdChars (void); int PruneTree (Tree *t); -int RandResolve (Tree *destination, PolyTree *t, safeLong *seed); +int RandResolve (Tree *destination, PolyTree *t, long *seed); # if defined (MPI_ENABLED) int ReassembleMoveInfo (void); int ReassembleSwapInfo (void); # endif int RecreateTree (Tree *t, char *s); -int RemovePartition (PFNODE *r, safeLong *p, int runId); +int RemovePartition (PFNODE *r, long *p, int runId); int RemoveTreeFromPartitionCounters (Tree *tree, int treeId, int runId); int RemoveTreeSamples (int from, int to); int ReopenMBPrintFiles (void); int RequestAbortRun(void); int ResetScalers (void); -int RunChain (safeLong *seed); +int RunChain (long int *seed); int SaveSprintf(char **target, int *targetLen, char *fmt, ...); int SetAARates (void); int SetChainParams (void); @@ -454,9 +454,9 @@ int *compColPos; /* column position in compressed matrix */ int *termState = NULL; /* index to terminal state ti:s */ int *isPartAmbig = NULL; /* does terminal taxon have partial ambiguity */ -safeLong *compMatrix; /* compressed character matrix */ -safeLong *parsMatrix = NULL; /* parsimony (bitset) matrix for terminals */ -safeLong *parsSets = NULL; /* parsimony (bitset) matrix for int nodes */ +long int *compMatrix; /* compressed character matrix */ +long int *parsMatrix = NULL; /* parsimony (bitset) matrix for terminals */ +long int *parsSets = NULL; /* parsimony (bitset) matrix for int nodes */ CLFlt *numSitesOfPat; /* no. sites of each pattern */ CLFlt *termCondLikes = NULL; /* cond likes for terminals */ CLFlt *chainCondLikes; /* cond likes for chains */ @@ -473,16 +473,16 @@ int *nAccepted; /* counter of accepted moves */ CLFlt **chainCLPtrSpace; /* space holding pointers to cond likes */ CLFlt ***condLikePtr; /* pointers to cond likes for chain and node */ -safeLong **parsPtrSpace = NULL; /* space holding pointers to parsimony sets */ -safeLong ***parsPtr = NULL; /* pointers to pars state sets for chain & node */ +long **parsPtrSpace = NULL; /* space holding pointers to parsimony sets */ +long ***parsPtr = NULL; /* pointers to pars state sets for chain & node */ CLFlt *parsNodeLengthSpace = NULL; /* space for parsimony node lengths */ CLFlt **parsNodeLen = NULL; /* pointers to pars node lengths for chains */ char *printString; /* string for printing to a file */ size_t printStringSize; /* length of printString */ -safeLong *sprParsMatrix; /* SPR parsimony (bitset) matrix for terminals */ -safeLong *sprParsSets; /* SPR parsimony (bitset) matrix for all nodes */ -safeLong **sprParsPtrSpace; /* space holding pointers to SPR parsimony sets */ -safeLong ***sprParsPtr; /* ptrs to SPR pars state sets for chain & node */ +long int *sprParsMatrix; /* SPR parsimony (bitset) matrix for terminals */ +long int *sprParsSets; /* SPR parsimony (bitset) matrix for all nodes */ +long **sprParsPtrSpace; /* space holding pointers to SPR parsimony sets */ +long ***sprParsPtr; /* ptrs to SPR pars state sets for chain & node */ int sprParsMatrixRowSize; /* row size of SPR parsimony matrix */ CLFlt *treeScalerSpace; /* space holding tree scalers */ CLFlt **treeScaler; /* pointers to tree scalers for each chain */ @@ -535,7 +535,7 @@ /*MrBFlt*/int abortMove; /* flag determining whether to abort move */ PFNODE **partFreqTreeRoot; /* root of tree(s) holding partition freqs */ int nLongsNeeded; /* number of longs needed for partitions */ -safeLong **partition; /* matrix holding partitions */ +long **partition; /* matrix holding partitions */ MrBFlt *maxLnL0 = NULL; /* maximum likelihood */ FILE *fpMcmc = NULL; /* pointer to .mcmc file */ FILE **fpParm = NULL; /* pointer to .p file(s) */ @@ -561,7 +561,7 @@ int i, j, k, d, numIncompatible, numDeleted, numStdChars, oldRowSize, newRowSize, numDummyChars, newColumn, newChar, oldColumn, oldChar, isCompat, *tempChar, numIncompatibleChars; - safeLong *tempMatrix; + long *tempMatrix; CLFlt *tempSitesOfPat; ModelInfo *m; ModelParams *mp; @@ -626,7 +626,7 @@ numCompressedChars += numDummyChars; /* allocate space for new data */ - tempMatrix = (safeLong *) calloc (numLocalTaxa * newRowSize, sizeof(safeLong)); + tempMatrix = (long *) calloc (numLocalTaxa * newRowSize, sizeof(long)); tempSitesOfPat = (CLFlt *) calloc (numCompressedChars, sizeof(CLFlt)); tempChar = (int *) calloc (compMatrixRowSize, sizeof(int)); if (!tempMatrix || !tempSitesOfPat || !tempChar) @@ -838,7 +838,7 @@ /* AddPartition: Add a partition to the tree keeping track of partition frequencies */ -PFNODE *AddPartition (PFNODE *r, safeLong *p, int runId) +PFNODE *AddPartition (PFNODE *r, long *p, int runId) { int i, comp; @@ -935,7 +935,7 @@ int AddTreeSamples (int from, int to) { int i, j, k, longestLine; - safeLong lastBlock; + long lastBlock; char *word, *s, *lineBuf; FILE *fp; Tree *t; @@ -1115,7 +1115,7 @@ -int AttemptSwap (int swapA, int swapB, safeLong *seed) +int AttemptSwap (int swapA, int swapB, long int *seed) { @@ -1583,15 +1583,15 @@ /*---------------------------------------------------------------- | -| Bit: return 1 if bit n is set in safeLong *p +| Bit: return 1 if bit n is set in long *p | else return 0 | -----------------------------------------------------------------*/ -int Bit (int n, safeLong *p) +int Bit (int n, long *p) { - safeLong x; + long x; p += n / nBitsInALong; x = 1 << (n % nBitsInALong); @@ -1617,11 +1617,11 @@ { int i, j, k, k1, nLongsNeeded, nextNode, nextActiveConstraint; - safeLong *constraintPartition, *mask; + long int *constraintPartition, *mask; PolyNode *pp, *qq, *rr, *ss, *tt; nLongsNeeded = (numLocalTaxa / nBitsInALong) + 1; - constraintPartition = (safeLong *) calloc (2*nLongsNeeded, sizeof(safeLong)); + constraintPartition = (long int *) calloc (2*nLongsNeeded, sizeof(long int)); if (!constraintPartition) { MrBayesPrint ("%s Problems allocating constraintPartition in BuildConstraintTree", spacer); @@ -1898,7 +1898,7 @@ | BuildStartTree: Build one starting tree | ----------------------------------------------------------------*/ -int BuildStartTree (Tree *t, safeLong *seed) +int BuildStartTree (Tree *t, long int *seed) { @@ -1909,7 +1909,7 @@ PolyTree constraintTree; Tree *tempTree; char tempName[100]; - safeLong *bitsets; + long int *bitsets; /* set pointers allocated locally to NULL for correct exit on error */ tempNums = NULL; @@ -1955,7 +1955,7 @@ /* make random tree consistent with constraints */ /* first allocate space for partition specifiers and polytomous tree */ nLongsNeeded = (numLocalTaxa / nBitsInALong) + 1; - bitsets = (safeLong *) calloc (2*numLocalTaxa*nLongsNeeded, sizeof(safeLong)); + bitsets = (long int *) calloc (2*numLocalTaxa*nLongsNeeded, sizeof(long int)); if (bitsets == NULL) { MrBayesPrint ("%s Problem allocating space for bitsets in BuildStartTree", spacer); @@ -2595,7 +2595,7 @@ { int c, i, j, nRates, posit; - safeLong inHMM; + long int inHMM; MrBFlt logScaler, max, prob, *F, *oldF, *tempF, fSpace[2][MAX_GAMMA_CATS]; MrBFlt *rP; @@ -3054,15 +3054,15 @@ { int a, b, i, j, k, nLongsNeeded; - safeLong *constraintPartition, *mask, *bitsets; + long int *constraintPartition, *mask, *bitsets; TreeNode *p=NULL; /* allocate space */ nLongsNeeded = (numLocalTaxa / nBitsInALong) + 1; - bitsets = (safeLong *) calloc ((t->nNodes + 1)*nLongsNeeded + /*1*/ + bitsets = (long int *) calloc ((t->nNodes + 1)*nLongsNeeded + /*1*/ 1+numLocalTaxa/nBitsInALong+1, - sizeof(safeLong)); + sizeof(long int)); if (!bitsets) { @@ -3494,12 +3494,12 @@ { int a, b, i, j, k, nLongsNeeded, foundIt, nextActiveConstraint; - safeLong *constraintPartition, *mask, *bitsets; + long int *constraintPartition, *mask, *bitsets; TreeNode *p; /* allocate space */ nLongsNeeded = (numLocalTaxa / nBitsInALong) + 1; - bitsets = (safeLong *) calloc (2*nLongsNeeded*numLocalTaxa + 2, sizeof(safeLong)); + bitsets = (long int *) calloc (2*nLongsNeeded*numLocalTaxa + 2, sizeof(long int)); if (!bitsets) { MrBayesPrint ("%s Problems allocating bitsets in CheckSetConstraints", spacer); @@ -3730,7 +3730,7 @@ int a, c, d, i, j, k, t, col[3], isSame, newRow, newColumn, *isTaken, *tempSitesOfPat, *tempChar; - safeLong *tempMatrix; + long *tempMatrix; ModelInfo *m; ModelParams *mp; @@ -3780,7 +3780,7 @@ /* allocate space for temporary matrix, tempSitesOfPat, */ /* vector keeping track of whether a character has been compressed, */ /* and vector indexing first original char for each compressed char */ - tempMatrix = (safeLong *) calloc (numLocalTaxa * numLocalChar, sizeof(safeLong)); + tempMatrix = (long *) calloc (numLocalTaxa * numLocalChar, sizeof(long)); tempSitesOfPat = (int *) calloc (numLocalChar, sizeof(int)); isTaken = (int *) calloc (numChar, sizeof(int)); tempChar = (int *) calloc (numLocalChar, sizeof(int)); @@ -3967,10 +3967,10 @@ MrBayesPrint ("%s compMatrix not free in CompressData\n", spacer); goto errorExit; } - compMatrix = (safeLong *) calloc (compMatrixRowSize * numLocalTaxa, sizeof(safeLong)); + compMatrix = (long *) calloc (compMatrixRowSize * numLocalTaxa, sizeof(long)); if (!compMatrix) { - MrBayesPrint ("%s Problem allocating compMatrix (%d)\n", spacer, compMatrixRowSize * numLocalTaxa * sizeof(safeLong)); + MrBayesPrint ("%s Problem allocating compMatrix (%d)\n", spacer, compMatrixRowSize * numLocalTaxa * sizeof(long)); goto errorExit; } memAllocs[ALLOC_COMPMATRIX] = YES; @@ -6913,7 +6913,7 @@ int i, j, k, d, nParsStatesForCont, nuc1, nuc2, nuc3, newColumn, codingNucCode, allNucCode, allAmbig; - safeLong x, x1, x2, x3, *longPtr; + long x, x1, x2, x3, *longPtr; ModelInfo *m; ModelParams *mp; @@ -6932,7 +6932,7 @@ mp = &modelParams[d]; m->parsMatrixStart = parsMatrixRowSize; - /* find how many parsimony ints (safeLong) are needed for each model site */ + /* find how many parsimony ints (long) are needed for each model site */ if (mp->dataType == CONTINUOUS) { /* scale continuous characters down to an ordered parsimony character */ @@ -6953,7 +6953,7 @@ MrBayesPrint ("%s parsMatrix not free in CreateParsMatrix\n", spacer); return (ERROR); } - parsMatrix = (safeLong *) calloc (parsMatrixRowSize * numLocalTaxa, sizeof(safeLong)); + parsMatrix = (long *) calloc (parsMatrixRowSize * numLocalTaxa, sizeof(long)); if (!parsMatrix) { MrBayesPrint ("%s Problem allocating parsMatrix\n", spacer); @@ -7227,7 +7227,7 @@ { - safeLong seed, numGlobalChains; + long int seed, numGlobalChains; int rc; # if defined (MPI_ENABLED) @@ -8662,7 +8662,7 @@ | FillNormalParams: Allocate and fill in non-tree parameters | -------------------------------------------------------------------------*/ -int FillNormalParams (safeLong *seed) +int FillNormalParams (long int *seed) { @@ -9559,7 +9559,7 @@ | FillTreeParams: Fill in trees and branch lengths | ------------------------------------------------------------------*/ -int FillTreeParams (safeLong *seed) +int FillTreeParams (long int *seed) { @@ -9894,14 +9894,14 @@ /*----------------------------------------------------------------- | -| FlipOneBit: flip bit n in safeLong *p +| FlipOneBit: flip bit n in long *p | ------------------------------------------------------------------*/ -void FlipOneBit (int n, safeLong *p) +void FlipOneBit (int n, long *p) { - safeLong x; + long x; p += n/nBitsInALong; x = 1 << (n % nBitsInALong); @@ -10562,7 +10562,7 @@ { int c, i, n, division; - safeLong *pL, *pR, *pP, *pA, x; + long *pL, *pR, *pP, *pA, x; CLFlt *nSitesOfPat; TreeNode *p; ModelInfo *m; @@ -10635,7 +10635,7 @@ { int c, i, n, division; - safeLong *pL, *pR, *pP, x; + long *pL, *pR, *pP, x; CLFlt *nSitesOfPat; TreeNode *p; ModelInfo *m; @@ -10684,7 +10684,7 @@ { int c, i, n, division; - safeLong *pL, *pR, *pP, *pA, x; + long *pL, *pR, *pP, *pA, x; CLFlt *nSitesOfPat; MrBFlt length; TreeNode *p; @@ -10759,7 +10759,7 @@ { int c, i, n, division; - safeLong *pD, *pP, *pA, x; + long *pD, *pP, *pA, x; TreeNode *p; ModelInfo *m; @@ -10994,7 +10994,7 @@ -int GetRandomEmbeddedSubtree (Tree *t, int nTerminals, safeLong *seed, int *nEmbeddedTrees) +int GetRandomEmbeddedSubtree (Tree *t, int nTerminals, long *seed, int *nEmbeddedTrees) { @@ -11142,7 +11142,7 @@ { int i, j, c, d; - safeLong *cl, *clL, *clR, *clA, *clU, *clM, x, y, z; + long *cl, *clL, *clR, *clA, *clU, *clM, x, y, z; CLFlt temp1, temp2=0.0; CLFlt *nSitesOfPat; TreeNode *p, *q; @@ -11506,7 +11506,7 @@ int i, j, k, n, c, d, s, chain, nObs, chosen, oneMatSize, nNodes, nScalerNodes, numReps; - safeLong *charBits; + long *charBits; ModelInfo *m; ModelParams *mp; CLFlt *clPtr; @@ -12232,7 +12232,7 @@ { int c, d, i, s, invCondLikeSize, isConstant; - safeLong *charBits; + long int *charBits; MrBFlt *cI; ModelInfo *m; ModelParams *mp; @@ -12384,7 +12384,7 @@ { int i, j, k, d, chain, nIntNodes, nNodes, nParsSets; - safeLong *ptr; + long *ptr; ModelInfo *m; /* Calculate number of nodes and number of internal nodes for rooted tree (worst case) */ @@ -12417,9 +12417,9 @@ MrBayesPrint ("%s Space for parsimony state sets not free in InitParsSets\n", spacer); return ERROR; } - parsSets = (safeLong *) calloc (numLocalChains * nIntNodes * nParsSets * 2, sizeof(safeLong)); - parsPtrSpace = (safeLong **) SafeMalloc (numLocalChains * nNodes * sizeof(safeLong *)); - parsPtr = (safeLong ***) SafeMalloc (numLocalChains * sizeof(safeLong **)); + parsSets = (long *) calloc (numLocalChains * nIntNodes * nParsSets * 2, sizeof(long)); + parsPtrSpace = (long **) SafeMalloc (numLocalChains * nNodes * sizeof(long *)); + parsPtr = (long ***) SafeMalloc (numLocalChains * sizeof(long **)); parsNodeLengthSpace = (CLFlt *) calloc (numLocalChains * parsNodeLenRowSize * 2, sizeof (CLFlt)); parsNodeLen = (CLFlt **) SafeMalloc (numLocalChains * sizeof(CLFlt *)); if (!parsSets || !parsPtrSpace || !parsPtr || !parsNodeLengthSpace || !parsNodeLen) @@ -12520,7 +12520,7 @@ { int c, i, j, d, chain, nIntNodes, nNodes; - safeLong *ptr, x; + long *ptr, x; ModelInfo *m; /* Calculate number of nodes and number of internal nodes for rooted tree (worst case) */ @@ -12537,10 +12537,10 @@ MrBayesPrint ("%s Space for SPR parsimony state sets not free in InitSprParsSets\n", spacer); return ERROR; } - sprParsMatrix = (safeLong *) calloc (sprParsMatrixRowSize * numLocalTaxa, sizeof(safeLong)); - sprParsSets = (safeLong *) calloc (numLocalChains * nNodes * sprParsMatrixRowSize * 3, sizeof(safeLong)); - sprParsPtrSpace = (safeLong **) SafeMalloc (numLocalChains * nNodes * sizeof(safeLong *)); - sprParsPtr = (safeLong ***) SafeMalloc (numLocalChains * sizeof(safeLong **)); + sprParsMatrix = (long *) calloc (sprParsMatrixRowSize * numLocalTaxa, sizeof(long)); + sprParsSets = (long *) calloc (numLocalChains * nNodes * sprParsMatrixRowSize * 3, sizeof(long)); + sprParsPtrSpace = (long **) SafeMalloc (numLocalChains * nNodes * sizeof(long *)); + sprParsPtr = (long ***) SafeMalloc (numLocalChains * sizeof(long **)); if (!sprParsMatrix || !sprParsSets || !sprParsPtrSpace || !sprParsPtr) { if (sprParsMatrix) @@ -12653,7 +12653,7 @@ int c, d, i, j, k, s, maxRates, numReps, oneMatSize, corrModel[MAX_NUM_DIVS]; - safeLong *charBits; + long int *charBits; CLFlt *cL; ModelInfo *m; ModelParams *mp=NULL; @@ -12970,11 +12970,11 @@ -int IsBitSet (int i, safeLong *bits) +int IsBitSet (int i, long *bits) { - safeLong x; + long x; bits += i / nBitsInALong; @@ -13341,9 +13341,9 @@ /* LastBlock: Return file position of last block in file */ -safeLong LastBlock (FILE *fp, char *lineBuf, int longestLine) +long LastBlock (FILE *fp, char *lineBuf, int longestLine) { - safeLong lastBlock; + long lastBlock; char *word; lastBlock = 0L; @@ -14085,7 +14085,7 @@ { int c, i, nStates; - safeLong done, *pL, *pR, *pP, *pA, *oldpP, x; + long done, *pL, *pR, *pP, *pA, *oldpP, x; CLFlt nParsChars, treeLength; CLFlt length, *nSitesOfPat, *newNodeLength, oldNodeLength; Tree *t; @@ -14266,7 +14266,7 @@ { int c, i, *nStates; - safeLong *pL, *pR, *pP, *pA, *oldpP, x; + long *pL, *pR, *pP, *pA, *oldpP, x; CLFlt *treeLength; CLFlt *nSitesOfPat; Tree *t; @@ -15095,7 +15095,7 @@ -int Move_Aamodel (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Aamodel (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -15212,7 +15212,7 @@ -int Move_Adgamma (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Adgamma (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -15280,7 +15280,7 @@ -int Move_Beta (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Beta (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -15411,7 +15411,7 @@ | TODO: Smart update of tiprobs, rnd insert both ends of | the moved branch on attachment branch ----------------------------------------------------------------*/ -int Move_BiasedSpr (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_BiasedSpr (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -16013,7 +16013,7 @@ -int Move_BrLen (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_BrLen (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -16095,7 +16095,7 @@ -int Move_TreeHeight (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_TreeHeight (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -16294,7 +16294,7 @@ -int Move_Extinction (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Extinction (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -16389,7 +16389,7 @@ -int Move_Extinction_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Extinction_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -16484,7 +16484,7 @@ -int Move_ExtSPR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_ExtSPR1 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -17020,7 +17020,7 @@ -int Move_ExtSPR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_ExtSPR2 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -17562,7 +17562,7 @@ -int Move_ExtSPRClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_ExtSPRClock (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -17927,7 +17927,7 @@ -int Move_ExtSS (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_ExtSS (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -18471,7 +18471,7 @@ -int Move_ExtTBR (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_ExtTBR (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -18934,7 +18934,7 @@ -int Move_ExtTBR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_ExtTBR1 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -19456,7 +19456,7 @@ -int Move_ExtTBR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_ExtTBR2 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -20032,7 +20032,7 @@ -int Move_ExtTBR3 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_ExtTBR3 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -20648,7 +20648,7 @@ -int Move_ExtTBR4 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_ExtTBR4 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -21171,7 +21171,7 @@ -int Move_GammaShape_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_GammaShape_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -21261,7 +21261,7 @@ -int Move_Growth (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Growth (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -21382,7 +21382,7 @@ | the boundary conditions into account | ----------------------------------------------------------------*/ -int Move_Local (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Local (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -21699,7 +21699,7 @@ | does not change tree height. | ----------------------------------------------------------------*/ -int Move_LocalClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_LocalClock (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -22186,7 +22186,7 @@ /* change topology using NNI */ -int Move_NNI (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_NNI (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -22259,7 +22259,7 @@ /* change topology with unlinked brlens using NNI */ -int Move_NNI_Hetero (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_NNI_Hetero (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -22465,7 +22465,7 @@ | -------------------------------------------------------------------------------------*/ -int Move_NodeSlider (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_NodeSlider (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { MrBFlt tuning, maxV, minV, oldM, newM, brlensPrExp=0.0, newMin, newMax, oldMin, oldMax; @@ -22558,7 +22558,7 @@ | -------------------------------------------------------------------------------------*/ -int Move_NodeSliderClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_NodeSliderClock (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { MrBFlt window, minV, minDepth, maxDepth, oldDepth, newDepth, oldLnPrior, newLnPrior, theta=0.0, growth=0.0, sR=0.0, eR=0.0, sF=0.0; @@ -22772,7 +22772,7 @@ | Note that this is appropriate when omegavar=equal | ----------------------------------------------------------------*/ -int Move_Omega (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Omega (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -22854,7 +22854,7 @@ | omegavar=equal | ----------------------------------------------------------------*/ -int Move_Omega_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Omega_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -22937,7 +22937,7 @@ | appropriate whenomegavar=M10 | ----------------------------------------------------------------*/ -int Move_OmegaBeta_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_OmegaBeta_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -23025,7 +23025,7 @@ | appropriate whenomegavar=M10 | ----------------------------------------------------------------*/ -int Move_OmegaGamma_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_OmegaGamma_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -23120,7 +23120,7 @@ #undef DO_DIR_CAT_PROP -int Move_OmegaCat (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_OmegaCat (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -23288,7 +23288,7 @@ | for neutral sites | ----------------------------------------------------------------*/ -int Move_OmegaNeu (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_OmegaNeu (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -23371,7 +23371,7 @@ | for positively selected sites | ----------------------------------------------------------------*/ -int Move_OmegaPos (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_OmegaPos (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -23477,7 +23477,7 @@ | for purifying selection sites | ----------------------------------------------------------------*/ -int Move_OmegaPur (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_OmegaPur (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -23569,7 +23569,7 @@ | Programmed by FR 2004-10-23-- | ----------------------------------------------------------------*/ -int Move_ParsEraser1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_ParsEraser1 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -23854,7 +23854,7 @@ -int Move_Pinvar (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Pinvar (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -23918,7 +23918,7 @@ -int Move_RanSPR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_RanSPR1 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -24486,7 +24486,7 @@ -int Move_RanSPR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_RanSPR2 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -25066,7 +25066,7 @@ -int Move_RanSPR3 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_RanSPR3 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -25714,7 +25714,7 @@ -int Move_RanSPR4 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_RanSPR4 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -26416,7 +26416,7 @@ | proposal. | ----------------------------------------------------------------*/ -int Move_RateMult_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_RateMult_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -26531,7 +26531,7 @@ | mechanism. | ----------------------------------------------------------------*/ -int Move_Revmat_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Revmat_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -26632,7 +26632,7 @@ -int Move_Speciation (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Speciation (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -26726,7 +26726,7 @@ -int Move_Speciation_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Speciation_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -26829,7 +26829,7 @@ | Programmed by JH 2002-11-18 | ----------------------------------------------------------------*/ -int Move_SPRClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_SPRClock (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -27474,7 +27474,7 @@ -int Move_Statefreqs (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Statefreqs (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -27560,7 +27560,7 @@ -int Move_StatefreqsSymDirMultistate (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_StatefreqsSymDirMultistate (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -27653,7 +27653,7 @@ -int Move_SwitchRate (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_SwitchRate (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -27742,7 +27742,7 @@ -int Move_SwitchRate_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_SwitchRate_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -27831,7 +27831,7 @@ -int Move_Theta (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Theta (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -27917,7 +27917,7 @@ -int Move_Tratio_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_Tratio_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -28017,7 +28017,7 @@ | Programmed by JH 2003-08-13 | ----------------------------------------------------------------*/ -int Move_UnrootedSlider (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) +int Move_UnrootedSlider (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) { @@ -28979,7 +28979,7 @@ -int PickProposal (safeLong *seed) +int PickProposal (long int *seed) { @@ -30162,7 +30162,7 @@ { int i, j=0, k, c, d, printWidth, nextColumn, nChars, inputChar; - safeLong x, y; + long x, y; char ch, tempName[200]; ModelInfo *m; ModelParams *mp; @@ -32379,7 +32379,7 @@ | RandResolve: Randomly resolve a polytomous tree | ---------------------------------------------------------------------*/ -int RandResolve (Tree *destination, PolyTree *t, safeLong *seed) +int RandResolve (Tree *destination, PolyTree *t, long *seed) { @@ -32646,7 +32646,7 @@ /* RemovePartition: Remove a partition from the tree keeping track of partition frequencies */ -int RemovePartition (PFNODE *r, safeLong *p, int runId) +int RemovePartition (PFNODE *r, long *p, int runId) { int i, comp; @@ -32728,7 +32728,7 @@ int RemoveTreeSamples (int from, int to) { int i, j, k, longestLine; - safeLong lastBlock; + long lastBlock; char *word, *s, *lineBuf=0; FILE *fp; Tree *t; @@ -33079,7 +33079,7 @@ -int RunChain (safeLong *seed) +int RunChain (long int *seed) { @@ -35289,10 +35289,10 @@ -void SetBit (int i, safeLong *bits) +void SetBit (int i, long int *bits) { - safeLong x; + long x; bits += i / nBitsInALong; @@ -39329,13 +39329,13 @@ MrBayesPrint ("%s ERROR: pfcounters not free in SetUpPartitionCounters\n", spacer); return ERROR; } - partition = (safeLong **) calloc (2*numLocalTaxa, sizeof (safeLong *)); + partition = (long **) calloc (2*numLocalTaxa, sizeof (long *)); if (partition == NULL) { MrBayesPrint ("%s Failed to allocate partition in SetUpPartitionCounters\n", spacer); return ERROR; } - partition[0] = (safeLong *) calloc (2*numLocalTaxa * nLongsNeeded, sizeof(safeLong)); + partition[0] = (long *) calloc (2*numLocalTaxa * nLongsNeeded, sizeof(long)); if (partition[0] == NULL) { free (partition); @@ -39381,7 +39381,7 @@ { int i, j, k, n, c, d, x=0, nReps; - safeLong *p; + long int *p; ModelInfo *m; ModelParams *mp; @@ -39859,7 +39859,7 @@ if (temp == NULL) return NULL; - temp->partition = (safeLong *) calloc (nLongsNeeded, sizeof (safeLong)); + temp->partition = (long *) calloc (nLongsNeeded, sizeof (long)); if (temp->partition == NULL) { free (temp); diff -ur mrbayes-3.1.2.new/mcmc.h mrbayes-3.1.2/mcmc.h --- mrbayes-3.1.2.new/mcmc.h 2006-08-08 16:01:53.000000000 +0200 +++ mrbayes-3.1.2/mcmc.h 2005-12-22 22:34:40.000000000 +0100 @@ -10,5 +10,5 @@ int MoveCalculationRoot (Tree *t, int outgroup); FILE *OpenNewMBPrintFile (char *fileName); int RootTree (Tree *t); -void SetBit (int i, safeLong *bits); +void SetBit (int i, long *bits); void SetUpMoveTypes (void); diff -ur mrbayes-3.1.2.new/sumt.c mrbayes-3.1.2/sumt.c --- mrbayes-3.1.2.new/sumt.c 2006-08-08 16:01:53.000000000 +0200 +++ mrbayes-3.1.2/sumt.c 2005-12-23 17:26:29.000000000 +0100 @@ -51,7 +51,7 @@ struct stnode *left, *right, *anc; int memoryIndex, index, upDateCl, upDateTi, marked, x, y, scalerNode, taxonName; - safeLong scalersSet, clSpace, tiSpace; + long scalersSet, clSpace, tiSpace; char label[100]; MrBFlt length; } @@ -66,8 +66,8 @@ /* local prototypes */ int AddTreeToList (int whichList); int AllocBits (int n); -void AssignIntPart (safeLong *lft, safeLong *rht, safeLong *p); -void AssignTipPart (int n, safeLong *p); +void AssignIntPart (long *lft, long *rht, long *p); +void AssignTipPart (int n, long *p); int BrlensVals (int treeNo, char *s, int longestLineLength, int lastTreeBlockBegin, int lastTreeBlockEnd); void CalculateTreeToTreeDistance (int *lst[2], MrBFlt *lngs[2], int nnds, int hasBrlens, MrBFlt *d1, MrBFlt *d2, MrBFlt *d3); int CheckSumtSpecies (void); @@ -76,7 +76,7 @@ int FindParts (void); int FindTree (void); void FinishSumtTree (SumtNode *p, int *i, int isThisTreeRooted); -int FirstTaxonInPartition (safeLong *partition, int length); +int FirstTaxonInPartition (long *partition, int length); int FreeBits (void); void GetConDownPass (PolyNode **downPass, PolyNode *p, int *i); int GetPartitions (void); @@ -85,20 +85,20 @@ int OpenBrlensFile (int treeNo); int OpenComptFiles (void); int OpenSumtFiles (int treeNo); -int PartFinder (safeLong *p, MrBFlt bl, int *partID); +int PartFinder (long *p, MrBFlt bl, int *partID); int PrintBrlensToFile (void); -void PrintParts (FILE *fp, safeLong *p, int nTaxaToShow); +void PrintParts (FILE *fp, long *p, int nTaxaToShow); int PruneSumt (void); int RealloateBits (void); int RealloateFullCompTrees (int whichList); int RealloateFullTrees (void); int ReorderParts (void); int RootSumtTree (SumtNode *p, int n, int out); -void ShowBits (safeLong *p, int nBitsToShow); +void ShowBits (long *p, int nBitsToShow); void ShowConNodes (int nNodes, PolyNode *root); int ShowConTree (FILE *fp, int nNodes, PolyNode *root, int screenWidth, int showSupport); int ShowConPhylogram (FILE *fp, int nNodes, PolyNode *root, int screenWidth); -void ShowParts (safeLong *p, int nTaxaToShow); +void ShowParts (long *p, int nTaxaToShow); void ShowSumtNodes (SumtNode *p, int indent, int isThisTreeRooted); void SortIndParts (int *item, MrBFlt *assoc, int count, int descendingOrder); void SortIndParts2 (int *item, MrBFlt *assoc, int left, int right, int descendingOrder); @@ -122,7 +122,7 @@ *prunedTaxa, *absentTaxa, *firstPrunedTaxa, *firstAbsentTaxa, comparingFiles, fileNum, numCompTrees[2], numCompTreesSampled[2], numFullCompTreesFound[2], numFullCompTreesAllocated[2], *fullCompTreePartIds1, *fullCompTreePartIds2, numBrlens, printingBrlens, runIndex; -safeLong *treeBits, *treePartsFound, *taxonMask; +long int *treeBits, *treePartsFound, *taxonMask; MrBFlt *aBrlens, *sBrlens, *treePartLengths, *fullCompTreePartLengths1, *fullCompTreePartLengths2, *brlens, *aWithinBrlens, *sWithinBrlens, *sumB, *sumsqB; SumtNode *pSumtPtr, *qSumtPtr, *sumtRoot, *sumtNodes; @@ -185,11 +185,11 @@ { int i, j, offSet; - safeLong x, y; + long x, y; /* decide how many unsigned ints are going to be needed to represent a taxon number */ - taxonLongsNeeded = (n / (sizeof(safeLong)*8)) + 1; + taxonLongsNeeded = (n / (sizeof(long int)*8)) + 1; /* how many partitions have been allocated */ numPartsAllocated = MAX_PARTITIONS; @@ -208,11 +208,11 @@ treeBits = NULL; treePartNums = NULL; treePartLengths = NULL; - treeBits = (safeLong *)SafeMalloc((size_t) (2 * n * taxonLongsNeeded * sizeof(safeLong))); + treeBits = (long *)SafeMalloc((size_t) (2 * n * taxonLongsNeeded * sizeof(long))); treePartNums = (int *)SafeMalloc((size_t) (2 * n * sizeof(int))); if (!treeBits || !treePartNums) { - MrBayesPrint ("%s Problem allocating treeBits (%d)\n", spacer, 2 * n * taxonLongsNeeded * sizeof(safeLong)); + MrBayesPrint ("%s Problem allocating treeBits (%d)\n", spacer, 2 * n * taxonLongsNeeded * sizeof(long)); goto errorExit; } treePartLengths = (MrBFlt *)SafeMalloc((size_t) (2 * n * sizeof(MrBFlt))); @@ -249,10 +249,10 @@ goto errorExit; } treePartsFound = NULL; - treePartsFound = (safeLong *)SafeMalloc((size_t) (taxonLongsNeeded * MAX_PARTITIONS * sizeof(safeLong))); + treePartsFound = (long *)SafeMalloc((size_t) (taxonLongsNeeded * MAX_PARTITIONS * sizeof(long))); if (!treePartsFound) { - MrBayesPrint ("%s Problem allocating treePartsFound (%d)\n", spacer, taxonLongsNeeded * MAX_PARTITIONS * sizeof(safeLong)); + MrBayesPrint ("%s Problem allocating treePartsFound (%d)\n", spacer, taxonLongsNeeded * MAX_PARTITIONS * sizeof(long)); goto errorExit; } memAllocs[ALLOC_TREEPARTS] = YES; @@ -457,10 +457,10 @@ goto errorExit; } taxonMask = NULL; - taxonMask = (safeLong *)SafeMalloc((size_t) (taxonLongsNeeded * sizeof(safeLong))); + taxonMask = (long *)SafeMalloc((size_t) (taxonLongsNeeded * sizeof(long))); if (!taxonMask) { - MrBayesPrint ("%s Problem allocating taxonMask (%d)\n", spacer, taxonLongsNeeded * sizeof(safeLong)); + MrBayesPrint ("%s Problem allocating taxonMask (%d)\n", spacer, taxonLongsNeeded * sizeof(long)); goto errorExit; } memAllocs[ALLOC_TAXONMASK] = YES; @@ -478,7 +478,7 @@ prunedTaxa = (int *)SafeMalloc((size_t) (i * sizeof(int))); if (!prunedTaxa) { - MrBayesPrint ("%s Problem allocating prunedTaxa (%d)\n", spacer, i * sizeof(safeLong)); + MrBayesPrint ("%s Problem allocating prunedTaxa (%d)\n", spacer, i * sizeof(long)); goto errorExit; } absentTaxa = prunedTaxa + numTaxa; @@ -579,11 +579,11 @@ -void AssignTipPart (int n, safeLong *p) +void AssignTipPart (int n, long *p) { - safeLong x; + long x; p += n / nBitsInALong; x = 1 << (n % nBitsInALong); @@ -595,7 +595,7 @@ -void AssignIntPart (safeLong *lft, safeLong *rht, safeLong *p) +void AssignIntPart (long *lft, long *rht, long *p) { @@ -992,7 +992,7 @@ { int i, j, targetNode, nBits, nextConNode, isCompat, localOutgroupNum, numTerminalsEncountered; - safeLong x, *mask = NULL, *partition = NULL, *ingroupPartition = NULL, *outgroupPartition = NULL; + long x, *mask = NULL, *partition = NULL, *ingroupPartition = NULL, *outgroupPartition = NULL; MrBFlt freq; char tempName[100]; PolyNode *cp, *q, *r, *ql, *rl, *pl, **downPass = NULL; @@ -1054,7 +1054,7 @@ MrBayesPrint ("%s outgroupPartition is already allocated\n", spacer); goto errorExit; } - outgroupPartition = (safeLong *) calloc (3 * taxonLongsNeeded, sizeof(safeLong)); + outgroupPartition = (long *) calloc (3 * taxonLongsNeeded, sizeof(long)); if (!outgroupPartition) { MrBayesPrint ("%s Could not allocate outgroupPartition\n", spacer); @@ -1687,8 +1687,8 @@ longestLineLength1, longestLineLength2, xaxis, yaxis, starHolder[80], *treePartList[2], minNumTrees, screenWidth, screenHeigth, numY[60], nSamples, nCompPartitions, numIncludedTaxa1, numIncludedTaxa2, oldSumtBrlensDef, brlensDef; - safeLong temporarySeed, len; - safeLong *x; + long int temporarySeed, len; + long *x; MrBFlt xProb, yProb, xInc, yInc, xUpper, xLower, yUpper, yLower, *treeLengthList[2], *dT1=NULL, *dT2=NULL, *dT3=NULL, d1, d2, d3, meanY[60], xVal, yVal, minX, minY, maxX, maxY, sums[3]; char *s=NULL, tempStr[100], tempName[100], prCh; @@ -2725,7 +2725,7 @@ /* calculate average tree-to-tree distances */ curTime = time(NULL); - temporarySeed = (safeLong)curTime; + temporarySeed = (long int)curTime; if (temporarySeed < 0) temporarySeed = -temporarySeed; sums[0] = sums[1] = sums[2] = 0.0; @@ -2937,7 +2937,7 @@ maxWidthNumberPartitions, tableWidth, unreliable, oneUnreliable, firstSumtBrlensDef=0, numTotalTreesSampled; MrBFlt var=0.0, f, var_s, sum_s, stddev_s=0.0, sumsq_s, varB, varW=0.0, sqrt_R=0.0; - safeLong *x; + long *x; char *s=NULL, tempName[100], tempStr[100], fileName[100]; FILE *fp; @@ -5187,14 +5187,14 @@ -int FirstTaxonInPartition (safeLong *partition, int length) +int FirstTaxonInPartition (long *partition, int length) { int i, j, nBits, taxon; - safeLong x; + long x; - nBits = sizeof(safeLong) * 8; + nBits = sizeof(long) * 8; for (i=taxon=0; i