Script MakePach para correção de platarforma 32 bits para 64
Publicado por José Cleydson Ferreira da Silva (última atualização em 25/05/2010)
[ Hits: 4.074 ]
Homepage: geminivirus.org
Este script faz a correção de um arquivo Makefile do software Mr Bayes da plataforma 32 bits para 64 incluindo suporte ao MPI.
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 ?= yes
-_64BIT ?= yes
# 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 @@
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