path: root/sci-biology/tree-puzzle/files/tree-puzzle-5.2-C99-decls.patch

--- a/src/consensus.c
+++ b/src/consensus.c
@@ -32,7 +32,7 @@
 /******************************************************************************/
 
 /* prepare for consensus tree analysis */
-void initconsensus()
+void initconsensus(void)
 {
 #	if ! PARALLEL
 		biparts = new_cmatrix(Maxspc-3, Maxspc);
--- a/src/consensus.h
+++ b/src/consensus.h
@@ -65,7 +65,7 @@
 /******************************************************************************/
 
 /* prepare for consensus tree analysis */
-void initconsensus();
+void initconsensus(void);
 
 /* recursive function to get bipartitions */
 /* traversal should be optimazable (HAS) */
--- a/src/ml1.c
+++ b/src/ml1.c
@@ -244,7 +244,7 @@
 /***************************** exported functions *****************************/
 
 
-void evaluateseqs()
+void evaluateseqs(void)
 {	
 	ivector ali;
 
@@ -1018,7 +1018,7 @@
 
 
 /* compute 1 PAM rate matrix, its eigensystem, and the inverse matrix thereof */
-void tranprobmat()
+void tranprobmat(void)
 {
 	eigensystem(Eval, Evec); /* eigensystem of 1 PAM rate matrix */
 	luinverse(Evec, Ievc, tpmradix); /* inverse eigenvectors are in Ievc */
@@ -1324,7 +1324,7 @@
 
 
 /* initialize distance matrix */
-void initdistan()
+void initdistan(void)
 {
 	int i, j, k, diff, x, y;
 	double obs, temp;
@@ -1478,7 +1478,7 @@
 
 #else /* not PARALLEL */
 
-void computedistan()
+void computedistan(void)
 {
 	int i, j;
 
--- a/src/ml2.c
+++ b/src/ml2.c
@@ -1036,7 +1036,7 @@
 
 
 /* preparation for ML analysis */
-void mlstart()
+void mlstart(void)
 {
 	/* number of states and code length */
 	tpmradix = gettpmradix();
@@ -1098,7 +1098,7 @@
 
 
 /* cleanup after ML analysis */
-void mlfinish()
+void mlfinish(void)
 {
 	if (Ctree != NULL)
 		free_tree(Ctree, Numspc);
@@ -1566,7 +1566,7 @@
                              int bestratefound,
                              int ncats)    /* numcats */
 #endif
-void findbestratecombination()
+void findbestratecombination(void)
 {
 	int k, u;
 	double bestvalue, fv2;
@@ -2147,7 +2147,7 @@
 } /* clock_lklhd */
 
 /* find out the edge containing the root */
-int findrootedge()
+int findrootedge(void)
 {
 	int e, ebest;
 	double logbest, logtest;
--- a/src/mlparam.c
+++ b/src/mlparam.c
@@ -70,7 +70,7 @@
 }
 
 /* compute rates of each category when rates are Gamma-distributed */
-void updaterates()
+void updaterates(void)
 {
 	int i;
 	double alpha;
@@ -190,7 +190,7 @@
 }
 
 /* estimate substitution process parameters - random quartets */
-void optimseqevolparamsquart()
+void optimseqevolparamsquart(void)
 {
 	double tsmeanold, yrmeanold;
 	dvector tslist, yrlist;
@@ -320,7 +320,7 @@
 
 
 /* optimize substitution process parameters - tree */
-void optimseqevolparamstree()
+void optimseqevolparamstree(void)
 {
 	twodimenmin(EPSILON_SUBSTPARAM,
 		(SH_optn || nuc_optn) && optim_optn && (data_optn == 0),
@@ -379,7 +379,7 @@
 
 
 /* optimize rate heterogeneity parameters */
-void optimrateparams()
+void optimrateparams(void)
 {	
 	twodimenmin(EPSILON_RATEPARAM,
 		fracinv_optim,
@@ -396,7 +396,7 @@
 
 /* estimate parameters of substitution process and rate heterogeneity - no tree
    n-taxon tree is not needed because of quartet method or NJ tree topology */
-void estimateparametersnotree()
+void estimateparametersnotree(void)
 {
 	int it, nump, change;
 	double TSold, YRold, FIold, GEold;
@@ -495,7 +495,7 @@
 
 /* estimate parameters of substitution process and rate heterogeneity - tree
    same as above but here the n-taxon tree is already in memory */
-void estimateparameterstree()
+void estimateparameterstree(void)
 {
 	int it, nump, change;
 	double TSold, YRold, FIold, GEold;
--- a/src/model1.c
+++ b/src/model1.c
@@ -31,7 +31,7 @@
 #include "ml.h"
 
 /* number of states of the selected model */ 
-int gettpmradix()
+int gettpmradix(void)
 {
 	if (data_optn == 0) { /* nucleotides */
 		if (nuc_optn) return 4;
--- a/src/puzzle1.c
+++ b/src/puzzle1.c
@@ -345,7 +345,7 @@
 /******************************************************************************/
 
 /* compute TN parameters according to F84 Ts/Tv ratio */
-void makeF84model()
+void makeF84model(void)
 {
 	double rho, piA, piC, piG, piT, piR, piY, ts, yr;
 	
@@ -390,7 +390,7 @@
 } /* makeF84model */
 
 /* compute number of quartets used in LM analysis */
-void compnumqts()
+void compnumqts(void)
 {
 	if (lmqts == 0) {
 		if (numclust == 4)
@@ -407,7 +407,7 @@
 } /* compnumqts */
 
 /* set options interactively */
-void setoptions()
+void setoptions(void)
 {	
 	int i, valid;
 	double sumfreq;
@@ -1718,7 +1718,7 @@
 } /* closefile */
 
 /* symmetrize doublet frequencies */
-void symdoublets()
+void symdoublets(void)
 {
 	int i, imean;
 	double mean;
@@ -1769,7 +1769,7 @@
 } /* symdoublets */
 
 /* show Ts/Tv ratio and Ts Y/R ratio */
-void computeexpectations()
+void computeexpectations(void)
 {
 	double AlphaYBeta, AlphaRBeta, piR, piY, num, denom, pyr, pur;
 	
@@ -4604,7 +4604,7 @@
 /* Reconstruct a tree with QP */
 /* (parameter estimation already done) */
 
-void recon_tree()
+void recon_tree(void)
 {
 	int i;
 	unsigned char tmpweight;
@@ -4848,7 +4848,7 @@
 
 /***************************************************************/ 
 
-void map_lklhd()
+void map_lklhd(void)
 {	
 	int i, a, a1, a2, b, b1, b2, c, c1, c2, d;
 	uli nq;
@@ -5101,7 +5101,7 @@
 
 /***************************************************************/ 
 
-void setdefaults() {
+void setdefaults(void) {
 
   strcpy(INFILE,     INFILEDEFAULT);
   strcpy(OUTFILE,    OUTFILEDEFAULT);
@@ -6027,7 +6027,7 @@
 
 /***************************************************************/ 
 
-void memcleanup() { 
+void memcleanup(void) { 
 	if (puzzlemode == QUARTPUZ && typ_optn == TREERECON_OPTN) {
 		free(splitfreqs);
 		free(splitpatterns);
--- a/src/puzzle2.c
+++ b/src/puzzle2.c
@@ -860,7 +860,7 @@
 
 
 /* estimate mean base frequencies from translated data set */
-void estimatebasefreqs()
+void estimatebasefreqs(void)
 {
 	int tpmradix, i, j;
 	uli all, *gene;
@@ -903,7 +903,7 @@
 
 
 /* guess model of substitution */
-void guessmodel()
+void guessmodel(void)
 {
 	double c1, c2, c3, c4, c5, c6;
 	dvector f;
@@ -1160,7 +1160,7 @@
 } /* callocquartets */
 
 /* free quartet memory */
-void freequartets()
+void freequartets(void)
 {	
 	free(quartetinfo);
 } /* freequartets */
@@ -1357,7 +1357,7 @@
 /*************************/
 
 /* checks out all possible quartets */
-void computeallquartets()
+void computeallquartets(void)
 {	
 	double onethird;
 	uli nq;
--- a/src/sprng/makeseed.c
+++ b/src/sprng/makeseed.c
@@ -1,10 +1,6 @@
 #include <time.h>
 
-#ifdef __STDC__
-int make_new_seed()
-#else
-int make_new_seed()
-#endif
+int make_new_seed(void)
 {
   time_t tp;
   struct tm *temp;
--- a/src/sprng/primes-lcg64.c
+++ b/src/sprng/primes-lcg64.c
@@ -1,5 +1,6 @@
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
 #include "primes-lcg64.h"
 #include "primelist-lcg64.h"
 
--- a/src/treesort.c
+++ b/src/treesort.c
@@ -487,7 +487,7 @@
 /**********/
 
 /* malloc new tree list item */
-treelistitemtype *gettreelistitem()
+treelistitemtype *gettreelistitem(void)
 {
 	treelistitemtype *tmpptr;
 	tmpptr = (treelistitemtype *)calloc((size_t) 1, sizeof(treelistitemtype));
--- a/src/treesort.h
+++ b/src/treesort.h
@@ -84,7 +84,7 @@
 /**********/
 
 /* allocate memory for ctree 3 ints pointer plus 1 check byte */
-int *initctree();
+int *initctree(void);
 
 /**********/
 
@@ -174,7 +174,7 @@
 /**********/
 
 /* malloc new tree list item */
-treelistitemtype *gettreelistitem();
+treelistitemtype *gettreelistitem(void);
 
 /**********/
 
--- a/src/util.c
+++ b/src/util.c
@@ -507,7 +507,7 @@
 #define EPS 1.2e-7
 #define RNMX (1.0-EPS)
 
-double randomunitintervall()
+double randomunitintervall(void)
 /* Long period (> 2e18) random number generator. Returns a uniform random
    deviate between 0.0 and 1.0 (exclusive of endpoint values).
 
@@ -734,7 +734,7 @@
 /* Reads characters from stdin until a newline character or EOF
    is received.  The newline is not made part of the string.
    If an error occurs a null string \0 is returned */
-cvector mygets()
+cvector mygets(void)
 {
 	int c, n;
 	cvector str;