SmartBuffer *reallocSB(SmartBuffer *sb, size_t incr) {
SmartBuffer *sbNew;
size_t i;
if (sb == NULL) {
sbNew = (SmartBuffer*) gblock((size_t) sizeof(SmartBuffer));
(sbNew -> buff) = cvector(0, incr - 1);
(sbNew -> size) = incr;
sbNew -> ptr = sbNew -> buff;
}
else {
sbNew = (SmartBuffer*) gblock((size_t) sizeof(SmartBuffer));
(sbNew -> buff) = cvector(0, (sb -> size) + incr - 1);
(sbNew -> size) = (sb -> size) + incr;
sb -> ptr = sb -> buff;
sbNew -> ptr = sbNew -> buff;
for (i = 1; i <= sb -> size; i++) {
*(sbNew -> ptr) = *(sb -> ptr);
++(sbNew -> ptr);
++(sb -> ptr);
}
freeSB(sb);
}
sbNew -> delim = ',';
sbNew -> tokenCnt = 0;
sbNew -> tokenSize = 0;
sbNew -> token = NULL;
return sbNew;
}
void mpsqrt(unsigned char w[], unsigned char u[], unsigned char v[], int n,
int m)
{
void mplsh(unsigned char u[], int n);
void mpmov(unsigned char u[], unsigned char v[], int n);
void mpmul(unsigned char w[], unsigned char u[], unsigned char v[], int n,
int m);
void mpneg(unsigned char u[], int n);
void mpsdv(unsigned char w[], unsigned char u[], int n, int iv, int *ir);
int i,ir,j,mm;
float fu,fv;
unsigned char *r,*s;
r=cvector(1,n<<1);
s=cvector(1,n<<1);
mm=IMIN(m,MF);
fv=(float) v[mm];
for (j=mm-1;j>=1;j--) {
fv *= BI;
fv += v[j];
}
fu=1.0/sqrt(fv);
for (j=1;j<=n;j++) {
i=(int) fu;
u[j]=(unsigned char) i;
fu=256.0*(fu-i);
}
for (;;) {
mpmul(r,u,u,n,n);
mplsh(r,n);
mpmul(s,r,v,n,IMIN(m,n));
mplsh(s,n);
mpneg(s,n);
s[1] -= 253;
mpsdv(s,s,n,2,&ir);
for (j=2;j<n;j++) {
if (s[j]) {
mpmul(r,s,u,n,n);
mpmov(u,&r[1],n);
break;
}
}
if (j<n) continue;
mpmul(r,u,v,n,IMIN(m,n));
mpmov(w,&r[1],n);
free_cvector(s,1,n<<1);
free_cvector(r,1,n<<1);
return;
}
}
SmartBuffer *parseLineSB(FILE *fPtr, char delim, size_t sbSize) {
size_t size;
SmartBuffer *sb = readLineSB(fPtr, sbSize);
(sb -> delim) = delim;
size = 0;
while((*(sb -> ptr)) != '\0') {
if ((*(sb -> ptr)) == delim) {
(sb -> tokenCnt) ++;
if (size > (sb -> tokenSize)) {
(sb -> tokenSize) = size;
}
size = 0;
}
else {
++ size;
}
++(sb -> ptr);
}
if ((sb -> tokenCnt) > 0) {
(sb -> tokenCnt) ++;
(sb -> token) = cvector(0, sb -> tokenSize);
}
sb -> ptr = sb -> buff;
return sb;
}
void mpinv(unsigned char u[], unsigned char v[], int n, int m)
{
void mpmov(unsigned char u[], unsigned char v[], int n);
void mpmul(unsigned char w[], unsigned char u[], unsigned char v[], int n,
int m);
void mpneg(unsigned char u[], int n);
unsigned char *rr,*s;
int i,j,maxmn,mm;
float fu,fv;
maxmn=IMAX(n,m);
rr=cvector(1,1+(maxmn<<1));
s=cvector(1,maxmn);
mm=IMIN(MF,m);
fv=(float) v[mm];
for (j=mm-1;j>=1;j--) {
fv *= BI;
fv += v[j];
}
fu=1.0/fv;
for (j=1;j<=n;j++) {
i=(int) fu;
u[j]=(unsigned char) i;
fu=256.0*(fu-i);
}
for (;;) {
mpmul(rr,u,v,n,m);
mpmov(s,&rr[1],n);
mpneg(s,n);
s[1] -= 254;
mpmul(rr,s,u,n,n);
mpmov(u,&rr[1],n);
for (j=2;j<n;j++)
if (s[j]) break;
if (j==n) {
free_cvector(s,1,maxmn);
free_cvector(rr,1,1+(maxmn<<1));
return;
}
}
}
CHARVECTOR *new_charvector( long nh)
{
CHARVECTOR *m;
m=(CHARVECTOR *)malloc(sizeof(CHARVECTOR));
if (!m) t_error("allocation failure in CHARVECTOR()");
m->isdynamic=isDynamic;
m->nl=NL;
m->nh=nh;
m->co=cvector(m->nl,nh);
return m;
}
void int_split(char *s,int *nums,int num)
{
int cnt=0,i;
char *p;
p=cvector(0,MAXLINE-1);
while(*s !='\0'&&cnt<num)
{ while(isspace(*s)) ++s; //skip white space
if(*s!='\0') //found a word
{ i=0;
while(!isspace(*s)&&*s!='\0') //translate the word into float number
{ p[i++]=*s++;}
p[i]='\0';
nums[cnt++]=atoi(p);
}
}
free_cvector(p,0,MAXLINE-1);
}
int main(void)
{
int k;
unsigned long i,j,lc,lcode=MAXLINE,n,nch,nrad,nt,nfreq[257],tmp,zero=0;
unsigned char *code,mess[MAXLINE],ness[MAXLINE];
arithcode acode;
FILE *fp;
code=cvector(0,MAXLINE);
acode.ilob=lvector(1,NWK);
acode.iupb=lvector(1,NWK);
acode.ncumfq=lvector(1,MC+2);
if ((fp = fopen("text.dat","r")) == NULL)
nrerror("Input file text.dat not found.\n");
for (j=1;j<=256;j++) nfreq[j]=0;
while ((k=getc(fp)) != EOF) {
if ((k -= 31) >= 1) nfreq[k]++;
}
fclose(fp);
nch=96;
nrad=256;
/* here is the initialization that constructs the code */
arcmak(nfreq,(int)nch,(int)nrad,&acode);
/* now ready to prompt for lines to encode */
for (;;) {
printf("Enter a line:\n");
if (gets((char *)&mess[1]) == NULL) break;
n=strlen((char *)&mess[1]);
/* shift from 256 character alphabet to 96 printing characters */
for (j=1;j<=n;j++) mess[j] -= 32;
/* message initialization */
lc=1;
arcode(&zero,&code,&lcode,&lc,0,&acode);
/* here we arithmetically encode mess(1:n) */
for (j=1;j<=n;j++) {
tmp=mess[j];
arcode(&tmp,&code,&lcode,&lc,1,&acode);
}
/* message termination */
arcode(&nch,&code,&lcode,&lc,1,&acode);
printf("Length of line input, coded= %lu %lu\n",n,lc-1);
/* here we decode the message, hopefully to get the original back */
lc=1;
arcode(&zero,&code,&lcode,&lc,0,&acode);
for (j=1;j<=lcode;j++) {
arcode(&i,&code,&lcode,&lc,-1,&acode);
if (i == nch) break;
else ness[j]=(unsigned char)i;
}
if (j > lcode) nrerror("Arith. coding: Never get here");
nt=j-1;
printf("Decoded output:\n");
for (j=1;j<=nt;j++) printf("%c",(char)(ness[j]+32));
printf("\n");
if (nt != n) printf("Error ! j decoded != n input.\n");
}
free_cvector(code,0,MAXLINE);
free_lvector(acode.ncumfq,1,MC+2);
free_lvector(acode.iupb,1,NWK);
free_lvector(acode.ilob,1,NWK);
printf("Normal completion\n");
return 0;
}
/*
* Function read_init is used to read in the initial values of selfing rates (S) for MCMC updating
* Input argument: initialfilename is the directory of the file containing the initial values,
* if it is NULL,then using random number generator to generate the INIT structure
* chainnum is the number of MCMC chains, determining the number of sets of initial values
* popnum is the number of subpopulation assumed
* chainnum and popnum determines the dimensions of the "initd" element of the INIT struture
* Output argument: this application returns an INIT structure, which contains the "chainnum" sets of initial values for F per subpopulation
* The data in the file should be ranged as:
* >chain_name1 each set of the initial values should begin with ">S"
* num1 num2..
*
* >chain_name2
* ....
*/
INIT read_init(char *initialfilename,int chainnum,int popnum,long update,long burnin,int thinning)
{
//char sign='#';
int i,j,temp,cnt_chn=0;
FILE *initfp;
char *line;
INIT initial;
initial.chainnum=chainnum;
initial.update=update;
initial.burnin=burnin;
initial.thinning=thinning;
initial.popnum=popnum;
initial.initd=matrix(0,chainnum-1,0,popnum-1);
initial.name_len=ivector(0,chainnum-1);
initial.chn_name=cmatrix(0,chainnum-1,0,MAXLEN-1);
if(initialfilename==NULL)
{
for(i=0;i<chainnum;i++)
{
for(j=0;j<popnum;j++)
initial.initd[i][j]=ran1();
strcpy(initial.chn_name[i],"Chain#");
strcat(initial.chn_name[i],int_to_string(i+1));
initial.name_len[i]=strlen(initial.chn_name[i])+1;
initial.chn_name[i][initial.name_len[i]-1]='\0';
}
}
else{
if((initfp=fopen(initialfilename,"r"))==NULL)
{ nrerror("Cannot open inital file!");}
line=cvector(0,MAXLINE-1);
cnt_chn=0;
for(i=0;i<chainnum&&(!feof(initfp));i++)
{
while(!feof(initfp))
{
fgets(line,MAXLINE,initfp);
if(line[0]=='>') break;
}
for(j=1;j<strlen(line)&&line[j]!='\n';j++)
{
initial.chn_name[i][j-1]=line[j];
}
initial.chn_name[j]='\0';
//printf("%s\n",initial.chn_name[i]);
initial.name_len[i]=j;
fgets(line,MAXLINE,initfp);
temp=word_cnt(line);
if(temp!=popnum)
{
nrerror("The number of initial values for selfing rates is not equal the number of subpopulation assumed!\n");
}
word_split(line,initial.initd[cnt_chn],popnum);
cnt_chn++;
}
if(cnt_chn<=chainnum)
{
for(i=cnt_chn;i<chainnum;i++)
{
for(j=0;j<popnum;j++)
initial.initd[i][j]=ran1();
strcpy(initial.chn_name[i],"Chain#");
strcat(initial.chn_name[i],int_to_string(i+1));
initial.name_len[i]=strlen(initial.chn_name[i])+1;
initial.chn_name[i][initial.name_len[i]-1]='\0';
}
}
if(cnt_chn>chainnum)
{
nrerror("The number of chain starting points is greater than the number of chains!\n");
}
fclose(initfp);
free_cvector(line,0,MAXLINE-1);
}
/*for(i=0;i<chainnum;i++)
{
for(j=0;j<popnum;j++)
fprintf(stdout,"%f\t",initial.initd[i][j]);
fprintf(stdout,"\n");
}*/
return(initial);
}