double readResult(string result,string rate,string date,int nb_tree){
FILE *f = fopen(result.c_str(),"rt");
if (f!=NULL){
FILE *w = fopen(rate.c_str(),"wt");
FILE *wd = fopen(date.c_str(),"wt");
string s= readWord(f,result);
while (s.compare("Exit)")!=0) s = readWord(f,result);
for (int y=0;y<nb_tree;y++){
s = readWord(f,result);
while (s.compare("rate")!=0) s = readWord(f,result);
double r=readdouble(f,result);
while (s.compare("tMRCA")!=0) s = readWord(f,result);
double t=readdouble(f,result);
fprintf(w,"%f\n",r);
fprintf(wd,"%f\n",t);
}
while (s.compare("time:")!=0) s = readWord(f,result);
double time=readdouble(f,result);
fclose(f);
fclose(w);
fclose(wd);
return time;
}
else{
cout<<"Impossible to open file "<<result<<endl;
exit (EXIT_FAILURE);
}
}
void Estudiant::llegir_estudiant()
{
DNI= readint();
if (DNI<0) throw PRO2Excepcio(ER4);
double x = readdouble();
if (x >= 0 and x <= MAX_NOTA) nota = x;
else nota=-1;
}
void tree2dataS(FILE * tree,int n,int m,int* &P,double* &B,string* &Support,string* &leaves){
int inode = 0;//number of internal nodes;
stack<int> pileNode;
char c = readBracket(tree,"input tree");
int a=1;
int countleaf=n;
P[0]=-1;
B[0]=-1;
do{
c = readChar(tree,"input tree");
if (c==')'){
a--;inode++;
int s1=pileNode.top();pileNode.pop();
int s2=pileNode.top();pileNode.pop();
P[s1]=n-inode;
P[s2]=n-inode;
if (a>0){
Support[n-inode]=readSupport(tree,"input tree");
B[n-inode]=readdouble(tree,"input tree");
}
else while (!pileNode.empty()){
int s=pileNode.top();pileNode.pop();
P[s]=n-inode;
}
pileNode.push(n-inode);
}
else if (c!='(' && c!=',' && c!=-1 && c!=';' && c!='\n'){
string lb=readLabel(c,tree);
pileNode.push(countleaf);
leaves[countleaf]=lb;
B[countleaf]=readdouble(tree,"input tree");
Support[countleaf]="";
countleaf++;
}
else if (c=='(') {a++;}
} while (a>0);
}
bool SmallConf::GetDouble(double *v,
SmallConf *root,
SmallConf *local,
SmallConf *artif,
SmallConf *param) const
{
if (alias_on)
return (alias_on->GetDouble(v, root, local, artif, param));
if (distant_double)
{
*v = *distant_double;
return (true);
}
if (expression && (root || local || artif || param))
{
if (expr_compute((SmallConf&)*this, NULL, false, root, local, artif, param) == false)
return (false);
}
if (have_value == false)
{
if (array.size() == 1)
{
if (array[0]->GetDouble(v, root, local, artif, param) == false)
return (false);
converted = *v;
return (true);
}
return (false);
}
if (is_converted == false)
{
int tmp;
ssize_t i = 0;
if (readdouble(original_value.c_str(), i, converted) == false)
{
if (readinteger(original_value.c_str(), i, tmp) == false)
return (false);
converted = tmp;
}
is_converted = true;
}
*v = converted;
return (true);
}
bool tree2data(FILE * tree,string date,int n,int m,int* &P,double* &B,string* &Support,double* &T,string* &leaves){
int inode = 0;//number of internal nodes;
stack<int> pileNode;
char c = readBracket(tree,"input tree");
int a=1;
int countleaf=n;
P[0]=-1;
B[0]=-1;
bool all=false;
do{
c = readChar(tree,"input tree");
if (c==')'){
a--;inode++;
int s1=pileNode.top();pileNode.pop();
int s2=pileNode.top();pileNode.pop();
P[s1]=n-inode;
P[s2]=n-inode;
if (a>0){
Support[n-inode]=readSupport(tree,"input tree");
B[n-inode]=readdouble(tree,"input tree");
}
else
while (!pileNode.empty()){
int s=pileNode.top();pileNode.pop();
P[s]=n-inode;
}
pileNode.push(n-inode);
}
else if (c!='(' && c!=',' && c!=-1 && c!=';' && c!='\n'){
string lb=readLabel(c,tree);
pileNode.push(countleaf);
leaves[countleaf]=lb;
B[countleaf]=readdouble(tree,"input tree");
Support[countleaf]="";
countleaf++;
}
else if (c=='(') {a++;}
} while (a>0);
FILE * dateFile = fopen(date.c_str(),"rt");
if (dateFile == NULL) cout << "Can not open the file " <<date<< endl;
else{
int ino=readInt(dateFile,"Error in the date file, the file should begin with an integer (the number of dated tips)");
for (int i=0;i<=m;i++) T[i]=-1;
int count=0;
double first=-1;
for (int i=0;i<ino;i++){
string s=readWord(dateFile,date);
double lt=readdouble(dateFile,date);
int k = getPosition(leaves,s,n,m+1);
if (k!=-1) {
if (count==0) first=lt;
else if (lt!=first) all=true;
T[k]=lt;
count++;
}
}
if (count<countleaf-n){
cout<<"The dates of some taxa are missing. If the input tree contains some outgroups, use option -g to specify the file name of outgroups. "<<endl;
exit(EXIT_FAILURE);
}
fclose(dateFile);
}
return all;
}
double EMUFILE::readdouble()
{
double temp;
readdouble(&temp);
return temp;
}
/* init: initializes global variables. */
void init(char* infilename) {
char keyword[101];
FILE *infile = fopen(infilename, "r");
int i, j;
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
if (rank == 0) {
assert(infile);
readint(infile, "nx", &nx);
readdouble(infile, "k", &k);
readint(infile, "nsteps", &nsteps);
readint(infile, "wstep", &wstep);
printf("Diffusion1d with nx=%d, k=%f, nsteps=%d, wstep=%d nprocs=%d\n",
nx, k, nsteps, wstep, nprocs);
}
MPI_Bcast(&nx, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&k, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
MPI_Bcast(&nsteps, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&wstep, 1, MPI_INT, 0, MPI_COMM_WORLD);
assert(nx>=nprocs); /* is this necessary ? */
assert(k>0 && k<.5);
assert(nx>=2);
assert(nsteps>=1);
// nxl: number actual points (incl. end-points)
// nxl+2: size of array (incl. ghost cells)
first = firstForProc(rank);
nxl = countForProc(rank);
if (first == 0 || nxl == 0) left = MPI_PROC_NULL; else left = OWNER(first-1);
if (first+nxl >= nx || nxl == 0) right = MPI_PROC_NULL; else right = OWNER(first+nxl);
u = (double*)malloc((nxl+2)*sizeof(double));
assert(u!=NULL);
u_new = (double*)malloc((nxl+2)*sizeof(double));
assert(u_new);
if (rank == 0) {
buf = (double*)malloc((1+nx/nprocs)*sizeof(double));
for (i=1; i <= nxl; i++){
if (fscanf(infile, "%lf", u+i) != 1) quit();
}
for (i=1; i < nprocs; i++){
for (j=0; j<countForProc(i); j++){
if (fscanf(infile, "%lf", buf+j) != 1) quit();
}
MPI_Send(buf, countForProc(i), MPI_DOUBLE, i, 0, MPI_COMM_WORLD);
}
}
else {
MPI_Recv(u+1, nxl, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
}
if (rank == OWNER(0)) {
start = 2;
}
else {
start = 1;
}
if (rank == OWNER(nx-1)) {
stop = nxl - 1;
}
else {
stop = nxl;
}
if (rank == 0) {
buf = (double*)malloc((1+nx/nprocs)*sizeof(double));
assert(buf);
file = fopen("./parout/out.gif", "wb");
assert(file);
colors = (int*)malloc(MAXCOLORS*sizeof(int));
assert(colors);
} else {
buf = NULL;
}
}
void
nextnode (void)
{
FileOffset offset = nextoffset;
char b;
int marked, err;
err = fread(&b,sizeof(char),1,f); nextoffset+=1;
if (err!=1) return;
if (rmode || xmode) {
marked = ismarked(b);
if (marked) {
cleartag(&b);
newtagat(&b, offset);
}
if (amode) printf("%s", (marked ? "=> " : " "));
}
{
int k = lo5(b);
if ((ExpDoStmt<k && k<AtomVariable) || k>ListCons) {
fprintf(stderr, "strange tag %d at byte offset 0x%x\n",
k, offset);
exit(1);
} else if (smode) {
count[k]++;
if (rmode && marked) reachcount[k]++;
}
switch (k) {
case ListCons:
if (gmode) printf("%d [label=\"0x%x ListCons\"]\n", offset, offset);
if (amode) printf("0x%x: %-20s\t", offset, tag2str(k));
if (amode) printf("elem=");
dopointer(NONZERO, ANYEXP, readpointer(), k, offset, "e");
if (amode) printf(" tail=");
dopointer(MAYBEZERO, ListCons, readpointer(), k, offset, "t");
break;
case Module:
if (amode) {
if (tracedModule(b))
printf("0x%x: Module (suspect) \t", offset);
else printf("0x%x: Module (trusted) \t", offset);
}
{ char *s = readstring(); if (amode) printf("%s\t", s); }
{ char *s = readstring(); if (amode) printf("\"%s\"", s); }
break;
case SrcPos:
if (amode) printf("0x%x: SrcPos\t\t\t", offset);
dopointer(NONZERO, Module, readpointer(), k, offset, "");
{ char *p = readposn(); if (amode) printf(" %s", p); }
break;
case AtomVariable:
if (amode) {
if (localDef(b))
printf("0x%x: AtomVariable (local)\t", offset);
else printf("0x%x: AtomVariable (toplevel)\t", offset);
}
if (gmode) printf("%d [label=\"0x%x AtomVariable", offset, offset);
dopointer(NONZERO, Module, readpointer(), k, offset, "");
{ char *p = readposn(); if (amode) printf(" %s", p); }
{ char *fp = readfixpri(); if (*fp!='\0' && amode) printf("%s ", fp); }
{ unsigned int a = readarity();
if (amode || gmode) printf(amode ? " arity=%u," : " %u", a); }
{ char *n = readstring(); if (amode || gmode) printf(" %s", n); }
if (gmode) printf("\"]\n");
break;
case AtomConstructor:
if (amode) printf("0x%x: %-20s\t", offset, tag2str(k));
if (gmode) printf("%d [label=\"0x%x AtomConstructor", offset, offset);
dopointer(NONZERO, Module, readpointer(), k, offset, "");
{ char *p = readposn(); if (amode) printf(" %s", p); }
{ char *fp = readfixpri(); if (*fp!='\0' && amode) printf("%s", fp); }
{ unsigned int a = readarity();
if (amode || gmode) printf(amode ? " arity=%u," : " %u", a);
{ char *n = readstring(); if (amode || gmode) printf(" %s", n); }
if (gmode) printf("\"]\n");
if hasFields(b) {
int i;
if (amode) printf(" fields:");
for (i=1; i<=a; i++) {
dopointer(NONZERO, AtomVariable, readpointer(), k, offset,
(gmode ? (sprintf(stringbuf,"%d",i), stringbuf) : "")
);
}
}
}
break;
case AtomAbstract:
if (amode) printf("0x%x: %-20s\t", offset, tag2str(k));
if (gmode) printf("%d [label=\"0x%x AtomAbstract ", offset, offset);
{ char *s = readstring(); if (amode || gmode) printf("%s", s); }
if (gmode) printf("\"]\n");
break;
default: {
if (amode) printf("0x%x: %-20s\t", offset, tag2str(k));
if (hasSrcPos(b)) {
if (amode) printf("use=");
dopointer(NONZERO, SrcPos, readpointer(), k, offset, "");
if (amode) printf(" ");
}
// if (amode && (ExpChar <= k) && (k <= ExpConstUse)) {
// printf("(");
// if (!isEntered(b)) printf("not ");
// printf("entered) ");
// }
switch (k) {
case ExpApp:
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
if (amode) printf(" result=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "r");
if (amode) printf(" fun=");
dopointer(NONZERO, ANYEXP, readpointer(), k, offset, "f");
if (gmode) printf("%d [label=\"0x%x ExpApp", offset, offset);
{ unsigned int a = readarity();
int i;
if (amode || gmode)
printf(amode ? " arity=%u, args " : " %u\"]\n",a);
for (i=1; i<=a; i++)
dopointer(NONZERO, ANYEXP, readpointer(), k, offset,
(gmode ? (sprintf(stringbuf,"%d",i), stringbuf) : "")
);
}
break;
case ExpValueApp:
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
if (amode) printf(" fun=");
dopointer(NONZERO, ANYATOM, readpointer(), k, offset, "f");
if (gmode) printf("%d [label=\"0x%x ExpValueApp", offset, offset);
{ unsigned int a = readarity();
int i;
if (amode || gmode)
printf(amode ? " arity=%u, args " : " %u\"]\n",a);
for (i=1; i<=a; i++)
dopointer(NONZERO, ANYEXP, readpointer(), k, offset,
(gmode ? (sprintf(stringbuf,"%d",i), stringbuf) : "")
);
}
break;
case ExpChar:
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
{ char c = nextbyte();
if (gmode) printf("%d [label=\"ExpChar", offset);
if (amode || gmode) printf(" '%c'", c);
if (gmode) printf("\"]\n");
}
break;
case ExpInt:
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
{ int i; i = readfourbytes();
if (gmode) printf("%d [label=\"ExpInt", offset);
if (amode || gmode) printf(" %d", i);
if (gmode) printf("\"]\n");
}
break;
case ExpInteger:
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
{ char* i; i = readinteger();
if (gmode) printf("%d [label=\"ExpInteger", offset);
if (amode || gmode) printf(" %s", i);
if (gmode) printf("\"]\n");
}
break;
case ExpRat:
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
{ int n,d; n=readfourbytes(); d=readfourbytes();
if (gmode) printf("%d [label=\"ExpRat", offset);
if (amode || gmode) printf(" %d%%%d", n,d);
if (gmode) printf("\"]\n");
}
break;
case ExpRational:
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
{ char* r = readrational();
if (gmode) printf("%d [label=\"ExpRational", offset);
if (amode || gmode) printf(" %s", r);
if (gmode) printf("\"]\n");
}
break;
case ExpFloat:
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
{ float f = readfloat();
if (gmode) printf("%d [label=\"ExpFloat", offset);
if (amode || gmode) printf(" %f", f);
if (gmode) printf("\"]\n");
}
break;
case ExpDouble:
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
{ double d = readdouble();
if (gmode) printf("%d [label=\"ExpDouble", offset);
if (amode || gmode) printf(" %f", d);
if (gmode) printf("\"]\n");
}
break;
case ExpValueUse:
if (gmode) printf("%d [label=\"0x%x ExpValueUse\"]\n", offset, offset);
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
if (amode) printf(" value=");
dopointer(MAYBELAMBDA, ANYATOM, readpointer(), ExpValueUse, offset,"v");
break;
case ExpConstUse:
if (gmode) printf("%d [label=\"0x%x ExpConstUse\"]\n", offset, offset);
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
if (amode) printf(" const=");
dopointer(NONZERO, ExpConstDef, readpointer(), k, offset, "c");
break;
case ExpConstDef:
if (gmode) printf("%d [label=\"0x%x ExpConstDef\"]\n", offset, offset);
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
if (amode) printf(" result=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "r");
if (amode) printf(" var=");
dopointer(NONZERO, AtomVariable, readpointer(), k, offset, "v");
break;
case ExpGuard:
case ExpCase:
case ExpIf:
if (gmode) printf("%d [label=\"0x%x %s\"]\n", offset, offset,
k==ExpGuard ? "ExpGuard" : k==ExpCase ? "ExpCase" : "ExpIf");
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
if (amode) printf(" result=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "r");
if (amode) printf(" cond=");
dopointer(NONZERO, ANYEXP, readpointer(), k, offset, "c");
break;
case ExpFieldUpdate:
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
if (amode) printf(" result=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "r");
if (amode) printf(" arg=");
dopointer(NONZERO, ANYEXP, readpointer(), k, offset, "a");
{ unsigned int i, arity = readarity();
if (gmode) printf("%d [label=\"0x%x ExpFieldUpdate %u\"]\n", offset, offset, arity);
if (amode) printf(" arity=%u, binders ",arity);
for (i=0; i<arity; i++) {
dopointer(NONZERO, AtomVariable, readpointer(), k, offset, "");
}
if (amode) printf(", bindees ",arity);
for (i=0; i<arity; i++) {
dopointer(NONZERO, ANYEXP, readpointer(), k, offset, "");
}
}
break;
case ExpProjection:
if (gmode) printf("%d [label=\"0x%x ExpProjection\"]\n", offset, offset);
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
if (amode) printf(" exp=");
dopointer(NONZERO, ANYEXP, readpointer(), k, offset, "e");
break;
case ExpHidden:
if (gmode) printf("%d [label=\"0x%x ExpHidden\"]\n", offset, offset);
if (amode) printf("parent=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "p");
if (amode) printf(" result=");
dopointer(MAYBEZERO, ANYEXP, readpointer(), k, offset, "r");
if (amode) printf(" children=");
dopointer(MAYBEZERO, ListCons, readpointer(), k, offset, "c");
break;
case ExpForward:
if (gmode) printf("%d [label=\"0x%x ExpForward\"]\n", offset, offset);
if (amode) printf("result=");
dopointer(NONZERO, ANYEXP, readpointer(), k, offset, "r");
break;
case ExpDoStmt:
if (gmode) printf("%d [label=\"0x%x ExpDoStmt\"]\n", offset, offset);
if (amode) printf("stmt=");
dopointer(NONZERO, ANYEXP, readpointer(), k, offset, "s");
break;
}
}}
if (amode) printf("\n");
if (smode) space[k] += nextoffset - offset;
}
}
void checkRooted(Pr* opt){
FILE * tree = fopen(opt->inFile.c_str(),"rt");
if (tree==NULL){
cout<<"Error: can not open the input file"<<endl;
exit(EXIT_FAILURE);
}
stack<int> pileNode;
char c = readBracket(tree,"input tree");
int a=1;
int s=0;
int nbChild=0;
int n=0;
int m=0;
do{
c = readChar(tree,"input tree");
if (c==')'){
a--;
s=0;
nbChild=0;
while (!pileNode.empty() && s!=-1) {
s=pileNode.top();pileNode.pop();
if (s!=-1){
nbChild++;
}
}
string sp=readSupport(tree,"input tree");
if (a>0) {
double d = readdouble(tree,"input tree");
}
pileNode.push(1);
n++;
m++;
}
else if (c!='(' && c!=',' && c!=-1 && c!=';' && c!='\n'){
string s= readLabel(c,tree,a);
pileNode.push(1);
double d =readdouble(tree,"input tree");
m++;
}
else if (c=='(') {a++;pileNode.push(-1);}
else if (c=='\n') {
c=readChar(tree,"input tree");
}
} while (a>0);
fclose(tree);
m--;
opt->nbINodes=n;
opt->nbBranches=m;
if (m==2*n) {
opt->rooted=true;
}
else if (m==2*n+1 && nbChild==3){
opt->rooted=false;
}
else if (nbChild==2) {
opt->rooted=true;
}
else{
opt->rooted=false;
}
}
