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rf.cpp
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/*
int a = 0;
* --------------------------------------------*
* Computation of the Robinson and Foulds *
* topological distance between two (or more) *
* trees given their distance matrices *
* *
* Input data file format: *
* 1. Number of objects (matrix size) n *
* 2. A sequence of m squared additive *
* distance matrices of size n by n *
* assosiated with trees *
* *
* Output data: *
* 1. A sequence of m-1 integer numbers *
* containing the Robinson and Foulds *
* distances between the tree associated *
* with the first matrix and all the other *
* trees associated with the following ones *
* *
* Vladimir Makarenkov *
* University of Montreal, September 1999 *
* --------------------------------------------*
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include <string.h>
#pragma warning(disable:4996)
#define INFINI 999999.99
// 1024*1024*500 element
#define SEUIL 104857600
//unsigned int n;
FILE *Output1;
int a;
/* Function's Propotypes */
void odp(double**,int*,int*,int*,int n);
int Bipartition_Table(double **, int **,int*,int n);
int Table_Comparaison(int**,int**,int*,int*,int,int,int n);
int nbSpeciesPhylip(const char *fichier){
FILE *in;
int nbItem;
in = fopen(fichier,"r+");
fscanf(in,"%d",&nbItem);
fclose(in);
a=0;
if((nbItem > 10000) || (nbItem < 3))
exit(8);
return nbItem;
}
int fileInNewickFormat(char *fichier){
char car;
// int retour;
int i=0;
FILE *in = fopen(fichier,"r+");
//= rechercher le premier caractere
do{
fscanf(in,"%c",&car);
i++;
if(i > SEUIL) exit(-1);
}while((car == ' ') || (car == '\t') || (car == '\n') || (car == '\r'));
fclose(in);
a=0;
if (car=='(') return 1;
else return 0;
}
void filtrerMatrice2(double **dissSpecies, double **dissGene, char **nomsSpecies, char **nomsGene,int nbSpecies, int nbGene, char * fichier){
int i,j,temoin;
/*FILE * out;
if((out = fopen(fichier,"a+")) == NULL){
printf("Can't open %s",fichier);
exit(-1);
}
fprintf(out,"\n=>Filtre");
*/
for(i=1;i<=nbSpecies;i++){
//printf("\n%s -",nomsSpecies[i]);
temoin = 0;
for(j=1;j<=nbGene;j++){
//printf(" %s",nomsGene[j]);
if(strcmp(nomsSpecies[i],nomsGene[j])==0)
temoin=1;
}
if(temoin == 0){
//fprintf(out,"\nSpecies:%s",nomsSpecies[i]);
for(j=1;j<=nbSpecies;j++){
dissSpecies[i][j] = dissSpecies[j][i] = -1;
}
strcpy(nomsSpecies[i],"");
}
}
//printf("==============");
for(i=1;i<=nbGene;i++){
//printf("\n%s -",nomsGene[i]);
temoin = 0;
for(j=1;j<=nbSpecies;j++){
// printf(" %s",nomsSpecies[j]);
//if(strlen(nomsSpecies[j]) > 1)
if(strcmp(nomsSpecies[j],nomsGene[i])==0)
temoin=1;
}
if(temoin == 0){
//fprintf(out,"\nGene:%s",nomsGene[i]);
for(j=1;j<=nbGene;j++){
dissGene[i][j] = dissGene[j][i] = -1;
}
strcpy(nomsGene[i],"");
}
}
//fclose(out);
}
void filtrerMatrice(double **dissSpecies, double **dissGene, char **nomsSpecies, char **nomsGene,int nbSpecies, int nbGene){
int i,j,temoin;
//printf("\nn=%d",nbSpecies);
for(i=1;i<=nbSpecies;i++){
// printf("\n%s -",nomsSpecies[i-1]);
temoin = 0;
for(j=1;j<=nbGene;j++){
//printf(" %s",nomsGene[j-1]);
if(strcmp(nomsSpecies[i-1],nomsGene[j-1])==0)
temoin=1;
}
if(temoin == 0){
// printf("*");
for(j=1;j<=nbSpecies;j++){
//dissSpecies[i+1][j+1] = dissSpecies[j+1][i+1] = -1;
dissSpecies[i][j] = dissSpecies[j][i] = -1;
}
strcpy(nomsSpecies[i-1],"");
}
}
// printf("\n\nn=%d",nbGene);
for(i=1;i<=nbGene;i++){
// printf("\n%s -",nomsGene[i-1]);
temoin = 0;
for(j=1;j<=nbSpecies;j++){
// printf(" %s",nomsSpecies[j]);
// if(strlen(nomsSpecies[j]) > 1)
if(strcmp(nomsSpecies[j-1],nomsGene[i-1])==0)
temoin=1;
}
if(temoin == 0){
// printf("*");
for(j=1;j<=nbGene;j++){
//dissGene[i+1][j+1] = dissGene[j+1][i+1] = -1;
dissGene[i][j] = dissGene[j][i] = -1;
}
strcpy(nomsGene[i-1],"");
}
}
}
int ecrireMatrice2(double **source,double**dest,int taille,char **nomsSource,char **nomsDest){
int i,ii,j,jj,finalTaille;
// FILE *out;
finalTaille=0;
for(i=0;i<taille;i++)
if(strcmp(nomsSource[i],"")!=0)
finalTaille = finalTaille+1;
if(finalTaille < 3){
printf("There are less than 3 same species !");
exit(5);
}
ii=1;
for(i=0;i<taille;i++){
if(strcmp(nomsSource[i],"") != 0){//if(strlen(noms[i]) > 1){
strcpy(nomsDest[ii-1],nomsSource[i]);
jj=1;
for(j=0;j<taille;j++)
if(source[i+1][j+1] != -1){
dest[ii][jj] = source[i+1][j+1];
jj++;
}
ii++;
}
}
return finalTaille;
}
//=========================================================
//
//=========================================================
double ** createDoubleMatrix(int size){
double ** matrice;
int i;
matrice = (double **) malloc((size)*sizeof(double *));
for(i=0;i<size;i++)
matrice[i] = (double *)malloc(size*sizeof(double));
return matrice;
}
//==========================================================
//
//==========================================================
void freeDoubleMatrix(double **matrice,int size){
int i;
for(i=0;i<size;i++)
free(matrice[i]);
//free(matrice);
}
char ** createStringMatrix(int nbString,int stringSize){
char ** noms;
int i;
noms = (char **)malloc(nbString*sizeof(char *));
for(i=0;i<nbString;i++)
noms[i] = (char *)malloc(stringSize);
return noms;
}
int nbSpeciesNewick(char *fichier){
FILE *data;
int i=0;
int n = 0;
char symbol;
char symbolOld =' ';
int temoin=0;
if ((data=fopen(fichier,"r"))==0) { printf("\n%s:Open Failed....",fichier); return -1; }
//Correctness of the Newick format verification
do
{
symbol=getc(data);
if (symbol==':') i++;
if(symbol == ':' && symbolOld !=')' && temoin != 1) n++;
if(symbol >= '0' && symbol <= '9' && symbolOld==')') temoin=1;
if(symbol==':' && temoin==1) temoin=0;
symbolOld = symbol;
} while(symbol != ';');
/*
while ((symbol=getc(data))!=';')
{
if (symbol==':') i++;
if (symbol == ':' && symbolOld != ')') n++;
symbolOld = symbol;
}
*/
fclose(data);
return n;
}
void TreeMatrix(double **DISS, long int *ARETE, double *LONGUEUR,int n,int kt)
{
int i,j,k,A,B;
double **Adjacence;
double longueur;
Adjacence = (double**) malloc ((2*n-1) * sizeof(double*));
for (i=0;i<=2*n-2;i++)
{
Adjacence[i] = (double*) malloc ((2*n-1) * sizeof(double));
}
for(i=1;i<=2*n-2;i++)
for(j=1;j<=2*n-2;j++)
Adjacence[i][j] = INFINI;
for (i=1;i<=2*n-3-kt;i++)
{
A = ARETE[2*i-2];
B = ARETE[2*i-1];
longueur = LONGUEUR[i-1];
Adjacence[A][B] = Adjacence[B][A] = longueur;
}
for(i=1;i<=2*n-2;i++)
for(j=i+1;j<=2*n-2;j++)
{
DISS[i][j] = DISS[j][i] = Adjacence[i][j];
}
for(i=1;i<=2*n-2;i++)
DISS[i][i] = 0.0;
//int bidon;
for(i=1;i<=2*n-2;i++)
for(j=1;j<=2*n-2;j++)
for(k=1;k<=2*n-2;k++)
{
if((DISS[j][i] + DISS[i][k]) < DISS[j][k])
DISS[j][k] = DISS[k][j] = DISS[j][i] + DISS[i][k];
}
// afficherMatriceDouble(DISS,n);
// free(Adjacence);
/* for(i=1;i<=2*n-2;i++)
for(j=1;j<=2*n-2;j++)
DISS[i-1][j-1] = DISS[i][j];*/
}
static void xtoa (unsigned long val,char *buf,unsigned radix,int is_neg){
char *p; /* pointer to traverse string */
char *firstdig; /* pointer to first digit */
char temp; /* temp char */
unsigned digval; /* value of digit */
p = buf;
if (is_neg) {
/* negative, so output '-' and negate */
*p++ = '-';
val = (unsigned long)(-(long)val);
}
firstdig = p; /* save pointer to first digit */
do {
digval = (unsigned) (val % radix);
val /= radix; /* get next digit */
/* convert to ascii and store */
if (digval > 9)
*p++ = (char) (digval - 10 + 'a'); /* a letter */
else
*p++ = (char) (digval + '0'); /* a digit */
} while (val > 0);
/* We now have the digit of the number in the buffer, but in reverse
order. Thus we reverse them now. */
*p-- = '\0'; /* terminate string; p points to last digit */
do {
temp = *p;
*p = *firstdig;
*firstdig = temp; /* swap *p and *firstdig */
--p;
++firstdig; /* advance to next two digits */
} while (firstdig < p); /* repeat until halfway */
}
/* Actual functions just call conversion helper with neg flag set correctly,
and return pointer to buffer. */
char * itoa(int val,char *buf,int radix){
if (radix == 10 && val < 0)
xtoa((unsigned long)val, buf, radix, 1);
else
xtoa((unsigned long)(unsigned int)val, buf, radix, 0);
return buf;
}
//===============================================================================================
//
//===============================================================================================
int lectureNewick(const char * fichier, long int * ARETE, double * LONGUEUR, char ** lesNoms, int *kt)
{
int n;
int cpt_x;
// Ce sous programme permet de lire un arbre au format newick et de le transcrire dans
// des vecteurs arete-longueur commencant à 1
// ATTENTION: les noms commencent à 0
// 7 octobre 2004
// Elmaestro
//printf("\nlecture Newick : ");
// TODO: Add your command handler code here
int FAIL =-1;
int i,j,j1,k, a, a1, a2,a3, VertexNumber,numero;
char symbol, *string, *string1, *string2/* *string3,c ,**Et*/;
int taxaPos; // le nombre de taxas recupéré
int aretePos; // le nombre d'aretes recupéré
char symbolOld =' ';
int zz, xx,jj,ii;
double longueur;
char * tempString;
int cpt=0;
int na;
char *string4 = (char*) malloc(1000);
int temoin=0;
char *newick = (char*)malloc(10000);
//long int *ARETE;
//double *LONGUEUR;
FILE *data;
if ((data=fopen(fichier,"r"))==0) { printf("\n%s:Open Failed....",fichier); return FAIL; }
i=0;
while ((symbol=getc(data))!=EOF)
{
newick[i] = symbol;
i++;
}
newick[i] = '\0';
fclose(data);
//printf(" fclose(data)");
a=0;
//Correctness of the Newick format verification
i=0;
n = 0;
do
{
symbol = newick[cpt++];
if (symbol==':') i++;
if(symbol == ':' && symbolOld !=')' && temoin != 1) n++;
if(symbol >= '0' && symbol <= '9' && symbolOld==')') temoin=1;
if(symbol==':' && temoin==1) temoin=0;
symbolOld = symbol;
} while(symbol != '\0');
cpt=0;
na=i;
if(i<=2*n-3)(*kt)=i;
else (*kt)=2*n-3;
if (i == 0) { printf("Incorrect Newick file format. Edge lengths must be indicated after a ':' characters."); return FAIL;}
if ((i>2*n-3) || (i<n)){
//printf("Unable to read your input data, please check it and try again...");
//exit(-1);
}
j=0;
do{
symbol=newick[cpt++];
if (symbol=='(') j++;
}while(symbol != '\0');
cpt=0;
j1=0;
do{
symbol=newick[cpt++];
if (symbol==')') j1++;
}while(symbol != '\0');
cpt=0;
// verification des arités de l'arbre
if (j1!=j) { printf("Incorrect Newick file format. Number of right parentheses must be equal to number of left parentheses."); return FAIL;}
//else if (j!=n-2) { printf("Incorrect Newick file format. Only trees with vertices of degree 1 and 3 are allowed by T-REX."); fclose (data); return FAIL;}
k=0;
do{
symbol=newick[cpt++];
if (symbol==',') k++;
}while(symbol != '\0');
cpt=0;
//if (k!=(n-1)) { printf("Incorrect Newick file format. Number of objects must be equal to number of commas plus 1."); fclose (data); return FAIL;}
a=0;
do{
symbol=newick[cpt++];
if (symbol==';') a++;
}while(symbol != '\0');
cpt=0;
if (a==0) { printf("Incorrect Newick file format. Newick string must be followed by a ';' character."); return FAIL;}
else if (a>1) { printf("Incorrect Newick file format. Newick string must contain (in the end) only one ';' character."); return FAIL;}
a=0;
do{
symbol=newick[cpt++];a++;
}while(symbol == ' ');
cpt=0;
if (symbol!='(') { printf("Incorrect Newick file format. Newick string must begin with a '(' character."); return FAIL;}
a=0;
do{ symbol=newick[cpt++];
if (symbol=='%') a++;
}while(symbol != '\0');
cpt=0;
if (a>0) { printf("Incorrect Newick file format. Newick string cannot contain '%%' character."); return FAIL;}
do
{
symbol=newick[cpt++];
if ((symbol=='(')||(symbol==','))
{
symbol=newick[cpt++]; a=0;
if ((symbol!='(')&&(symbol!=',')&&(symbol!=';')&&(symbol!=':'))
{
cpt--;
do{
symbol=newick[cpt++];a++;
}while ((symbol!=':')&&(symbol!='\0'));
}
else cpt--;
if (a>50) { printf("Incorrect Newick file format. Names of objects must not exceed 50 characters."); return FAIL;}
}
}while(symbol != '\0');
cpt=0;
string = (char*)malloc((100000*n) * sizeof(char));
string2 = (char*)malloc((100000*n) * sizeof(char));
string1 = (char*)malloc((200000) * sizeof(char));
if ((string == NULL)||(string1 == NULL)||(string2 == NULL)/*||(string3 == NULL)*/)
{ printf("Input data are too large or not a correct Newick file chosen"); return FAIL;}
a=0;
do{
symbol=newick[cpt++];
if ((symbol!=' ')&&(symbol!='\n')&&(symbol!='\t')) { string[a++]=symbol; }
}while(symbol !='\0');
int boot_value;
int temoin3 = 0;
k=0; VertexNumber=n;
//a1 = 0;
//a2 = 0;
taxaPos =1; // nous allons commencer à mettre les taxas à la position 1
aretePos = 1;
boot_value=0;
while (string[0] == '(') // traiter toute la chaine
{
a1 = 0;
a2 = 0;
while( string[a2] != ')') // traiter la paire () la plus profonde
{
if(string[a2] == '(') a1 = a2; // retrouver ;a parenthèse ouvrante
a2++;
}
// a => contient la longueur de la chaine
// a1 => contient le debut d'un noeud à traiter
// a2 => contient la fin d'un noeud à traiter
// a3 => délimite le noeud et sa longueur
zz = a1+1;
VertexNumber++; // augmenter le nombre de noeuds
boot_value=0;
for ( ii = a1+1; ii <= a2; ii++)
{// decortiquer cette chaine
if (string[ii] == ':')
{
xx = 0;
a3 = ii+1;
if( string[zz] == '%')
{ // cela veut dire que c'est un noeud que l'on traite
for ( jj = zz+1; jj < ii; jj++)
{
if(string[jj] == '|')
break;
string1[xx++] = string[jj];
}
temoin3=1;
string1[xx++] = '\0';
numero = atoi(string1);
if(string[jj] == '|' ){
boot_value=1;
cpt_x=0;
jj++;
while(string[jj] != ':')
string4[cpt_x++] = string[jj++];
string4[cpt_x] = '\0';
}
}
else
{
// on recupère le nom du taxa
for(jj = zz; jj < ii; jj++)
{
lesNoms[taxaPos-1][xx++] = string[jj];
}
numero = taxaPos;
lesNoms[taxaPos-1][xx] = '\0'; // mettre la fin de chaine
taxaPos++; // augmenter le nombre de taxas pris
}
}
else if(string[ii] == ',' || string[ii] == ')')
{
xx = 0;
zz = ii +1; // faire pointer sur le prochain noeud
for ( jj = a3; jj < ii; jj++)
{
string1[xx++] = string[jj];
}
string1[xx++] = '\0';
longueur = atof(string1);
ARETE[aretePos++] = VertexNumber;
ARETE[aretePos++] = numero;
LONGUEUR[(aretePos-1)/ 2] = longueur;
if(boot_value == 1){
//printf("\n%d--%d : %lf (%s)",VertexNumber,numero,longueur,string4);
boot_value=0;
}
}
}
// fin for pour traiter noeud
//transcrire la nouvelle chaine
xx = 0;
for ( jj = 0; jj < (int)a1; jj++)
{string2[xx++] = string[jj];}
// ecrire le vertex
// char buffer[50];
itoa(VertexNumber,string1,10);
string2[xx++] = '%'; // indiquer que c'est un noeud
for( jj = 0; jj < (int) strlen(string1); jj++)
{string2[xx++] = string1[jj];}
int temoin=0;
// transcrire la fin
for( jj = a2+1; jj <= a; jj++) // il faut voir si c'est <= a ou c < a
{
if(string[jj] != ':' && temoin==0){
string2[xx++] = '|';
}
temoin = 1;
//if(temoin==1)
string2[xx++] = string[jj];
}
// remplacer string par string2 en remplacant les pointeurs
tempString = string;
string = string2;
string2 = tempString;
tempString = 0;
a = xx; // mettre la longueur à jour
} // fin du while pour traiter toute la string
/*for( jj=n;jj>0;jj--)
strcpy(lesNoms[jj],lesNoms[jj-1]);*/
int root_existance = -1;
//for( jj=n;jj>0;jj--){
for(jj=0;jj<n;jj++){
//strcpy(lesNoms[jj],lesNoms[jj+1]);
if (strcmp(lesNoms[jj],"Root") == 0)
root_existance = jj;
}
/*printf("\nRoot_existance = %d",root_existance);
for( jj=0;jj<n;jj++){
printf("\n(%d) - %s",jj,lesNoms[jj]);
}
*/
/*
printf("\n\naretePos=%d\n",aretePos);
for(i=1;i<=2*(2*n-3);i++){
printf("\n%d",ARETE[i]);
}
*/
ARETE[aretePos++] = 0;
ARETE[aretePos++] = 0;
/*for(i=1;i<=2*(na);i++){
ARETE[i-1] = ARETE[i];
}*/
i=0;
int cpt_branches=0;
do{
i++;cpt_branches++;
// printf("\n%d : %d",cpt_branches,ARETE[i]);
ARETE[i-1] = ARETE[i];
i++;
// printf("--%d",ARETE[i]);
ARETE[i-1] = ARETE[i];
}while(ARETE[i] != 0);
for(i=1;i<=na;i++){
LONGUEUR[i-1] = LONGUEUR[i];
}
//printf("\nNombre de branches dans l'arbre : %d",na);
/*
printf("\n\naretePos=%d,n=%d\n",aretePos,n);
for(i=1;i<=na;i++){
printf("\n%d : %d-%d",i,ARETE[2*i-2],ARETE[2*i-1]);
}*/
//== recherche des branches connexes a celle de la racine;
if( root_existance > 0){
int noeud_interne = -1;
for(i=1;i<=na;i++){
if(ARETE[2*i-1] == root_existance)
noeud_interne = ARETE[2*i-2];
if(ARETE[2*i-2] == root_existance)
noeud_interne = ARETE[2*i-1];
}
//printf("\n[%d,%d]",noeud_interne,root_existance);
for(i=1;i<=na;i++){
if((ARETE[2*i-1] != root_existance) && (noeud_interne == ARETE[2*i-2])){
LONGUEUR[i-1] = 50;
// printf("\n[%d,%d]",noeud_interne,ARETE[2*i-1]);
}
if((ARETE[2*i-2] != root_existance) && (noeud_interne == ARETE[2*i-1])){
LONGUEUR[i-1] = 50;
// printf("\n[%d,%d]",noeud_interne,ARETE[2*i-2]);
}
}
}
//=== on teste si il y a un noeud de degre 2 et un noeud de degre 1
/* printf("\nn=%d",n);
for(i=1;i<=na;i++){
printf("\n%d : %d-%d --> %lf",i,ARETE[2*i-1],ARETE[2*i-2],LONGUEUR[i-1]);
}
printf("\n");
*/
int * tableau = (int*)malloc((2*n)*sizeof(int));
int deg2=-1,deg1=-1;
for(i=1;i<=2*n;i++)
tableau[i-1] = 0;
for(i=1;i<=na;i++){
tableau[ARETE[2*i-1]]++;
tableau[ARETE[2*i-2]]++;
}
// printf("\n");
i=n+1;
while(tableau[i] > 0){
//printf("\n%d-->%d",i,tableau[i]);
if(tableau[i] == 2) deg2 = i;
if(tableau[i] == 1) deg1 = i;
i++;
}
//printf("\ndeg2=%d , deg1=%d",deg2,deg1);
int pos_racine=-1;
for(i=1;i<=na;i++){
if(ARETE[2*i-1] == deg1){ ARETE[2*i-1] = deg2; pos_racine=i; break;}
if(ARETE[2*i-2] == deg1){ ARETE[2*i-2] = deg2; pos_racine=i; break;}
}
if(pos_racine != -1){
LONGUEUR[pos_racine-1] = 100;
}
else if(deg2 != -1){
int pos1=-1,pos2=-1;
for(i=1;i<=na;i++){
if((ARETE[2*i-1] == deg2 || ARETE[2*i-2] == deg2) && pos1==-1){ pos1=i;}
else if((ARETE[2*i-1] == deg2 || ARETE[2*i-2] == deg2) && pos1 != -1){ pos2=i;}
}
//printf("\npos1=%d, pos2=%d",pos1,pos2);
//== modification de la branche pos1
if(ARETE[2*pos1-1] == deg2)
ARETE[2*pos1-1] = (ARETE[2*pos2-1] == deg2)?ARETE[2*pos2-2]:ARETE[2*pos2-1];
else
ARETE[2*pos1-2] = (ARETE[2*pos2-1] == deg2)?ARETE[2*pos2-2]:ARETE[2*pos2-1];
//== suppression de la branche pos2
for(i=pos2;i<=na;i++){
LONGUEUR[i-1] = LONGUEUR[i];
ARETE[2*i-1] = ARETE[2*(i+1)-1];
ARETE[2*i-2] = ARETE[2*(i+1)-2];
}
na--;
}
/*printf("\nn=%d",n);
for(i=1;i<=na;i++){
printf("\n%d : %d-%d --> %lf",i,ARETE[2*i-1],ARETE[2*i-2],LONGUEUR[i-1]);
}
printf("\n");*/
(*kt) = 2*n-3 - (*kt);
//printf ("\nkt=%d,na=%d,n=%d",*kt,na,n);
return n;
//=== on teste si il y a un noeud de degre 2 et un noeud de degre 1
//int * tableau = (int*)malloc((2*n)*sizeof(int));
//int deg2=0,deg1=0;
for(i=n+1;i<=2*n;i++)
tableau[i-1] = 0;
for(i=1;i<=2*n-3-(*kt);i++){
tableau[ARETE[2*i-1]]++;
tableau[ARETE[2*i-2]]++;
}
// printf("\n");
i=n+1;
while(tableau[i] > 0){
printf("\n%d-->%d",i,tableau[i]);
if(tableau[i] == 2) deg2 = i;
if(tableau[i] == 1) deg1 = i;
i++;
}
for(i=1;i<=2*n-3-(*kt);i++){
if(ARETE[2*i-1] == deg1) ARETE[2*i-1] = deg2;
if(ARETE[2*i-2] == deg1) ARETE[2*i-2] = deg2;
}
printf("\nn=%d",n);
for(i=1;i<=na;i++){
printf("\n%d : %d-%d --> %lf",i,ARETE[2*i-1],ARETE[2*i-2],LONGUEUR[i-1]);
}
free(string);
free(string1);
free(string2);
free(newick);
//free(string3);
return n;
}
//===============================================================================================
//
//===============================================================================================
int lectureNewick_(char * fichier, long int * ARETE, double * LONGUEUR, char ** lesNoms,int *kt)
{
int n;
printf("\nlecture Newick : ");
// Ce sous programme permet de lire un arbre au format newick et de le transcrire dans
// des vecteurs arete-longueur commencant à 1
// ATTENTION: les noms commencent à 0
// 7 octobre 2004
// Elmaestro
// TODO: Add your command handler code here
int FAIL =-1;
int i,j,j1,k,NewickValid=1, a, a1, a2,a3, VertexNumber,numero;
char symbol, *string, *string1, *string2/* *string3,c ,**Et*/;
int taxaPos; // le nombre de taxas recupéré
int aretePos; // le nombre d'aretes recupéré
char symbolOld =' ';
int zz, xx,jj,ii;
double longueur;
char * tempString;
//long int *ARETE;
//double *LONGUEUR;
FILE *data;
if ((data=fopen(fichier,"r"))==0) { printf("\n%s:Open Failed....",fichier); return FAIL; }
//Correctness of the Newick format verification
i=0;
n = 0;
while ((symbol=getc(data))!=EOF)
{
if (symbol==':') i++;
if (symbol == ':' && symbolOld != ')') n++;
symbolOld = symbol;
}
fseek(data,0,0);
(*kt) = i;
if (i == 0) { printf("Incorrect Newick file format. Edge lengths must be indicated after a ':' characters."); fclose (data); return FAIL;}
j=0;
while ((symbol=getc(data))!=EOF)
{ if (symbol=='(') j++; }
fseek(data,0,0);
j1=0;
while ((symbol=getc(data))!=EOF)
{ if (symbol==')') j1++; }
fseek(data,0,0);
// verification des arités de l'arbre
if (j1!=j) { printf("Incorrect Newick file format. Number of right parentheses must be equal to number of left parentheses."); fclose (data); return FAIL;}
//else if (j!=n-2) { printf("Incorrect Newick file format. Only trees with vertices of degree 1 and 3 are allowed by T-REX."); fclose (data); return FAIL;}
k=0;
while ((symbol=getc(data))!=EOF)
{ if (symbol==',') k++; }
fseek(data,0,0);
//if (k!=(n-1)) { printf("Incorrect Newick file format. Number of objects must be equal to number of commas plus 1."); fclose (data); return FAIL;}
a=0;
while ((symbol=getc(data))!=EOF)
{ if (symbol==';') a++; }
fseek(data,0,0);
if (a==0) { printf("Incorrect Newick file format. Newick string must be followed by a ';' character."); fclose (data); return FAIL;}
else if (a>1) { printf("Incorrect Newick file format. Newick string must contain (in the end) only one ';' character."); fclose (data); return FAIL;}
a=0;
while ((symbol=getc(data))==' ') a++;
fseek(data,0,0);
if (symbol!='(') { printf("Incorrect Newick file format. Newick string must begin with a '(' character."); fclose (data); return FAIL;}
a=0;
while ((symbol=getc(data))!=EOF)
{ if (symbol=='%') a++; }
fseek(data,0,0);
if (a>0) { printf("Incorrect Newick file format. Newick string cannot contain '%%' character."); fclose (data); return FAIL;}
while ((symbol=getc(data))!=EOF)
{
if ((symbol=='(')||(symbol==','))
{
symbol=getc(data); a=0;
if ((symbol!='(')&&(symbol!=',')&&(symbol!=';')&&(symbol!=':'))
{ fseek(data,-1,1); while (((symbol=getc(data))!=':')&&(symbol!=EOF)) a++; }
else fseek(data,-1,1);
if (a>50) { printf("Incorrect Newick file format. Names of objects must not exceed 50 characters."); fclose (data); return FAIL;}
}
}
fseek(data,0,0);
string = (char*)malloc((1000*n) * sizeof(char));
string2 = (char*)malloc((1000*n) * sizeof(char));
//string3 = (char*)malloc((1000*n) * sizeof(char));
string1 = (char*)malloc((2000) * sizeof(char));
if ((string == NULL)||(string1 == NULL)||(string2 == NULL)/*||(string3 == NULL)*/)
{ printf("Input data are too large or not a correct Newick file chosen"); fclose (data); return FAIL;}
a=0;
while ((symbol=getc(data))!=EOF)
{ if ((symbol!=' ')&&(symbol!='\n')&&(symbol!='\t')) { string[a++]=symbol; } }
fclose (data);
printf(" fclose(data)");
k=0; VertexNumber=n;
//a1 = 0;
//a2 = 0;
taxaPos =1; // nous allons commencer à mettre les taxas à la position 1
aretePos = 1;
while (string[0] == '(') // traiter toute la chaine
{
a1 = 0;
a2 = 0;
while( string[a2] != ')') // traiter la paire () la plus profonde
{
if(string[a2] == '(') a1 = a2; // retrouver ;a parenthèse ouvrante
a2++;
}
// a => contient la longueur de la chaine
// a1 => contient le debut d'un noeud à traiter
// a2 => contient la fin d'un noeud à traiter
// a3 => délimite le noeud et sa longueur
zz = a1+1;
VertexNumber++; // augmenter le nombre de noeuds