Convertir un program c en c++
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samsouma04
Messages postés
60
Date d'inscription
samedi 26 juillet 2008
Statut
Membre
Dernière intervention
17 mai 2009
-
20 avril 2009 à 14:19
fiddy Messages postés 11069 Date d'inscription samedi 5 mai 2007 Statut Contributeur Dernière intervention 23 avril 2022 - 15 mai 2013 à 23:07
fiddy Messages postés 11069 Date d'inscription samedi 5 mai 2007 Statut Contributeur Dernière intervention 23 avril 2022 - 15 mai 2013 à 23:07
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13 réponses
Nabla's
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18203
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mercredi 4 juin 2008
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28 avril 2014
3 193
20 avril 2009 à 14:21
20 avril 2009 à 14:21
le compilateur C++ comprend très bien le C. Tu n'as rien a faire ! (renomer le fichier si tu veux)
si tu veux vraiment transcrire ton programme, alors il faire des classes, etc.. mais ce n'est pas une nécessité
si tu veux vraiment transcrire ton programme, alors il faire des classes, etc.. mais ce n'est pas une nécessité
samsouma04
Messages postés
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Date d'inscription
samedi 26 juillet 2008
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20 avril 2009 à 14:22
20 avril 2009 à 14:22
Merci mais jai pensé que ca pose un probleme puisque la compilation me donne des erreurs!!!
Nabla's
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18203
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mercredi 4 juin 2008
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28 avril 2014
3 193
20 avril 2009 à 14:29
20 avril 2009 à 14:29
le mieux serai de nous fournir le code (ou la partie concernée)et les messages d'erreur, pour qu'on puisse t'aider...
samsouma04
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samedi 26 juillet 2008
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20 avril 2009 à 14:32
20 avril 2009 à 14:32
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <stdlib.h>
#include <math.h>
#define MAXNAMES 20
#define MAXSEQ 1000
#define MAXLEN 5000
#define MAXLINE 2048
#define Boolean short
#define TRUE 1
#define FALSE 0
#define EOS '\0'
#define INT_SCALE_FACTOR 100 /* Scaling factor to convert float to integer for profile scores */
#define NUMRES 32 /* max size of comparison matrix */
#define LEFT 1
#define RIGHT 2
#define NODE 0
#define LEAF 1
typedef struct node { /* phylogenetic tree structure */
struct node *left;
struct node *right;
struct node *parent;
float dist;
int leaf;
int order;
char name[64];
} stree, *treeptr;
/* trees.c */
void guide_tree(FILE *tree,int nseqs);
int SeqGCGCheckSum(char *seq, int len);
Boolean keyword(char *line,char *code);
int getargs(char *line,char *args[],int max);
int parse_repart(char *str);
Boolean blankline(char *line);
void readmsf(FILE *fin);
void readref(FILE *fin);
void score_ref(void);
int countmsf(FILE *fin);
void columnscore(Boolean verbose);
void readref(FILE *fin);
int read_annotation(FILE *fin);
int countref(FILE *ifd);
void code_refseq(int i);
void code_seq(int i);
void aln_seq(int i);
void ref_gaps(int cutoff);
/* arrays for storing reference alignment */
char refnames[MAXSEQ][MAXNAMES+1];
char refseq_array[MAXSEQ][MAXLEN];
int refseq_code[MAXSEQ][MAXLEN];
int refseq_col[MAXLEN];
int refseqlength;
int refnseqs;
/* arrays for storing text alignment */
char names[MAXSEQ][MAXNAMES+1];
char seq_array[MAXSEQ][MAXLEN];
int seq_code[MAXSEQ][MAXLEN];
int seq_aln[MAXSEQ][MAXLEN];
int seqlength;
int seq_xref[MAXSEQ];
int nseqs;
Boolean verbose;
int refscore;
/* number of gaps in a column in the reference alignment */
int gap[MAXLEN];
/* cutoff for number of gaps allowed in a column in the reference alignment
for column to be included in alignment score */
int cutoff;
/* core block data read in from annotation file */
int nblocks;
typedef struct Block {
int s;
int e;
int nseqs;
} Block;
Block blocks[100];
/* alignment scores - mean square score, total column score and percentage
of correctly aligned pairs of residues */
float ms_score,tc_score;
float maxscore,maxpc_res;
float pc_res;
void main(int argc, char **argv)
{
FILE *ifd,*tfd,*afd;
int err,i,j,ires,iseq=0;
int ix;
char t[MAXLINE+1];
char seq[MAXLINE+1];
char clen[MAXLINE+1];
char cvar[MAXLINE+1];
char cprog[MAXLINE+1];
char method;
Boolean eof,found;
if(argc<3) {
fprintf(stderr,"Usage: %s ref_aln test_aln [annot_file] [-v]\n",argv[0]);
fprintf(stderr," where ref_aln reference alignment in msf format \n");
fprintf(stderr," test_aln test alignment in msf format \n");
fprintf(stderr," annot_file optional BAliBASE annotation file\n");
fprintf(stderr," -v verbose mode\n");
//return;
}
/* open the reference aln file */
if((ifd=fopen(argv[1],"r"))==NULL) {
fprintf(stderr,"Cannot open reference aln file [%s]",argv[1]);
//return;
}
/* open the test aln file */
if((tfd=fopen(argv[2],"r"))==NULL) {
fprintf(stderr,"Cannot open test aln file [%s]",argv[2]);
return;
}
/* open the annotation file */
/* plus a bit of trickery to decide if an annotation file is supplied */
/* set method="C" if no annotation file ie. we're all the columns in the
alignment (minus the columns with gaps in!) */
verbose=FALSE;
method='C';
if(argc>=4)
{
if(argv[3][0]=='-')
verbose=TRUE;
else
{
if((afd=fopen(argv[3],"r"))==NULL) {
fprintf(stderr,"Cannot open annotation file [%s]",argv[3]);
return;
}
method='B';
if(argc>=5) verbose=TRUE;
}
}
/* read the reference alignment into refnames,refseq_array,refseqlength */
refnseqs=countmsf(ifd);
if(refnseqs==0) {
fprintf(stderr,"Error: no sequences in %s\n",argv[1]);
return;
}
readref(ifd);
/* read the test alignment into names, seq_array, seqlength */
nseqs = countmsf(tfd);
if(nseqs==0) {
fprintf(stderr,"Error: no sequences in %s\n",argv[2]);
return;
}
readmsf(tfd);
if(nseqs != refnseqs) {
fprintf(stderr,"Error: %d sequences in %s and %d in %s",refnseqs,argv[1],nseqs,argv[2]);
return;
}
/* if no annotation file supplied, only consider columns with less than 'cutoff'
gaps. Here we use 20% of the number of sequences */
if(method=='C')
{
cutoff=(float)refnseqs*20.0/100.0;
if(cutoff<1) cutoff=1;
ref_gaps(cutoff);
}
/* cross-reference the sequence refnames, in case they're not in the same order
in the reference and test alignment files */
for(i=0;i<refnseqs;i++)
seq_xref[i]=-1;
for(i=0;i<refnseqs;i++)
{
found=FALSE;
for(j=0;j<nseqs;j++)
{
if(strcasecmp(names[j],refnames[i])==0)
{
found=TRUE;
seq_xref[j]=i;
break;
}
}
if(found==FALSE) {
fprintf(stderr,"Error: sequence %s not found in test aln %s\n",refnames[i],argv[2]);
return;
}
}
fprintf(stdout,"\nComparing test alignment in %s\nwith reference alignment in %s\n",argv[2],argv[1]);
if(method=='B')
fprintf(stdout,"\nUsing core blocks defined in %s\n",argv[3]);
/* code the reference alignment - assign to each residue the number of the column it's in */
for(i=0;i<refnseqs;i++)
code_refseq(i);
/* read the annotation file */
if(method=='B')
{
err=read_annotation(afd);
if(err<0) fprintf(stderr,"No motif positions in %s: using all conserved columns\n",argv[4]);
}
/* calculate the max score possible ie the score for the reference alignment */
score_ref();
/* code the test alignment - look up each residue from the test alignment in the reference
alignment and assign the reference column number */
for(i=0;i<nseqs;i++)
if ( seq_xref[i] != -1) code_seq(i);
/* calculate the scores */
columnscore(verbose);
ms_score/=maxscore;
pc_res/=maxpc_res;
fprintf(stdout,"\n\tSP score= %.3f\n",pc_res);
fprintf(stdout,"\n\tTC score= %.3f\n",tc_score);
}
void code_refseq(int seq)
{
int i,j;
/* assign column no. in reference alignment to each residue */
for(i=0;i<refseqlength;i++)
{
if(refseq_array[seq][i]=='-')
{
refseq_code[seq][i]=0;
}
else
{
refseq_code[seq][i]=i+1;
}
}
}
void ref_gaps(int cutoff)
{
int i,j;
/* find columns with gaps in the reference sequnce - set refseq_col[]=0
if gaps, =nseqs otherwise */
for(i=0;i<refseqlength;i++)
{
gap[i]=0;
for(j=0;j<refnseqs;j++)
if(refseq_array[j][i]=='-')
{
gap[i]++;
}
}
for(i=0;i<refseqlength;i++)
{
if(gap[i]>=cutoff) refseq_col[i]=0;
else refseq_col[i]=refnseqs;
}
}
void score_ref(void)
{
int i,j;
/* calculates the maximum score possible for an alignment */
for(i=0;i<refseqlength;i++)
{
if(refseq_col[i]>1)
{
maxscore+=refseq_col[i]*refseq_col[i];
maxpc_res+=refseq_col[i]*(refseq_col[i]-1)/2.0;
}
}
}
void code_seq(int seq)
{
int i,j,ix;
/* find the first residue in the reference sequence */
ix=0;
for(j=0;j<refseqlength;j++)
if(refseq_array[seq_xref[seq]][j]!='-')
{
ix=refseq_code[seq_xref[seq]][j];
break;
}
for(i=0;i<seqlength;i++)
{
if(seq_array[seq][i]=='-')
{
seq_code[seq_xref[seq]][i]=0;
}
else
{
if (refseq_col[ix-1]>seq_xref[seq]) seq_code[seq_xref[seq]][i]=ix;
for(j+=1;j<refseqlength;j++)
if(refseq_array[seq_xref[seq]][j]!='-')
{
ix=refseq_code[seq_xref[seq]][j];
break;
}
}
}
}
void columnscore(Boolean verbose)
{
int i,j,k;
int iseq,ncols;
int scores[MAXSEQ];
int index[MAXSEQ];
int n;
float colscore[MAXLEN];
float colscore1[MAXLEN];
int pc;
int nblocks;
int blen=30;
Boolean found;
ms_score=tc_score=ncols=0;
for(j=0;j<seqlength;j++)
{
colscore[j]=0;
colscore1[j]=0;
}
for(i=0;i<seqlength;i++)
{
for(j=0;j<nseqs;j++)
scores[j]=0;
n=0;
for(j=0;j<nseqs;j++)
{
if(seq_code[j][i]!=0)
{
found=FALSE;
for(k=0;k<n;k++)
{
if(seq_code[j][i]==index[k])
{
scores[k]++;
found=TRUE;
break;
}
}
if(found==FALSE)
{
scores[n]=1;
index[n]=seq_code[j][i];
n++;
}
}
}
for(j=0;j<nseqs;j++)
{
if(scores[j]>1)
{
colscore[i]+=scores[j]*scores[j];
pc_res+=scores[j]*(scores[j]-1)/2.0;
}
}
/* count 1 for each column */
for(j=0;j<nseqs;j++)
if(seq_code[0][i]>0 && scores[j]>=refseq_col[seq_code[0][i]-1])
colscore1[i]=1;
if (seq_code[0][i]!=0) ncols++;
ms_score+=colscore[i];
tc_score+=colscore1[i];
}
if(verbose)
{
nblocks=seqlength/blen;
fprintf(stdout,"\n\n");
for(k=0;k<=nblocks;k++) {
for(i=0;i<nseqs;i++) {
fprintf(stdout,"%10s",names[i]);
for(j=0;j<blen && k*blen+j<seqlength;j++) {
fprintf(stdout," %c",seq_array[i][k*blen+j]);
}
fprintf(stdout,"\n");
}
fprintf(stdout,"\n ");
for(j=0;j<blen && k*blen+j<seqlength;j++) {
fprintf(stdout,"% 4.0f",colscore[k*blen+j]);
}
fprintf(stdout,"\n\n");
}
}
/* count 1 for each column */
tc_score/=(float)ncols;
}
void code_blockseq(int seq)
{
int i,j;
for(i=0,j=1;i<seqlength;i++)
{
if(seq_array[seq][i]=='-')
{
seq_code[seq][i]=0;
}
else
{
seq_code[seq][i]=j++;
}
}
}
int read_annotation(FILE *fin)
{
int i,j,k,s,e;
char c,line[MAXLINE+1];
char t[MAXLINE+1];
int numargs;
char *args[101];
Boolean g;
nblocks=0;
while(fgets(line,MAXLINE+1,fin)) {
if(keyword(line,"BPOS")) {
nblocks=0;
numargs = getargs(line,args,101);
for(i=1;i<numargs;i++)
{
s=sscanf(args[i],"%d%c%d",&blocks[nblocks].s,&c,&blocks[nblocks].e);
if(s==1) {
blocks[nblocks].e=blocks[nblocks].s;
}
else if(s!=3) {
break;
}
blocks[nblocks].nseqs=refnseqs;
nblocks++;
}
break;
}
}
while(fgets(line,MAXLINE+1,fin)) {
if(keyword(line,"BREPART")) {
numargs = getargs(line,args,101);
for(i=1;i<numargs;i++)
{
blocks[i-1].nseqs = 0;
sscanf(args[i],"%s",t);
blocks[i-1].nseqs = parse_repart(t);
}
}
}
for(i=0;i<refseqlength;i++)
refseq_col[i]=0;
for(i=0;i<nblocks;i++) {
if(blocks[i].nseqs > 0) {
for(j=0, k=0;j<refseqlength;j++)
{
if(isalpha(refseq_array[0][j]))
k++;
if(k==blocks[i].s) {
s=j;
break;
}
}
for(;j<refseqlength;j++)
{
if(isalpha(refseq_array[0][j]))
k++;
if(k==blocks[i].e) {
e=j+1;
break;
}
}
for(j=s;j<=e;j++)
refseq_col[j]=blocks[i].nseqs;
}
}
}
Boolean keyword(char *line,char *code)
{
int i;
char key[MAXLINE];
for(i=0;!isspace(line[i]) && line[i]!=EOS;i++)
key[i]=line[i];
key[i]=EOS;
return( strcmp(key,code) == 0 );
}
int getargs(char *line,char *args[],int max)
{
char *inptr;
int i;
inptr=line;
for (i=0;i<=max;i++)
{
if ((args[i]=strtok(inptr," \t\n"))==NULL)
break;
inptr=NULL;
}
if (i>max)
{
fprintf(stdout,"Too many args\n");
return(0);
}
return(i);
}
int parse_repart(char *str)
{
int len,s,e,i,ix,tot;
char t[MAXLINE+1];
/* string contains a number of substrings of format n<Hn or n, separated by + */
tot=0;
len=strlen(str);
for(ix=0;ix<len;)
{
for(;ix<len && !isalnum(str[ix]);ix++);
s=ix;
for(;ix<len && str[ix]!='+';ix++);
e=ix;
for(i=s;i<e;i++)
t[i-s]=str[i];
t[i-s]='\0';
/* now we have a string in t[] with format n<Hn or n */
if(toupper(t[0])=='H') {
sscanf(&t[1],"%d",&i);
if(i>0 && i<=refnseqs) tot += i;
else fprintf(stderr,"WARNING: bad format in repartition %s\n",str);
}
else {
sscanf(t,"%d",&i);
if(i>0 && i<=refnseqs) tot += i;
else fprintf(stderr,"WARNING: bad format in repartition %s\n",str);
}
}
return tot;
}
Boolean blankline(char *line)
{
int i;
for(i=0;line[i]!='\n' && line[i]!=EOS;i++) {
if( isdigit(line[i]) ||
isspace(line[i]) ||
(line[i] == '*') ||
(line[i] == ':') ||
(line[i] == '.'))
;
else
return FALSE;
}
return TRUE;
}
void readref(FILE *fin)
{
static char line[MAXLINE+1];
char seq[MAXLEN+1];
int len,seqno,i,j,k;
unsigned char c;
for(seqno=0;seqno<refnseqs;seqno++)
{
fseek(fin,0,0); /* start at the beginning */
len=0; /* initialise length to zero */
for(i=0;;i++) {
if(fgets(line,MAXLINE+1,fin)==NULL) return; /* read the title*/
if(line[0]=='/' && line[1]=='/') break;
}
while (fgets(line,MAXLINE+1,fin) != NULL) {
if(!blankline(line)) {
for(i=0;i<seqno;i++) fgets(line,MAXLINE+1,fin);
for(j=0;j<=strlen(line);j++) if(line[j] != ' ') break;
for(k=j;k<=strlen(line);k++) if(line[k] == ' ') break;
strncpy(refnames[seqno],line+j,k-j);
refnames[seqno][k-j]='\0';
refnames[seqno][MAXNAMES]='\0';
for(i=k;i<=MAXLINE;i++) {
c=line[i];
if(c == '.' || c == '~' ) c = '-';
if(c == '*') c = 'X';
if(c == '\n' || c == EOS) break; /* EOL */
if(isalpha(c) || c=='-') seq[len++]=c;
}
for(i=0;;i++) {
if(fgets(line,MAXLINE+1,fin)==NULL) break;
if(blankline(line)) break;
}
}
}
strcpy(refseq_array[seqno],seq);
if(seqno==0) refseqlength=len;
}
}
void readmsf(FILE *fin)
{
static char line[MAXLINE+1];
char seq[MAXLEN+1];
int len,seqno,i,j,k;
unsigned char c;
for(seqno=0;seqno<nseqs;seqno++)
{
fseek(fin,0,0); /* start at the beginning */
len=0; /* initialise length to zero */
for(i=0;;i++) {
if(fgets(line,MAXLINE+1,fin)==NULL) return; /* read the title*/
if(line[0]=='/' && line[1]=='/') break;
}
while (fgets(line,MAXLINE+1,fin) != NULL) {
if(!blankline(line)) {
for(i=0;i<seqno;i++) fgets(line,MAXLINE+1,fin);
for(j=0;j<=strlen(line);j++) if(line[j] != ' ') break;
for(k=j;k<=strlen(line);k++) if(line[k] == ' ') break;
strncpy(names[seqno],line+j,k-j);
names[seqno][k-j]='\0';
names[seqno][MAXNAMES]='\0';
for(i=k;i<=MAXLINE;i++) {
c=line[i];
if(c == '.' || c == '~' ) c = '-';
if(c == '*') c = 'X';
if(c == '\n' || c == EOS) break; /* EOL */
if(isalpha(c) || c=='-') seq[len++]=c;
}
for(i=0;;i++) {
if(fgets(line,MAXLINE+1,fin)==NULL) break;
if(blankline(line)) break;
}
}
}
strcpy(seq_array[seqno],seq);
if(seqno==0) seqlength=len;
}
}
int countmsf(FILE *fin)
{
/* count the number of sequences in a PILEUP alignment file */
char line[MAXLINE+1];
int lnseqs;
while (fgets(line,MAXLINE+1,fin) != NULL) {
if(line[0]=='/' && line[1]=='/') break;
}
while (fgets(line,MAXLINE+1,fin) != NULL) {
if(!blankline(line)) break; /* Look for next non- */
} /* blank line */
lnseqs = 1;
while (fgets(line,MAXLINE+1,fin) != NULL) {
if(blankline(line)) return lnseqs;
lnseqs++;
}
return 0; /* if you got to here-funny format/no seqs.*/
}
//Merci bcp
#include <string.h>
#include <ctype.h>
#include <stdlib.h>
#include <math.h>
#define MAXNAMES 20
#define MAXSEQ 1000
#define MAXLEN 5000
#define MAXLINE 2048
#define Boolean short
#define TRUE 1
#define FALSE 0
#define EOS '\0'
#define INT_SCALE_FACTOR 100 /* Scaling factor to convert float to integer for profile scores */
#define NUMRES 32 /* max size of comparison matrix */
#define LEFT 1
#define RIGHT 2
#define NODE 0
#define LEAF 1
typedef struct node { /* phylogenetic tree structure */
struct node *left;
struct node *right;
struct node *parent;
float dist;
int leaf;
int order;
char name[64];
} stree, *treeptr;
/* trees.c */
void guide_tree(FILE *tree,int nseqs);
int SeqGCGCheckSum(char *seq, int len);
Boolean keyword(char *line,char *code);
int getargs(char *line,char *args[],int max);
int parse_repart(char *str);
Boolean blankline(char *line);
void readmsf(FILE *fin);
void readref(FILE *fin);
void score_ref(void);
int countmsf(FILE *fin);
void columnscore(Boolean verbose);
void readref(FILE *fin);
int read_annotation(FILE *fin);
int countref(FILE *ifd);
void code_refseq(int i);
void code_seq(int i);
void aln_seq(int i);
void ref_gaps(int cutoff);
/* arrays for storing reference alignment */
char refnames[MAXSEQ][MAXNAMES+1];
char refseq_array[MAXSEQ][MAXLEN];
int refseq_code[MAXSEQ][MAXLEN];
int refseq_col[MAXLEN];
int refseqlength;
int refnseqs;
/* arrays for storing text alignment */
char names[MAXSEQ][MAXNAMES+1];
char seq_array[MAXSEQ][MAXLEN];
int seq_code[MAXSEQ][MAXLEN];
int seq_aln[MAXSEQ][MAXLEN];
int seqlength;
int seq_xref[MAXSEQ];
int nseqs;
Boolean verbose;
int refscore;
/* number of gaps in a column in the reference alignment */
int gap[MAXLEN];
/* cutoff for number of gaps allowed in a column in the reference alignment
for column to be included in alignment score */
int cutoff;
/* core block data read in from annotation file */
int nblocks;
typedef struct Block {
int s;
int e;
int nseqs;
} Block;
Block blocks[100];
/* alignment scores - mean square score, total column score and percentage
of correctly aligned pairs of residues */
float ms_score,tc_score;
float maxscore,maxpc_res;
float pc_res;
void main(int argc, char **argv)
{
FILE *ifd,*tfd,*afd;
int err,i,j,ires,iseq=0;
int ix;
char t[MAXLINE+1];
char seq[MAXLINE+1];
char clen[MAXLINE+1];
char cvar[MAXLINE+1];
char cprog[MAXLINE+1];
char method;
Boolean eof,found;
if(argc<3) {
fprintf(stderr,"Usage: %s ref_aln test_aln [annot_file] [-v]\n",argv[0]);
fprintf(stderr," where ref_aln reference alignment in msf format \n");
fprintf(stderr," test_aln test alignment in msf format \n");
fprintf(stderr," annot_file optional BAliBASE annotation file\n");
fprintf(stderr," -v verbose mode\n");
//return;
}
/* open the reference aln file */
if((ifd=fopen(argv[1],"r"))==NULL) {
fprintf(stderr,"Cannot open reference aln file [%s]",argv[1]);
//return;
}
/* open the test aln file */
if((tfd=fopen(argv[2],"r"))==NULL) {
fprintf(stderr,"Cannot open test aln file [%s]",argv[2]);
return;
}
/* open the annotation file */
/* plus a bit of trickery to decide if an annotation file is supplied */
/* set method="C" if no annotation file ie. we're all the columns in the
alignment (minus the columns with gaps in!) */
verbose=FALSE;
method='C';
if(argc>=4)
{
if(argv[3][0]=='-')
verbose=TRUE;
else
{
if((afd=fopen(argv[3],"r"))==NULL) {
fprintf(stderr,"Cannot open annotation file [%s]",argv[3]);
return;
}
method='B';
if(argc>=5) verbose=TRUE;
}
}
/* read the reference alignment into refnames,refseq_array,refseqlength */
refnseqs=countmsf(ifd);
if(refnseqs==0) {
fprintf(stderr,"Error: no sequences in %s\n",argv[1]);
return;
}
readref(ifd);
/* read the test alignment into names, seq_array, seqlength */
nseqs = countmsf(tfd);
if(nseqs==0) {
fprintf(stderr,"Error: no sequences in %s\n",argv[2]);
return;
}
readmsf(tfd);
if(nseqs != refnseqs) {
fprintf(stderr,"Error: %d sequences in %s and %d in %s",refnseqs,argv[1],nseqs,argv[2]);
return;
}
/* if no annotation file supplied, only consider columns with less than 'cutoff'
gaps. Here we use 20% of the number of sequences */
if(method=='C')
{
cutoff=(float)refnseqs*20.0/100.0;
if(cutoff<1) cutoff=1;
ref_gaps(cutoff);
}
/* cross-reference the sequence refnames, in case they're not in the same order
in the reference and test alignment files */
for(i=0;i<refnseqs;i++)
seq_xref[i]=-1;
for(i=0;i<refnseqs;i++)
{
found=FALSE;
for(j=0;j<nseqs;j++)
{
if(strcasecmp(names[j],refnames[i])==0)
{
found=TRUE;
seq_xref[j]=i;
break;
}
}
if(found==FALSE) {
fprintf(stderr,"Error: sequence %s not found in test aln %s\n",refnames[i],argv[2]);
return;
}
}
fprintf(stdout,"\nComparing test alignment in %s\nwith reference alignment in %s\n",argv[2],argv[1]);
if(method=='B')
fprintf(stdout,"\nUsing core blocks defined in %s\n",argv[3]);
/* code the reference alignment - assign to each residue the number of the column it's in */
for(i=0;i<refnseqs;i++)
code_refseq(i);
/* read the annotation file */
if(method=='B')
{
err=read_annotation(afd);
if(err<0) fprintf(stderr,"No motif positions in %s: using all conserved columns\n",argv[4]);
}
/* calculate the max score possible ie the score for the reference alignment */
score_ref();
/* code the test alignment - look up each residue from the test alignment in the reference
alignment and assign the reference column number */
for(i=0;i<nseqs;i++)
if ( seq_xref[i] != -1) code_seq(i);
/* calculate the scores */
columnscore(verbose);
ms_score/=maxscore;
pc_res/=maxpc_res;
fprintf(stdout,"\n\tSP score= %.3f\n",pc_res);
fprintf(stdout,"\n\tTC score= %.3f\n",tc_score);
}
void code_refseq(int seq)
{
int i,j;
/* assign column no. in reference alignment to each residue */
for(i=0;i<refseqlength;i++)
{
if(refseq_array[seq][i]=='-')
{
refseq_code[seq][i]=0;
}
else
{
refseq_code[seq][i]=i+1;
}
}
}
void ref_gaps(int cutoff)
{
int i,j;
/* find columns with gaps in the reference sequnce - set refseq_col[]=0
if gaps, =nseqs otherwise */
for(i=0;i<refseqlength;i++)
{
gap[i]=0;
for(j=0;j<refnseqs;j++)
if(refseq_array[j][i]=='-')
{
gap[i]++;
}
}
for(i=0;i<refseqlength;i++)
{
if(gap[i]>=cutoff) refseq_col[i]=0;
else refseq_col[i]=refnseqs;
}
}
void score_ref(void)
{
int i,j;
/* calculates the maximum score possible for an alignment */
for(i=0;i<refseqlength;i++)
{
if(refseq_col[i]>1)
{
maxscore+=refseq_col[i]*refseq_col[i];
maxpc_res+=refseq_col[i]*(refseq_col[i]-1)/2.0;
}
}
}
void code_seq(int seq)
{
int i,j,ix;
/* find the first residue in the reference sequence */
ix=0;
for(j=0;j<refseqlength;j++)
if(refseq_array[seq_xref[seq]][j]!='-')
{
ix=refseq_code[seq_xref[seq]][j];
break;
}
for(i=0;i<seqlength;i++)
{
if(seq_array[seq][i]=='-')
{
seq_code[seq_xref[seq]][i]=0;
}
else
{
if (refseq_col[ix-1]>seq_xref[seq]) seq_code[seq_xref[seq]][i]=ix;
for(j+=1;j<refseqlength;j++)
if(refseq_array[seq_xref[seq]][j]!='-')
{
ix=refseq_code[seq_xref[seq]][j];
break;
}
}
}
}
void columnscore(Boolean verbose)
{
int i,j,k;
int iseq,ncols;
int scores[MAXSEQ];
int index[MAXSEQ];
int n;
float colscore[MAXLEN];
float colscore1[MAXLEN];
int pc;
int nblocks;
int blen=30;
Boolean found;
ms_score=tc_score=ncols=0;
for(j=0;j<seqlength;j++)
{
colscore[j]=0;
colscore1[j]=0;
}
for(i=0;i<seqlength;i++)
{
for(j=0;j<nseqs;j++)
scores[j]=0;
n=0;
for(j=0;j<nseqs;j++)
{
if(seq_code[j][i]!=0)
{
found=FALSE;
for(k=0;k<n;k++)
{
if(seq_code[j][i]==index[k])
{
scores[k]++;
found=TRUE;
break;
}
}
if(found==FALSE)
{
scores[n]=1;
index[n]=seq_code[j][i];
n++;
}
}
}
for(j=0;j<nseqs;j++)
{
if(scores[j]>1)
{
colscore[i]+=scores[j]*scores[j];
pc_res+=scores[j]*(scores[j]-1)/2.0;
}
}
/* count 1 for each column */
for(j=0;j<nseqs;j++)
if(seq_code[0][i]>0 && scores[j]>=refseq_col[seq_code[0][i]-1])
colscore1[i]=1;
if (seq_code[0][i]!=0) ncols++;
ms_score+=colscore[i];
tc_score+=colscore1[i];
}
if(verbose)
{
nblocks=seqlength/blen;
fprintf(stdout,"\n\n");
for(k=0;k<=nblocks;k++) {
for(i=0;i<nseqs;i++) {
fprintf(stdout,"%10s",names[i]);
for(j=0;j<blen && k*blen+j<seqlength;j++) {
fprintf(stdout," %c",seq_array[i][k*blen+j]);
}
fprintf(stdout,"\n");
}
fprintf(stdout,"\n ");
for(j=0;j<blen && k*blen+j<seqlength;j++) {
fprintf(stdout,"% 4.0f",colscore[k*blen+j]);
}
fprintf(stdout,"\n\n");
}
}
/* count 1 for each column */
tc_score/=(float)ncols;
}
void code_blockseq(int seq)
{
int i,j;
for(i=0,j=1;i<seqlength;i++)
{
if(seq_array[seq][i]=='-')
{
seq_code[seq][i]=0;
}
else
{
seq_code[seq][i]=j++;
}
}
}
int read_annotation(FILE *fin)
{
int i,j,k,s,e;
char c,line[MAXLINE+1];
char t[MAXLINE+1];
int numargs;
char *args[101];
Boolean g;
nblocks=0;
while(fgets(line,MAXLINE+1,fin)) {
if(keyword(line,"BPOS")) {
nblocks=0;
numargs = getargs(line,args,101);
for(i=1;i<numargs;i++)
{
s=sscanf(args[i],"%d%c%d",&blocks[nblocks].s,&c,&blocks[nblocks].e);
if(s==1) {
blocks[nblocks].e=blocks[nblocks].s;
}
else if(s!=3) {
break;
}
blocks[nblocks].nseqs=refnseqs;
nblocks++;
}
break;
}
}
while(fgets(line,MAXLINE+1,fin)) {
if(keyword(line,"BREPART")) {
numargs = getargs(line,args,101);
for(i=1;i<numargs;i++)
{
blocks[i-1].nseqs = 0;
sscanf(args[i],"%s",t);
blocks[i-1].nseqs = parse_repart(t);
}
}
}
for(i=0;i<refseqlength;i++)
refseq_col[i]=0;
for(i=0;i<nblocks;i++) {
if(blocks[i].nseqs > 0) {
for(j=0, k=0;j<refseqlength;j++)
{
if(isalpha(refseq_array[0][j]))
k++;
if(k==blocks[i].s) {
s=j;
break;
}
}
for(;j<refseqlength;j++)
{
if(isalpha(refseq_array[0][j]))
k++;
if(k==blocks[i].e) {
e=j+1;
break;
}
}
for(j=s;j<=e;j++)
refseq_col[j]=blocks[i].nseqs;
}
}
}
Boolean keyword(char *line,char *code)
{
int i;
char key[MAXLINE];
for(i=0;!isspace(line[i]) && line[i]!=EOS;i++)
key[i]=line[i];
key[i]=EOS;
return( strcmp(key,code) == 0 );
}
int getargs(char *line,char *args[],int max)
{
char *inptr;
int i;
inptr=line;
for (i=0;i<=max;i++)
{
if ((args[i]=strtok(inptr," \t\n"))==NULL)
break;
inptr=NULL;
}
if (i>max)
{
fprintf(stdout,"Too many args\n");
return(0);
}
return(i);
}
int parse_repart(char *str)
{
int len,s,e,i,ix,tot;
char t[MAXLINE+1];
/* string contains a number of substrings of format n<Hn or n, separated by + */
tot=0;
len=strlen(str);
for(ix=0;ix<len;)
{
for(;ix<len && !isalnum(str[ix]);ix++);
s=ix;
for(;ix<len && str[ix]!='+';ix++);
e=ix;
for(i=s;i<e;i++)
t[i-s]=str[i];
t[i-s]='\0';
/* now we have a string in t[] with format n<Hn or n */
if(toupper(t[0])=='H') {
sscanf(&t[1],"%d",&i);
if(i>0 && i<=refnseqs) tot += i;
else fprintf(stderr,"WARNING: bad format in repartition %s\n",str);
}
else {
sscanf(t,"%d",&i);
if(i>0 && i<=refnseqs) tot += i;
else fprintf(stderr,"WARNING: bad format in repartition %s\n",str);
}
}
return tot;
}
Boolean blankline(char *line)
{
int i;
for(i=0;line[i]!='\n' && line[i]!=EOS;i++) {
if( isdigit(line[i]) ||
isspace(line[i]) ||
(line[i] == '*') ||
(line[i] == ':') ||
(line[i] == '.'))
;
else
return FALSE;
}
return TRUE;
}
void readref(FILE *fin)
{
static char line[MAXLINE+1];
char seq[MAXLEN+1];
int len,seqno,i,j,k;
unsigned char c;
for(seqno=0;seqno<refnseqs;seqno++)
{
fseek(fin,0,0); /* start at the beginning */
len=0; /* initialise length to zero */
for(i=0;;i++) {
if(fgets(line,MAXLINE+1,fin)==NULL) return; /* read the title*/
if(line[0]=='/' && line[1]=='/') break;
}
while (fgets(line,MAXLINE+1,fin) != NULL) {
if(!blankline(line)) {
for(i=0;i<seqno;i++) fgets(line,MAXLINE+1,fin);
for(j=0;j<=strlen(line);j++) if(line[j] != ' ') break;
for(k=j;k<=strlen(line);k++) if(line[k] == ' ') break;
strncpy(refnames[seqno],line+j,k-j);
refnames[seqno][k-j]='\0';
refnames[seqno][MAXNAMES]='\0';
for(i=k;i<=MAXLINE;i++) {
c=line[i];
if(c == '.' || c == '~' ) c = '-';
if(c == '*') c = 'X';
if(c == '\n' || c == EOS) break; /* EOL */
if(isalpha(c) || c=='-') seq[len++]=c;
}
for(i=0;;i++) {
if(fgets(line,MAXLINE+1,fin)==NULL) break;
if(blankline(line)) break;
}
}
}
strcpy(refseq_array[seqno],seq);
if(seqno==0) refseqlength=len;
}
}
void readmsf(FILE *fin)
{
static char line[MAXLINE+1];
char seq[MAXLEN+1];
int len,seqno,i,j,k;
unsigned char c;
for(seqno=0;seqno<nseqs;seqno++)
{
fseek(fin,0,0); /* start at the beginning */
len=0; /* initialise length to zero */
for(i=0;;i++) {
if(fgets(line,MAXLINE+1,fin)==NULL) return; /* read the title*/
if(line[0]=='/' && line[1]=='/') break;
}
while (fgets(line,MAXLINE+1,fin) != NULL) {
if(!blankline(line)) {
for(i=0;i<seqno;i++) fgets(line,MAXLINE+1,fin);
for(j=0;j<=strlen(line);j++) if(line[j] != ' ') break;
for(k=j;k<=strlen(line);k++) if(line[k] == ' ') break;
strncpy(names[seqno],line+j,k-j);
names[seqno][k-j]='\0';
names[seqno][MAXNAMES]='\0';
for(i=k;i<=MAXLINE;i++) {
c=line[i];
if(c == '.' || c == '~' ) c = '-';
if(c == '*') c = 'X';
if(c == '\n' || c == EOS) break; /* EOL */
if(isalpha(c) || c=='-') seq[len++]=c;
}
for(i=0;;i++) {
if(fgets(line,MAXLINE+1,fin)==NULL) break;
if(blankline(line)) break;
}
}
}
strcpy(seq_array[seqno],seq);
if(seqno==0) seqlength=len;
}
}
int countmsf(FILE *fin)
{
/* count the number of sequences in a PILEUP alignment file */
char line[MAXLINE+1];
int lnseqs;
while (fgets(line,MAXLINE+1,fin) != NULL) {
if(line[0]=='/' && line[1]=='/') break;
}
while (fgets(line,MAXLINE+1,fin) != NULL) {
if(!blankline(line)) break; /* Look for next non- */
} /* blank line */
lnseqs = 1;
while (fgets(line,MAXLINE+1,fin) != NULL) {
if(blankline(line)) return lnseqs;
lnseqs++;
}
return 0; /* if you got to here-funny format/no seqs.*/
}
//Merci bcp
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samsouma04
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samedi 26 juillet 2008
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20 avril 2009 à 14:40
20 avril 2009 à 14:40
c un prgram que jai eu d'internet.Merci pr votre aide
Nabla's
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20 avril 2009 à 14:59
20 avril 2009 à 14:59
et les messages d'erreur de ton compilo STP ?
samsouma04
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20 avril 2009 à 15:04
20 avril 2009 à 15:04
--------------------Configuration: score - Win32 Debug--------------------
Compiling...
scor.cpp
c:\documents and settings\soumaya\bureau\score\scor.cpp(184) : warning C4244: '=' : conversion from 'double' to 'int', possible loss of data
c:\documents and settings\soumaya\bureau\score\scor.cpp(198) : error C2065: 'strcasecmp' : undeclared identifier
c:\documents and settings\soumaya\bureau\score\scor.cpp(306) : warning C4244: '+=' : conversion from 'double' to 'float', possible loss of data
c:\documents and settings\soumaya\bureau\score\scor.cpp(357) : warning C4244: '=' : conversion from 'int' to 'float', possible loss of data
c:\documents and settings\soumaya\bureau\score\scor.cpp(395) : warning C4244: '+=' : conversion from 'double' to 'float', possible loss of data
c:\documents and settings\soumaya\bureau\score\scor.cpp(631) : warning C4018: '<=' : signed/unsigned mismatch
c:\documents and settings\soumaya\bureau\score\scor.cpp(632) : warning C4018: '<=' : signed/unsigned mismatch
c:\documents and settings\soumaya\bureau\score\scor.cpp(679) : warning C4018: '<=' : signed/unsigned mismatch
c:\documents and settings\soumaya\bureau\score\scor.cpp(680) : warning C4018: '<=' : signed/unsigned mismatch
Error executing cl.exe.
score.exe - 1 error(s), 8 warning(s)
Compiling...
scor.cpp
c:\documents and settings\soumaya\bureau\score\scor.cpp(184) : warning C4244: '=' : conversion from 'double' to 'int', possible loss of data
c:\documents and settings\soumaya\bureau\score\scor.cpp(198) : error C2065: 'strcasecmp' : undeclared identifier
c:\documents and settings\soumaya\bureau\score\scor.cpp(306) : warning C4244: '+=' : conversion from 'double' to 'float', possible loss of data
c:\documents and settings\soumaya\bureau\score\scor.cpp(357) : warning C4244: '=' : conversion from 'int' to 'float', possible loss of data
c:\documents and settings\soumaya\bureau\score\scor.cpp(395) : warning C4244: '+=' : conversion from 'double' to 'float', possible loss of data
c:\documents and settings\soumaya\bureau\score\scor.cpp(631) : warning C4018: '<=' : signed/unsigned mismatch
c:\documents and settings\soumaya\bureau\score\scor.cpp(632) : warning C4018: '<=' : signed/unsigned mismatch
c:\documents and settings\soumaya\bureau\score\scor.cpp(679) : warning C4018: '<=' : signed/unsigned mismatch
c:\documents and settings\soumaya\bureau\score\scor.cpp(680) : warning C4018: '<=' : signed/unsigned mismatch
Error executing cl.exe.
score.exe - 1 error(s), 8 warning(s)
fiddy
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20 avril 2009 à 19:11
20 avril 2009 à 19:11
Salut,
Le mieux, c'est de récrire ton code proprement. Ce sera surtout de l'adaptation. Du genre remplacer stdio.h par cstdio. Attention également à l'espace des noms (using namespace std; évitera la répétition de std::.)
strcasecmp fait partie de strings.h et non string.h. Ce qui peut expliquer ton message d'erreur.
Et enfin, main() renvoie un int. Donc : int main(int argc, char **argv)...
Cdlt
Le mieux, c'est de récrire ton code proprement. Ce sera surtout de l'adaptation. Du genre remplacer stdio.h par cstdio. Attention également à l'espace des noms (using namespace std; évitera la répétition de std::.)
strcasecmp fait partie de strings.h et non string.h. Ce qui peut expliquer ton message d'erreur.
Et enfin, main() renvoie un int. Donc : int main(int argc, char **argv)...
Cdlt
Nabla's
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20 avril 2009 à 15:10
20 avril 2009 à 15:10
ben tu n'as qu'une seulle erreur, le reste c'est des warning parce que c'est mal programmé...
error C2065: 'strcasecmp' : undeclared identifier -> tu essayes d'utiliser une fonction qui n'existe pas...
tu trouvera ici le code de la fonction
http://www.koders.com/c/fid9E0C73B87923AB861E42F6532D65B0FD2D94D2AE.aspx
error C2065: 'strcasecmp' : undeclared identifier -> tu essayes d'utiliser une fonction qui n'existe pas...
tu trouvera ici le code de la fonction
http://www.koders.com/c/fid9E0C73B87923AB861E42F6532D65B0FD2D94D2AE.aspx
samsouma04
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samedi 26 juillet 2008
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20 avril 2009 à 15:12
20 avril 2009 à 15:12
Merci mais le probleme que jai des doutes que ce pgrm est executable sur une plateforme linux et pas windows.
Nabla's
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20 avril 2009 à 15:21
20 avril 2009 à 15:21
ben vu ce que fait cette fonction, c'est pas difficile de la refaire!
tu verra bien si il y a des appels spécifiques à linux ...
tu verra bien si il y a des appels spécifiques à linux ...
samsouma04
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20 avril 2009 à 19:02
20 avril 2009 à 19:02
donc je fais quoi:-(??
samsouma04
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20 avril 2009 à 19:13
20 avril 2009 à 19:13
Merci bcp je fairai de tes conseils esperant que ca se resoue
essayer avec dev c++
fiddy
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15 mai 2013 à 23:07
15 mai 2013 à 23:07
Cela ne répond pas au post qui date de 4 ans !
20 avril 2009 à 18:58
Le compilateur C++ comprend très bien le C
Non, le langage C++ est bien différent du C de par la distinction des normes. Effectivement, il y a plein de points communs, mais il est possible que le compilateur C++ échoue là ou le compilateur C réussi.