obitools/sumalibs
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 10 Wiki Activity

Improved the fasta parser for better memory handling and better parsing

Browse Source 
of the last parts of fasta headers (definitions)
This commit is contained in:
Celine Mercier
2017-10-13 18:54:17 +02:00
parent 52e94bbea7
commit a258d334b1
5 changed files with 83 additions and 84 deletions
Download Patch File Download Diff File Expand all files Collapse all files

53
libfasta/fasta_header_parser.l
View File

@ -53,7 +53,7 @@ EQUAL =
(*p_header)[*nbf].value = (char*) malloc(sizeof(char)*size_needed);
strcpy(((*p_header)[*nbf]).value,yytext);
(*nbf)++;
p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
}
@ -66,7 +66,7 @@ EQUAL =
field = store_in_field(field,yytext,&free_size,&i);
}
<REGNAME>{SPACE} {
<REGNAME>{SPACE} { // TODO
/*fprintf(stderr,"\n<REGNAME>{SPACE} **%s**",yytext);*/
if (i != 0)
field = store_in_field(field,yytext,&free_size,&i);
@ -112,22 +112,19 @@ EQUAL =
<REGVAL><<EOF>> {
field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
(*nbf)++;
end_header_table(p_header, *nbf);
free(field);
BEGIN(INITIAL);
return 0;
}
<REGNAME><<EOF>> {
/*(*p_header)[*nbf].name = (char*) malloc(sizeof(char)*19);
strcpy((*p_header)[*nbf].name,"other_informations");
(*p_header)[*nbf].name = (char*) malloc(sizeof(char)*19);
strcpy((*p_header)[*nbf].name,"definition");
field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
*/
end_header_table(p_header, *nbf);
(*nbf)++;
end_header_table(p_header, nbf);
free(field);
BEGIN(INITIAL);
return 0;
@ -142,37 +139,31 @@ int header_yywrap()
element_from_header* header_parser_main(char *h)
{
int nbfields,memory_allocated;
int nbfields, memory_allocated;
element_from_header* header;
char* nbfields_n;
char* nbfields_v;
nbfields_n = (char*) malloc(9*sizeof(char));
nbfields_v = (char*) malloc(5*sizeof(char));
YY_BUFFER_STATE state;
state=yy_scan_string(h);
memory_allocated=MEMALLOCATED;
header = (element_from_header*) malloc(memory_allocated * sizeof(element_from_header));
nbfields_n = (char*) malloc(9*sizeof(char));
strcpy(nbfields_n, "nbfields");
header[0].name = nbfields_n;
// Initialize memory to store the number of fields
header[0].value = (char*) malloc(10*sizeof(char));
nbfields=1;
strcpy(nbfields_n, "nbfields");
strcpy(nbfields_v, "1");
header = (element_from_header*) malloc(memory_allocated * sizeof(element_from_header));
header[0].name = nbfields_n;
header[0].value = nbfields_v;
YY_BUFFER_STATE state;
state=yy_scan_string(h);
header_parser(&nbfields, &memory_allocated, &header);
yy_delete_buffer(state);
return header;
}