sumalibs first commit

libfasta/fasta_header_parser.l

@@ -0,0 +1,178 @@
+/*
+ * Add -ll in Makefile if you modify this file to convert to .c
+ */
+
+%x REGID
+%x REGNAME
+%x REGVAL
+
+%{
+
+#include <stdlib.h>
+#include <string.h>
+#include "header_mem_handler.h"
+#include "fasta_header_handler.h"
+
+#define MEMALLOCATED 10
+#define BUFFER 5
+	
+#define YY_DECL int header_parser(int *nbf, int *memory_allocated, element_from_header **p_header)
+
+	
+%}
+
+WORD				[[:alnum:]:\-.{},'_()\#\[\]\|\&\"\'\/\%\+]+
+WORDID				[[:alnum:]:\-.{},'_()\#\[\]\|\&\"\'\/\%\+=;]+
+SUP					>
+EOL                	\n
+SEP                 ;
+SPACE				[[:blank:]]+
+EQUAL				=
+
+%%
+
+	int i;
+	int size_needed;
+	int free_size;
+	char* field;
+	
+	
+<INITIAL>{SUP}	{	
+					/*printf("\n<INITIAL>{SUP},%s",yytext);*/
+					BEGIN(REGID);
+				}
+				
+<INITIAL,REGID>{WORDID}     {
+								i=0;						
+								
+								field = malloc_field(&free_size);
+								(*p_header)[*nbf].name = (char*) malloc(3*sizeof(char));
+								strcpy(((*p_header)[*nbf]).name,"id");
+										
+								size_needed = strlen(yytext)+1;
+								(*p_header)[*nbf].value = (char*) malloc(sizeof(char)*size_needed);
+								strcpy(((*p_header)[*nbf]).value,yytext);
+										
+								(*nbf)++;
+						  }
+
+
+<INITIAL,REGID>{SPACE}     {
+						BEGIN(REGNAME);
+					}
+
+<REGNAME>{WORD}      {
+						/*fprintf(stderr,"\n<REGNAME>{WORD} **%s**",yytext);*/
+						field = store_in_field(field,yytext,&free_size,&i);
+				    }
+
+<REGNAME>{SPACE}     {
+						/*fprintf(stderr,"\n<REGNAME>{SPACE} **%s**",yytext);*/
+						if (i != 0)
+							field = store_in_field(field,yytext,&free_size,&i);
+				    }
+
+<REGNAME>{EQUAL}     {
+						/*fprintf(stderr,"\n<REGNAME>{EQUAL},%s",yytext);*/
+						field = store_in_header_table(field, &((*p_header)[*nbf].name), &free_size, &i);
+						BEGIN(REGVAL);
+				    }
+
+<REGNAME>{SEP}       {
+						/*fprintf(stderr,"\n<REGNAME>{SEP},%s",yytext);*/
+						(*p_header)[*nbf].name = (char*) malloc(19*sizeof(char));
+						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);
+						BEGIN(REGNAME);
+				    }
+
+<REGVAL>{WORD}      {
+					/*fprintf(stderr,"\n<REGVAL>{WORD} **%s**\n",yytext);*/
+					field = store_in_field(field,yytext,&free_size,&i);
+				    }
+
+<REGVAL>{SPACE}     {
+					/*fprintf(stderr,"\n<REGVAL>{SPACE} **%s**\n",yytext);*/
+					field = store_in_field(field,yytext,&free_size,&i);
+				    }
+
+<REGVAL>{SEP}      {
+					/*fprintf(stderr,"\n<REGVAL>{SEP},%s\n",yytext);*/
+					
+					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);
+					BEGIN(REGNAME);
+				    }
+
+
+<REGVAL>{EQUAL}     {
+						/*fprintf(stderr, "\nWarning : separator ';' probably missing in header after %s",(*p_header)[*nbf].name);*/
+				    }
+
+<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);
+					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");
+						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);
+						
+						free(field);
+						BEGIN(INITIAL);
+						return 0;
+                	}
+
+%%
+
+int header_yywrap()
+{
+	return 1;
+}
+
+element_from_header* header_parser_main(char *h)
+{
+	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));
+	
+	memory_allocated=MEMALLOCATED;
+	
+	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;
+}
+
+
+
+