00001 00167 #ifndef READ_H 00168 #define READ_H 00169 00170 #include <stdio.h> 00171 #include <string.h> 00172 #include <stdlib.h> 00173 #include <math.h> 00174 #include "structs.h" 00175 00176 char *get_line(FILE *fp); 00177 00178 struct gotoh_arguments gotoh_readArguments(int argc, char *argv[]); 00179 00180 struct gotoh_settings gotoh_readSettings(gotoh_arguments ga); 00181 00182 struct gotoh_motifSingle gotoh_readMotifSingle(char *file); 00183 00184 struct gotoh_motif gotoh_readMotif2sided(char *file, gotoh_settings cfg); 00185 00186 /* init functions */ 00187 struct gotoh_arguments gotoh_initArguments(); 00188 00189 struct gotoh_settings gotoh_initSettings(); 00190 00191 /* print functions */ 00192 void gotoh_printArguments(gotoh_arguments ga); 00193 00194 void gotoh_printSettings(gotoh_settings gs); 00195 00196 void gotoh_printMotifSingle(struct gotoh_motifSingle m); 00197 00198 void gotoh_printMotif(struct gotoh_motif m); 00199 00200 void usage(); 00201 00202 void version(); 00203 00204 /* free functions */ 00205 void gotoh_freeArguments(gotoh_arguments ga); 00206 00207 void gotoh_freeSettings(gotoh_settings gs); 00208 00209 void gotoh_freeMotifSingle(gotoh_motifSingle gm); 00210 00211 /* void gotoh_freeMotif2sided(gotoh_motif gm); */ 00212 00213 void gotoh_freeMotif(gotoh_motif gm); 00214 00215 /* other functions */ 00216 void gotoh_Error(char *msg, int v); 00217 00218 void gotoh_Warning(char *msg, int v); 00219 00220 #endif