aln_input.h

Go to the documentation of this file.
00001 #ifndef ALN_INPUT_H
00002 #define ALN_INPUT_H
00003 
00004 #include <stdio.h>
00005 #include <ctype.h>
00006 #include "seqaln.h"
00007 
00008 #ifndef MAX_ARG_LEN
00009 #define MAX_ARG_LEN 2048
00010 #endif
00011 
00012 int load_distrib(char *fn, double *freq, struct SEQALN_IO *io);
00013 int load_mat(char *fn, struct SEQALN_CONSTANTS *scoring, struct SEQALN_IO *io);
00014 int load_pro(struct SEQALN_PROFILE *pro, struct SEQALN_CONSTANTS *scoring, 
00015                 struct SEQALN_IO *io);
00016 int load_seq(struct SEQALN_SEQUENCE *sequence,
00017                       struct SEQALN_CONSTANTS *scoring, struct SEQALN_IO *io);
00018 int load_seq_fromstr(struct SEQALN_SEQUENCE *sequence, 
00019                 struct SEQALN_CONSTANTS *scoring, const char *seqname,
00020                 const char *seqstring);
00021 int load_seq_lite(struct SEQALN_SEQUENCE *sequence);
00022 void parseargs(struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2,
00023                    struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results,
00024                            struct SEQALN_IO *io, int argc, char *argv[]);
00025 /* with the io */
00026 void parseargs_str_new(struct SEQALN_SEQUENCE *seq1,
00027                 struct SEQALN_SEQUENCE *seq2,
00028         struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results,
00029         char *seq1name, char *seq2name, char *seq1str, char *seq2str, 
00030         struct SEQALN_IO* io);
00031 void parseargs_str(struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2,
00032         struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results,
00033         char *seq1name, char *seq2name, char *seq1str, char *seq2str);
00034 void loadDeltaFunction(struct SEQALN_CONSTANTS* scoring);
00035 
00036 
00037 
00038 #endif