aln_input.h

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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);
00014 int load_mat(char *fn, struct SEQALN_CONSTANTS *scoring, struct SEQALN_IO *io);
00015 int load_pro(struct SEQALN_PROFILE *pro, struct SEQALN_CONSTANTS *scoring, 
00016                 struct SEQALN_IO *io);
00017 int load_seq(struct SEQALN_SEQUENCE *sequence,
00018                       struct SEQALN_CONSTANTS *scoring, struct SEQALN_IO *io);
00019 int load_seq_fromstr(struct SEQALN_SEQUENCE *sequence, 
00020                 struct SEQALN_CONSTANTS *scoring, const char *seqname,
00021                 const char *seqstring);
00022 int load_seq_lite(struct SEQALN_SEQUENCE *sequence);
00023 void parseargs(struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2,
00024                    struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results,
00025                            struct SEQALN_IO *io, int argc, char *argv[]);
00026 /* with the io */
00027 void parseargs_str_new(struct SEQALN_SEQUENCE *seq1,
00028                 struct SEQALN_SEQUENCE *seq2,
00029         struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results,
00030         char *seq1name, char *seq2name, char *seq1str, char *seq2str, 
00031         struct SEQALN_IO* io);
00032 void parseargs_str(struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2,
00033         struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results,
00034         char *seq1name, char *seq2name, char *seq1str, char *seq2str);
00035 void loadDeltaFunction(struct SEQALN_CONSTANTS* scoring);
00036 
00037 
00038 
00039 #endif