alnfn.h

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00001 #ifndef ALNFN_H
00002 #define ALNFN_H
00003 
00004 #include "seqaln.h"
00005 
00006 //char *newmem(int number, int size);
00007 // moved to util.h
00008 //void parseargs_str(struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2,
00009 //                 struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results,
00010 //                      char *seq1name, char *seq2name, char *seq1str, char *seq2str);
00011 //      return 1 if not getting enough memory
00012 //      return 0 for success
00013 int results_init(struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2, 
00014                    struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io);
00015 
00016 void localS(struct SEQALN_SEQUENCE *seq1, struct SEQALN_SEQUENCE *seq2,
00017                    struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io);
00018 //void rpt_align(struct SEQALN_SEQUENCE  *seq1, struct SEQALN_SEQUENCE *seq2,
00019 //                 struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io);
00020 void trace(struct SEQALN_SEQUENCE  *seq1, struct SEQALN_SEQUENCE *seq2,
00021                    struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io);
00022 //void print_trace(struct SEQALN_CONSTANTS *scoring,struct SEQALN_RESULTS *results, struct SEQALN_IO *io);
00023 void gen_align(struct SEQALN_SEQUENCE  *seq1, struct SEQALN_SEQUENCE *seq2,
00024                    struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io);
00025 void lsdeclump(struct SEQALN_SEQUENCE  *seq1, struct SEQALN_SEQUENCE *seq2,
00026                    struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io);
00027 //void rpt_scores(struct SEQALN_SEQUENCE  *seq1, struct SEQALN_SEQUENCE *seq2,
00028 //                 struct SEQALN_CONSTANTS *scoring, struct SEQALN_RESULTS *results, struct SEQALN_IO *io);
00029 //int load_seq_fromstr(struct SEQALN_SEQUENCE *sequence, struct SEQALN_CONSTANTS *scoring, char *seqname, char *seqstring);
00030 
00031 #endif