sim4b1.h

Go to the documentation of this file.
00001 #ifndef SIM4B1_H
00002 #define SIM4B1_H
00003 /* $Id: sim4b1.h,v 1.1.1.1 2007-07-13 03:44:06 kzhou Exp $ */
00004 
00005 extern const char *seq1, *seq2;
00006 extern int M, N, encoding[NACHARS];
00007 extern comparisonType file_type;
00008 extern coords last_GT, last_CT, last_AG, last_AC;
00009 extern sim4Args command;
00010 
00011 void link_to_data_list(Pointer,ValNodePtr *,ValNodePtr *);
00012 void ValNodeFreeData(ValNodePtr);
00013 int good_ratio(int);
00014 void flip_list(Exon **,Exon **);
00015 void free_list(Exon *);
00016 void free_table(void);
00017 void free_align(edit_script_list *);
00018 void complement_exons(Exon **,int,int);
00019 void print_exons(const Exon *);
00020 void print_pipmaker_exons(Exon *,edit_script_list *, const char *,int,int,int,int, const char *, const char*,int);
00021 void bld_table(const char *s, int len, int in_W, int type);
00022          //build table of W-tuples in one of the sequences 
00023 edit_script_list *SIM4(const kzseq &so1, const kzseq &so2, const sim4Args &cmd,int*,Exon**,sim4_stats_t *);
00024 //in_seq1 is genomic sequnece(string), in_seq2 is cDNA 
00025 #endif /* SIM4B1_H */