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/**
*
* io.h:
*
* 2004-08-30 Dorothea Emig Volker Menrad
*
*/
/************************************************/
/* */
/* structs */
/* */
/************************************************/
/************************************************/
/* */
/* global variable */
/* */
/************************************************/
/*********************************************/
/* */
/* functions from io.c */
/* */
/*********************************************/
void version(); // prints version on stdout
void print_scr_matrix(struct scr_matrix* aSmatrix);
struct scr_matrix* read_scr_matrix(char *filename);
void print_seq(struct seq* aSeq);
struct seq_col* read_fasta(char *filename);
void print_diag(struct diag* aDiag);
struct prob_dist* read_diag_prob_dist(struct scr_matrix* smatrix, char *filename);
void simple_print_alignment_default(struct alignment *algn);
void simple_print_alignment_dna_retranslate(struct alignment *algn);
//void simple_print_alignment_dna(struct alignment *algn);
void fasta_print_alignment_default(struct alignment *algn, char *filename);
void fasta_print_alignment_dna_retranslate(struct alignment *algn, char *filename);
//void fasta_print_alignment_dna(struct alignment *algn, char *filename);
char *print_info(struct alignment *align);
char *output_line(char *string);
char *output_line_left(char *string);
char *blank_line();
void print_pdist_matrix(struct prob_dist *sdist,char *filename);
void error(char *message);
void merror(char *msg1, char *msg2);
char* build_pathname(char *dir, char *file);
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