/******************************COPYRIGHT NOTICE*******************************/ /* (c) Centro de Regulacio Genomica */ /* and */ /* Cedric Notredame */ /* 12 Aug 2014 - 22:07. */ /*All rights reserved. */ /*This file is part of T-COFFEE. */ /* */ /* T-COFFEE is free software; you can redistribute it and/or modify */ /* it under the terms of the GNU General Public License as published by */ /* the Free Software Foundation; either version 2 of the License, or */ /* (at your option) any later version. */ /* */ /* T-COFFEE is distributed in the hope that it will be useful, */ /* but WITHOUT ANY WARRANTY; without even the implied warranty of */ /* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the */ /* GNU General Public License for more details. */ /* */ /* You should have received a copy of the GNU General Public License */ /* along with Foobar; if not, write to the Free Software */ /* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */ /*............................................... */ /* If you need some more information */ /* cedric.notredame@europe.com */ /*............................................... */ /******************************COPYRIGHT NOTICE*******************************/ #include #include #include #include #include #include typedef struct { int in_seq; FILE *fp; int font; int x0; int y0; int x; int y; int n_pages; int max_line_ppage; int n_line; int line; int eop; int in_html_span; char previous_html_color[100]; } FILE_format; typedef struct { float r; float g; float b; char html_color[30]; char html_color_class[30]; int ascii_value; } Color; Sequence * fill_sequence_struc ( int nseq, char **sequences, char **seq_name, Genomic_info *genome_co); Sequence * cw_read_sequences ( char *seq_name); Sequence * get_sequence_type (Sequence *S); Sequence * fast_get_sequence_type (Sequence *S); char * get_array_type (int n, char **s); Alignment* get_aln_type (Alignment *A); char * get_string_type (char *string); char *store_mode (char *val); char *retrieve_mode (); char *unset_mode (); char *set_mode (int mode, char *val); char *store_seq_type (char *val); char *retrieve_seq_type (); char *unset_seq_type (); char *set_seq_type (int mode, char *val); void get_sequence (char *seq_file,int *NSEQ, char ***SEQ, char ***SN, int **sl, int *min, int *max); int ** get_matrix ( char *name, char *format); int ** read_matrice (char *mat_name); int **neg_matrix2pos_matrix ( int **matrix); void print_aln ( Alignment *B); int output_raw_score (Alignment *A, Alignment *B, char *name); int output_reliability_ps ( Alignment *B,Alignment *S, char *name); int output_reliability_pdf ( Alignment *B,Alignment *S, char *name); int output_reliability_html ( Alignment *B,Alignment *S, char *name); int output_color_ps ( Alignment *B,Alignment *S, char *name); int output_color_pdf ( Alignment *B,Alignment *S, char *name); int output_color_html ( Alignment *B,Alignment *S, char *name); int output_hit_color_html (Alignment *B, float **ffPScoreTable, int nl, char *name); //JM_ADD void output_hit_matrix(char *fileName, float **ffpHitScoreMatrix, int nl); //JM_ADD void get_rgb_values(int val, Color *C); int output_reliability_format ( Alignment *B,Alignment *S, char *name, \ FILE_format *(*vfopen_format) ( char *),\ FILE_format *(*print_format_string) ( char * ,Color *, Color *, FILE_format*),\ FILE_format *(*print_format_char) ( int ,Color *, Color *, FILE_format*),\ void (*get_rgb_values_format) ( int ,Color *),\ FILE_format* (*vfclose_format) ( FILE_format *)); int output_score_format ( Alignment *B,Alignment *S, char *name, \ FILE_format *(*vfopen_format) ( char *),\ FILE_format *(*print_format_string) ( char * ,Color *, Color *, FILE_format*),\ FILE_format *(*print_format_char) ( int ,Color *, Color *, FILE_format*),\ void (*get_rgb_values_format) ( int ,Color *),\ FILE_format* (*vfclose_format) ( FILE_format *)); FILE_format * print_ps_string ( char *s , Color *box, Color *ink, FILE_format *f); FILE_format * print_ps_char ( int c, Color *box, Color *ink, FILE_format *f); FILE_format * print_ps_line (int len, Color *c, FILE_format *f); void get_rgb_values_ps ( int val, Color *C); FILE_format* vfopen_ps ( char *name); FILE_format* vfclose_ps ( FILE_format *fps); FILE_format *print_html_string( char *s, Color *box, Color *ink, FILE_format *fhtml); FILE_format * print_html_char ( int c, Color *box, Color *ink, FILE_format *f); void get_rgb_values_html ( int val, Color *C); FILE_format* vfopen_html ( char *name); FILE_format* vfclose_html ( FILE_format *fhtml); int output_reliability_ascii ( Alignment *B,Alignment *S, char *name); int output_reliability_fasta ( Alignment *B,Alignment *S, char *name); int output_color_ascii ( Alignment *B,Alignment *S, char *name); FILE_format *print_ascii_string( char *s, Color *box, Color *ink, FILE_format *fascii); FILE_format * print_ascii_char ( int c, Color *box, Color *ink, FILE_format *f); void get_rgb_values_ascii ( int val, Color *C); FILE_format* vfopen_ascii ( char *name); FILE_format* vfclose_ascii ( FILE_format *fascii); int output_seq_reliability_ascii ( Alignment *B,Alignment *S, char *name); int aln2compressed_ps (Alignment *A,char *file); int aln2compressed_pdf (Alignment *A,char *file);