--- /dev/null
+/******************************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 <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <string.h>
+#include <ctype.h>
+#include <stdlib.h>
+
+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);
git://source.jalview.org / jabaws.git / blobdiff