X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Ftcoffee%2Ft_coffee_source%2Fio_func.c;h=d9816e91b4e3c43de68ac0f725f0924af6ba2d38;hb=338caee91f39abcaef1ae33c3468bb65f4cc3165;hp=44ff9e4c08bab37890fe23c2a2adeca72ac5f724;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git diff --git a/binaries/src/tcoffee/t_coffee_source/io_func.c b/binaries/src/tcoffee/t_coffee_source/io_func.c index 44ff9e4..d9816e9 100644 --- a/binaries/src/tcoffee/t_coffee_source/io_func.c +++ b/binaries/src/tcoffee/t_coffee_source/io_func.c @@ -96,7 +96,7 @@ char * get_string_type (char *S) sprintf ( type, "PROTEIN"); } - else if ( dna>98 && rna>10)sprintf ( type, "RNA"); + else if ( dna>98 && rna>0)sprintf ( type, "RNA"); else if ( dna>98)sprintf ( type, "DNA"); else sprintf ( type, "PROTEIN"); @@ -268,13 +268,15 @@ int ** read_matrice (char *mat_name_in) { int a,b,c, l; - char AA[]="abcdefghiklmnpqrstvwxyz"; + char *AA; FILE *fp; int **matrice; int **matrix2; char mat_name[200]; int *vector=NULL; + AA=vcalloc (256, sizeof (char)); + sprintf (AA, "abcdefghiklmnpqrstvwxyz"); l=strlen(AA); @@ -330,6 +332,9 @@ int ** read_matrice (char *mat_name_in) else if (strm(mat_name, "ralpha_mat" ))vector=ralpha_mat; else if (strm(mat_name, "rcoil_mat" ))vector=rcoil_mat; else if (strm (mat_name, "jtttm250mt"))vector=jtttm250mt; + + else if (strm (mat_name, "promoter_tf1"))vector=promoter_tf1; + else if (strm (mat_name, "blosumR"))vector=blosumR; /*Header Matrices*/ if(vector) @@ -655,6 +660,23 @@ void get_rgb_values ( int val, Color *C) } + +// void output_tm_mark(FILE_format *fps) +// { +// Color *box_c=vcalloc ( 1, sizeof (Color)); +// Color *ink; +// get_rgb_values_format (INK_COLOR, (ink =vcalloc ( 1, sizeof (Color)))); +// +// get_rgb_values_format ( 5, box_c); +// fps=print_format_char ( " IN ", box_c,ink,fps); +// +// get_rgb_values_format ( 9, box_c); +// fps=print_format_char ( " HEL ", box_c,ink,fps); +// +// get_rgb_values_format ( 0, box_c); +// fps=print_format_char ( "OUT", box_c,ink,fps); +// } + int output_color_format ( Alignment *B,Alignment *Sin,char *name, \ FILE_format *(*vfopen_format) ( char *),\ FILE_format *(*print_format_string) ( char * ,Color *, Color *, FILE_format*),\ @@ -736,6 +758,19 @@ FILE_format* (*vfclose_format) ( FILE_format *)) sprintf (buf, "\n%s, %s(%s)\n%s\n",PROGRAM,VERSION,DATE, AUTHOR); fps=print_format_string ( buf,white, ink, fps); + if(B->output_tm == 1) + { + fps=print_format_char ( '\n', white, ink, fps); + get_rgb_values_format ( 5, box_c); + fps=print_format_string ( " IN ", box_c,ink,fps); + + get_rgb_values_format ( 9, box_c); + fps=print_format_string ( " HEL ", box_c,ink,fps); + + get_rgb_values_format ( 0, box_c); + fps=print_format_string ( " OUT ", box_c,ink,fps); + } + fps=print_format_string ( "\n\n",white,ink, fps); fps->line-=max_len; @@ -1153,7 +1188,12 @@ void output_hit_matrix(char *fileName, float **ffpHitScoreMatrix, int nl) } vfclose(fp); } - +int output_hit_color_format (Alignment *B, float **ffPScoreTable, int nl, 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_hit_color_html (Alignment *B, float **ffPScoreTable, int nl, char *name) { output_hit_color_format (B, ffPScoreTable, nl, name, vfopen_html,print_html_string,print_html_char,get_rgb_values_html, vfclose_html); @@ -1330,7 +1370,7 @@ FILE_format* vfopen_html ( char *name) fprintf(fhtml->fp,"\n