--- /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>
+#include "io_lib_header.h"
+#include "util_lib_header.h"
+#include "define_header.h"
+#include "matrices.h"
+
+#define DEFAULT_COLOR -1
+#define GAP_COLOR -2
+#define INK_COLOR -3
+
+Sequence * cw_read_sequences ( char *seq_name)
+ {
+ Sequence *S;
+
+
+ char **seq=NULL;
+ char **name=NULL;
+ int *len=NULL;
+ int nseq=0;
+ int min_len=0;
+ int max_len=0;
+ int a;
+
+ get_sequence ( seq_name, &nseq, &seq, &name, &len, &min_len, &max_len);
+
+ S=declare_sequence ( min_len, max_len, nseq);
+ for ( a=0; a< nseq; a++)sprintf ( S->file[a], "%s", seq_name);
+
+ for ( a=0; a<S->nseq; a++)
+ {
+ S->len[a]=len[a];
+ sprintf ( S->name[a],"%s", name[a]);
+ vfree ( name[a]);
+ sprintf ( S->seq[a], "%s", seq[a]);
+ vfree ( seq[a]);
+ }
+ vfree (seq);
+ vfree (name);
+ vfree (len);
+ S=get_sequence_type ( S);
+ return S;
+ }
+char * get_string_type (char *S)
+ {
+ int a, l;
+ int protein=0, dna=0,rna=0, tot=0;
+ char *type;
+ static char *ltype;
+ static int warning;
+
+ if ( !ltype)
+ declare_name(ltype);
+
+ declare_name(type);
+ l=(int)strlen (S);
+
+ if (l==0)
+ {
+ sprintf ( type, "UNKNOWN");
+ return type;
+ }
+
+ for ( a=0; a<l; a++)
+ {
+ if ( !is_gap(S[a]))
+ {
+ protein+=( is_aa (S[a]) && !is_dna(S[a]));
+ dna+= ( is_dna(S[a]));
+ rna+= ( is_rna(S[a]));
+ tot++;
+ }
+ }
+
+ protein=(protein*100)/tot;
+ dna=(dna*100)/tot;
+ rna=(rna*100)/tot;
+
+ if ( l<20 && warning==0)
+ {
+ /*add_warning ( stderr, "WARNING: short sequences, use -type=DNA or PROTEIN");*/
+ warning=1;
+ }
+ if ( l<20 && ltype && ltype[0])
+ {
+ if (dna==100)
+ {
+ sprintf ( type, "%s", ltype);
+ ltype[0]='\0';
+ }
+ else
+ sprintf ( type, "PROTEIN");
+
+ }
+ else if ( dna>98 && rna>0)sprintf ( type, "RNA");
+ else if ( dna>98)sprintf ( type, "DNA");
+ else sprintf ( type, "PROTEIN");
+
+ sprintf ( ltype, "%s", type);
+ return type;
+ }
+
+Alignment* get_aln_type (Alignment *A)
+ {
+ if ( !A) return A;
+
+ if ( A->S && !(A->S)->type)(A->S)->type=(char*)vcalloc (30, sizeof (char));
+
+ if ( A->S && (A->S)->type[0]!='\0')
+ {
+ ;
+ }
+ else if (A->S!=NULL && (A->S)->type[0]=='\0')
+ {
+ A->S=get_sequence_type (A->S);
+ }
+ else if (A->S==NULL)
+ {
+ A->S=aln2seq (A);
+ A->S=get_sequence_type(A->S);
+ }
+ return A;
+ }
+
+
+
+char *unset_mode ()
+{
+ return set_mode (UNSET, NULL);
+}
+char *store_mode (char *val)
+{
+ return set_mode (SET, val);
+}
+char *retrieve_mode ()
+{
+ return set_mode (GET,NULL);
+}
+char *set_mode (int mode, char *val)
+{
+ static char type[100];
+ if (mode==SET)
+ {
+ if (!val)printf_exit (EXIT_FAILURE, stderr, "Error: programme mode unset in io_func.c:set_seq_type");
+ sprintf ( type,"%s", val);
+ }
+ else if ( mode==GET)
+ {
+ ;
+ }
+ else if ( mode==UNSET)
+ {
+ type[0]='\0';
+ }
+ else
+ {
+ printf_exit (EXIT_FAILURE, stderr, "Error: unknown mode in function io_func.c:set_seq_type, use SET, GET or UNSET");
+ }
+ return type;
+}
+/************************************************************/
+
+
+
+char *unset_seq_type ()
+{
+ return set_seq_type (UNSET, NULL);
+}
+char *store_seq_type (char *val)
+{
+ return set_seq_type (SET, val);
+}
+char *retrieve_seq_type ()
+{
+ return set_seq_type (GET,NULL);
+}
+char *set_seq_type (int mode, char *val)
+{
+ static char type[100];
+ if (mode==SET)
+ {
+ if (!val)printf_exit (EXIT_FAILURE, stderr, "Error: sequence type unset in io_func.c:set_seq_type");
+ sprintf ( type,"%s", val);
+ }
+ else if ( mode==GET)
+ {
+ ;
+ }
+ else if ( mode==UNSET)
+ {
+ type[0]='\0';
+ }
+ else
+ {
+ printf_exit (EXIT_FAILURE, stderr, "Error: unknown mode in function io_func.c:set_seq_type, use SET, GET or UNSET");
+ }
+ return type;
+}
+char * get_array_type (int n, char **seq)
+{
+ char *buf, *buf2;
+ int a, tot=0;
+ buf2=(char*)vcalloc ( 100, sizeof (char));
+
+
+ for ( tot=0,a=0; a<n; a++)tot+=strlen (seq[a]);
+ buf=(char*)vcalloc (tot+1, sizeof (char));
+ for ( a=0; a<n; a++)strcat (buf, seq[a]);
+ sprintf ( buf2, "%s", get_string_type(buf));
+ vfree (buf);
+ return buf2;
+}
+Sequence *get_sequence_type (Sequence *S)
+{
+ if ( !S) return NULL;
+ else sprintf ( S->type, "%s", get_array_type (S->nseq, S->seq));
+ return S;
+}
+Sequence *fast_get_sequence_type (Sequence *S)
+{
+ if ( !S) return NULL;
+ else if (S->type && S->type[0])return S;
+ else return get_sequence_type(S);
+}
+
+
+void get_sequence (char *seq_file,int *NSEQ, char ***SEQ, char ***SN, int **sl, int *min, int *max)
+ {
+ int a,b;
+ int min_len;
+ int max_len;
+ int nseq;
+
+ int **SL;
+
+ nseq=NSEQ[0]= readseqs ( seq_file, SEQ, SN, &SL);
+ sl[0]=(int*)vcalloc ( nseq, sizeof (int));
+
+
+ min_len= max_len= (SL)[0][0];
+ for ( a=0; a<NSEQ[0]; a++)
+ {
+ sl[0][a]=SL[a][0];
+ for ( b=0; b<(SL)[a][0]; b++)
+ (SEQ[0])[a][b]=tolower ((SEQ[0])[a][b]);
+ }
+ for ( a=1; a<NSEQ[0]; a++)
+ {
+ min_len= ( min_len > (SL)[a][0])?(SL)[a][0]:min_len;
+ max_len= ( max_len < (SL)[a][0])?(SL)[a][0]:max_len;
+ }
+ min[0]=min_len;
+ max[0]=max_len;
+ }
+
+int ** get_matrix ( char *name, char *format)
+ {
+
+ if ( strm ( "blast", format))return read_blast_matrix ( name);
+ else if ( strm ( "clustalw", format))return read_matrice(name);
+ else
+ {
+ fprintf ( stderr, "\nError:\nUnknowm Format %s for Matrix %s[FATAL]", format, name);
+ myexit (EXIT_FAILURE);
+ }
+ return NULL;
+ }
+void display_matrix (int **mat);
+int ** read_matrice (char *mat_name_in)
+ {
+ int a,b,c, l;
+
+ char *AA;
+ FILE *fp;
+ int **matrice;
+ int **matrix2;
+ char mat_name[200];
+ int *vector=NULL;
+
+ AA=(char*)vcalloc (256, sizeof (char));
+ sprintf (AA, "abcdefghiklmnpqrstvwxyz");
+ l=strlen(AA);
+
+
+ if ( strcmp (mat_name_in, "list")==0)
+ {
+ fprintf ( stderr, "****List of available matrices\n");
+ fprintf ( stderr, "\tidmat\n");
+ fprintf ( stderr, "\tmd_40mt\n");
+ fprintf ( stderr, "\tmd_350mt\n");
+ fprintf ( stderr, "\tmd_250mt\n");
+ fprintf ( stderr, "\tpam120mt\n");
+ fprintf ( stderr, "\tpam160mt\n");
+ fprintf ( stderr, "\tpam350mt\n");
+
+ fprintf ( stderr, "\tblosum30mt\n");
+ fprintf ( stderr, "\tblosum40mt\n");
+ fprintf ( stderr, "\tblosum45mt\n");
+ fprintf ( stderr, "\tblosum50mt\n");
+ fprintf ( stderr, "\tblosum55mt\n");
+ fprintf ( stderr, "\tblosum62mt\n");
+ fprintf ( stderr, "\tblosum80mt\n");
+ myexit (EXIT_SUCCESS);
+
+ }
+ if ( strm2 (mat_name_in, "pam", "PAM"))sprintf ( mat_name, "pam250mt");
+ else if (strm2 (mat_name_in, "blosum", "BLOSUM"))sprintf ( mat_name, "blosum62mt");
+ else if (strm3 (mat_name_in, "id", "ID", "idmat"))sprintf ( mat_name, "idmat");
+ else sprintf ( mat_name, "%s", mat_name_in);
+
+ /*Read Header Matrices*/
+ if (strm(mat_name, "pam250mt"))vector=pam250mt;
+ else if (strm(mat_name, "idmat"))vector=idmat;
+ else if (strm(mat_name, "dna_idmat"))vector=idmat;
+ else if (strm(mat_name, "est_idmat"))vector=est_idmat;
+ else if (strm(mat_name, "md_350mt"))vector=md_350mt;
+ else if (strm(mat_name, "md_250mt"))vector=md_250mt;
+ else if (strm(mat_name, "md_120mt"))vector=md_120mt;
+ else if (strm(mat_name, "md_40mt" ))vector= md_40mt;
+ else if (strm(mat_name, "pam350mt" ))vector=pam350mt;
+ else if (strm(mat_name, "pam160mt" ))vector=pam160mt;
+ else if (strm(mat_name, "pam120mt" ))vector=pam120mt;
+
+ else if (strm(mat_name, "blosum80mt" ))vector=blosum80mt;
+ else if (strm(mat_name, "blosum62mt" ))vector=blosum62mt;
+ else if (strm(mat_name, "exon2mt" ))vector=blosum62mt;
+ else if (strm(mat_name, "blosum62mt3" ))vector=blosum62mt3;
+
+ else if (strm(mat_name, "blosum62mt2" ))vector=blosum62mt2;
+ else if (strm(mat_name, "blosum55mt" ))vector=blosum55mt;
+ else if (strm(mat_name, "blosum50mt" ))vector=blosum50mt;
+ else if (strm(mat_name, "blosum45mt" ))vector=blosum45mt;
+
+ else if (strm(mat_name, "blosum40mt" ))vector=blosum40mt;
+ else if (strm(mat_name, "blosum30mt" ))vector=blosum30mt;
+ else if (strm(mat_name, "beta_mat" ))vector=beta_mat;
+ else if (strm(mat_name, "alpha_mat" ))vector=alpha_mat;
+ else if (strm(mat_name, "coil_mat" ))vector=coil_mat;
+
+ else if (strm(mat_name, "rblosum80mt" ))vector=rblosum80mt;
+ else if (strm(mat_name, "rblosum62mt" ))vector=rblosum62mt;
+ else if (strm(mat_name, "rblosum30mt" ))vector=rblosum30mt;
+
+ else if (strm(mat_name, "rpam250mt" ))vector=rpam250mt;
+ else if (strm(mat_name, "rpam350mt" ))vector=rpam350mt;
+ else if (strm(mat_name, "rpam160mt" ))vector=rpam160mt;
+ else if (strm(mat_name, "rpam120mt" ))vector=rpam120mt;
+
+ else if (strm(mat_name, "tmpam250mt" ))vector=tmpam250mt;
+ else if (strm(mat_name, "rtmpam250mt" ))vector=rtmpam250mt;
+
+ else if (strm(mat_name, "rbeta_mat" ))vector=rbeta_mat;
+ 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)
+ {
+ matrice=declare_int ( 256, 256);
+ for (a=0; a<l; ++a)
+ {
+ for (b=0;b<=a;++b)
+ {
+ matrice[a][b]=matrice[b][a]=(vector[(a*a+a)/2+b]);
+ }
+ }
+ }
+
+ /*Hard coded Matrices*/
+
+ else if ( strm (mat_name, "exon_mt"))
+ {
+ matrice=declare_int ( 256, 256);
+ sprintf (AA, "bojx");
+ l=4;
+ for ( a=0; a<l-1; a++)
+ {
+ matrice[a][a]=10;
+ for ( b=a+1; b< l-2; b++)
+ {
+ matrice[a][b]=matrice[b][a]=5;
+ }
+ }
+
+ }
+ else if ( strm ( mat_name, "tdamat"))
+ {
+ int x, y;
+ matrice=declare_int ( 256, 256);
+ sprintf ( AA, "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ");
+ l=strlen (AA);
+ for ( x=0; x<l; x++)
+ for ( y=0; y<l; y++)matrice[x][y]=-10;
+ for ( x=0; x<l; x++) {matrice[x][x]=0; matrice[x][GAP_CODE]=-3;}
+ return matrice;
+ }
+ /*Blast Matrices*/
+ else if (strm (mat_name, "strikeP"))
+ {
+ double min=100000;
+
+ matrice=declare_int ( 256, 256);
+ for (a=0; a<26; ++a)
+ {
+ for (b=0;b<26;++b)
+ {
+ if (min>strikeP_mat[a][b])min=strikeP_mat[a][b];
+ }
+ }
+ for (a=0; a<26; ++a)
+ {
+ for (b=0;b<26;++b)
+ {
+
+ matrice[a+'a'][b+'a']=(int)((double)10*(strikeP_mat[a][b]-min));
+ matrice[a+'A'][b+'A']=(int)((double)10*(strikeP_mat[a][b]-min));
+ }
+ }
+ return matrice;
+ }
+ else if (strm (mat_name, "strikeR"))
+ {
+ matrice=declare_int ( 256, 256);
+ matrice['G']['A']=matrice['g']['a']=0;
+ matrice['G']['G']=matrice['g']['g']=0;
+ matrice['G']['C']=matrice['g']['c']=6;
+ matrice['G']['T']=matrice['g']['t']=2;
+ matrice['G']['U']=matrice['g']['u']=2;
+ matrice['C']['A']=matrice['g']['a']=0;
+ matrice['C']['G']=matrice['c']['g']=6;
+ matrice['C']['C']=matrice['c']['c']=0;
+ matrice['C']['T']=matrice['c']['t']=0;
+ matrice['C']['U']=matrice['c']['u']=0;
+ matrice['T']['A']=matrice['t']['a']=5;
+ matrice['T']['G']=matrice['t']['g']=0;
+ matrice['T']['C']=matrice['t']['c']=0;
+ matrice['T']['T']=matrice['t']['t']=0;
+ matrice['T']['U']=matrice['t']['u']=0;
+ matrice['U']['A']=matrice['u']['a']=5;
+ matrice['U']['G']=matrice['u']['g']=2;
+ matrice['U']['C']=matrice['u']['c']=0;
+ matrice['U']['T']=matrice['u']['t']=0;
+ matrice['U']['U']=matrice['u']['u']=0;
+ matrice['A']['A']=matrice['a']['a']=0;
+ matrice['A']['G']=matrice['a']['g']=0;
+ matrice['A']['C']=matrice['a']['c']=0;
+ matrice['A']['T']=matrice['a']['t']=5;
+ matrice['A']['U']=matrice['a']['u']=5;
+ return matrice;
+ }
+ else if ( check_file_exists(mat_name) && is_blast_matrix (mat_name))
+ {
+ matrice=read_blast_matrix ( mat_name);
+ }
+
+
+ else if ( check_file_exists(mat_name) && is_pavie_matrix (mat_name))
+ {
+
+ matrice=read_pavie_matrix ( mat_name);
+ return matrice;
+ }
+
+ else if ( check_file_exists(mat_name) && is_clustalw_matrix (mat_name))
+ {
+
+ fp=vfopen ( mat_name, "r");
+ while ( (c=fgetc (fp))!='$' && c!=EOF);
+ if ( c==EOF){vfclose (fp);return NULL;};
+
+ matrice=declare_int ( 256, 256);
+ fgetc(fp);
+ for ( a=0; a<l; a++)
+ {
+ for ( b=0; b<=a; b++)
+ if (fscanf ( fp, "%d,", &matrice[a][b])==0){vfclose (fp);free_int (matrice, -1);return NULL;};
+ fscanf ( fp, "\n");
+ }
+ fclose ( fp);
+ }
+ else {return NULL;}
+
+
+ matrix2=declare_int ( 256, 256);
+ for ( b=0; b<l; b++)
+ for ( c=0; c<l; c++)
+ {
+
+ matrix2[toupper(AA[b])-'A'][toupper(AA[c])-'A']=matrice[b][c];
+ matrix2[toupper(AA[b])-'A'][tolower(AA[c])-'A']=matrice[b][c];
+ matrix2[tolower(AA[b])-'A'][toupper(AA[c])-'A']=matrice[b][c];
+ matrix2[tolower(AA[b])-'A'][tolower(AA[c])-'A']=matrice[b][c];
+ }
+ if ( strm ( "exon2mt", mat_name))
+ {
+ char EE[4];
+ int v=(getenv ("EXONVALUE_4_TCOFFEE"))?atoi("EXONVALUE_4_TCOFFEE"):100;
+ sprintf (EE, "obj");
+ for (a=0; a<strlen (EE); a++)
+ {
+ matrix2[toupper(EE[a])-'A'][toupper(EE[a])-'A']=v;
+ matrix2[tolower(EE[a])-'A'][toupper(EE[a])-'A']=v;
+ matrix2[toupper(EE[a])-'A'][tolower(EE[a])-'A']=v;
+ matrix2[tolower(EE[a])-'A'][tolower(EE[a])-'A']=v;
+ }
+ }
+
+ /*Correct for RNA: Add the U cost*/
+ for (b=0; b<l; b++)
+ {
+
+ matrix2['U'-'A'][toupper(AA[b])-'A']=matrix2['T'-'A'][toupper(AA[b])-'A'];
+ matrix2[toupper(AA[b])-'A']['U'-'A']=matrix2[toupper(AA[b])-'A']['T'-'A'];
+ matrix2['U'-'A'][toupper(AA[b])-'A']=matrix2['t'-'A'][tolower(AA[b])-'A'];
+ matrix2[tolower(AA[b])-'A']['u'-'A']=matrix2[tolower(AA[b])-'A']['t'-'A'];
+
+ }
+ matrix2['U'-'A']['U'-'A']=matrix2['T'-'A']['T'-'A'];
+ matrix2['u'-'A']['U'-'A']=matrix2['t'-'A']['T'-'A'];
+ matrix2['U'-'A']['u'-'A']=matrix2['T'-'A']['t'-'A'];
+ matrix2['u'-'A']['u'-'A']=matrix2['t'-'A']['t'-'A'];
+
+ free_int (matrice, -1);
+ return (matrix2);
+
+ }
+
+void display_matrix (int **mat)
+{
+ int a, b;
+
+ for ( a=0; a< 26; a++)
+ {
+ fprintf ( stderr, "\n%c ", a+'a');
+ for ( b=0; b< 26; b++)
+ fprintf ( stderr, " %2d", mat[a][b]);
+ }
+}
+
+int **neg_matrix2pos_matrix ( int **matrix)
+ {
+ int b,c,l, min, max;
+ char AA[]="abcdefghiklmnpqrstvwxyzABCDEFGHIKLMNPQRSTVWXYZ";
+ l=strlen(AA);
+ min=max=matrix[AA[0]-'A'][AA[0]-'A'];
+ for ( b=0; b<l; b++)
+ for ( c=0; c<l; c++)
+ {
+ min=(matrix[AA[b]-'A'][AA[c]-'A']<min)?matrix[AA[b]-'A'][AA[c]-'A']:min;
+ max=(matrix[AA[b]-'A'][AA[c]-'A']<max)?matrix[AA[b]-'A'][AA[c]-'A']:max;
+ }
+ if (min>0)return matrix;
+ else
+ {
+ for ( b=0; b<l; b++)
+ for ( c=0; c<l; c++)
+ {
+ matrix[b][c]=matrix[b][c]-min;
+ }
+ }
+ return matrix;
+ }
+
+
+
+/*****************************************************************/
+void get_rgb_values ( int val, Color *C)
+ {
+
+ /*Colors can be modified, see the definition of
+ COLOR_FILE in prgogrammes_define.h
+ */
+
+ static char **html_code;
+ static float **ps_code;
+ float *r, *g, *b;
+ if (!html_code)
+ {
+ int rgb255=0;
+ int a, b;
+ int new_scheme=3;
+ int color_file=0;
+ FILE *fp;
+ int classC, n, c;
+ char *cs;
+
+ if ((cs=getenv ("COLOR_4_TCOFFEE")))
+ {
+ if ( strm (cs, "new")|| strm (cs, "NEW")||strm (cs, "monet"))new_scheme=3;
+ else if (strm (cs, "old")|| strm (cs, "OLD")||strm (cs, "delaunay"))new_scheme=0;
+ else if (strm (cs, "2"))new_scheme=2;
+ else if (strm (cs, "1"))new_scheme=1;
+ else
+ {
+ printf_exit ( EXIT_FAILURE,stderr, "\nERROR: color scheme %s is unknown",cs);
+ }
+ }
+
+ color_file=(check_file_exists(COLOR_FILE))?1:0;
+ html_code=declare_char(20, 10);
+ ps_code=declare_float (20, 3);
+
+ if (!color_file && new_scheme==3 )
+ {
+ n=0;
+ /*0*/
+ sprintf (html_code[n], "#9B92FF");//blue
+ ps_code[n][0]=155;
+ ps_code[n][1]=146;
+ ps_code[n][2]=255;
+ n++;
+
+
+
+ /*1*/
+ sprintf (html_code[n], "#B4FFB4");//green1
+ ps_code[n][0]=180;
+ ps_code[n][1]=255;
+ ps_code[n][2]=180;
+ n++;
+
+
+ /*2*/
+ sprintf (html_code[n], "#BEFFBE");//green2
+ ps_code[n][0]=190;
+ ps_code[n][1]=255;
+ ps_code[n][2]=190;
+ n++;
+
+ /*3*/
+ sprintf (html_code[n], "#C8FFC8");//green3
+ ps_code[n][0]=200;
+ ps_code[n][1]=255;
+ ps_code[n][2]=200;
+ n++;
+
+ /*4*/
+ sprintf (html_code[n], "#FFFFB7");//orange 1
+ ps_code[n][0]=255;
+ ps_code[n][1]=255;
+ ps_code[n][2]=183;
+ n++;
+
+ /*5*/
+ sprintf (html_code[n], "#FFFFAD");//orange 1
+ ps_code[n][0]=255;
+ ps_code[n][1]=255;
+ ps_code[n][2]=173;
+ n++;
+
+ /*6*/
+ sprintf (html_code[n], "#FFFFAD");//orange 2
+ ps_code[n][0]=255;
+ ps_code[n][1]=255;
+ ps_code[n][2]=173;
+ n++;
+
+ /*7*/
+ sprintf (html_code[n], "#FFE6E6");//red1
+ ps_code[n][0]=255;
+ ps_code[n][1]=230;
+ ps_code[n][2]=230;
+ n++;
+
+ /*8*/
+ sprintf (html_code[n], "#FFDCDC");//red2
+ ps_code[n][0]=255;
+ ps_code[n][1]=220;
+ ps_code[n][2]=220;
+ n++;
+
+ /*9*/
+ sprintf (html_code[n], "#FFC8C8");//red3
+ ps_code[n][0]=255;
+ ps_code[n][1]=200;
+ ps_code[n][2]=200;
+ n++;
+
+
+
+
+ }
+ else if (!color_file && new_scheme==2 )
+ {
+ n=0;
+ /*0*/
+ sprintf (html_code[n], "#008080");//blue
+ ps_code[n][0]=0.4;
+ ps_code[n][1]=0.4;
+ ps_code[n][2]=1;
+ n++;
+ /*0
+ sprintf (html_code[n], "#BC4400");//blue
+ ps_code[n][0]=0.4;
+ ps_code[n][1]=0.4;
+ ps_code[n][2]=1;
+ n++;
+ */
+
+
+ /*2*/
+ sprintf (html_code[n], "#D05800");//blue green
+ ps_code[n][0]=0.6;
+ ps_code[n][1]=1;
+ ps_code[n][2]=0;
+ n++;
+ /*2
+ sprintf (html_code[n], "#E46C03");//Green pea
+ ps_code[n][0]=0.6;
+ ps_code[n][1]=1;
+ ps_code[n][2]=0;
+ n++;
+ /*
+
+ /*3*/
+ sprintf (html_code[n], "#FF8A21");//lighter pink
+ ps_code[n][0]=0.8;
+ ps_code[n][1]=1;
+ ps_code[n][2]=0;
+ n++;
+
+ /*4*/
+ sprintf (html_code[n], "#FF9E35");//light pink
+ ps_code[n][0]=1.0;
+ ps_code[n][1]=1.0;
+ ps_code[n][2]=0;
+ n++;
+
+ /*5*/
+ sprintf (html_code[n], "#FFB249");//light orange
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.85;
+ ps_code[n][2]=0;
+ n++;
+
+ /*6*/
+ sprintf (html_code[n], "#FFC65D");//light orange/bown
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.7;
+ ps_code[n][2]=0;
+ n++;
+
+ /*7*/
+ sprintf (html_code[n], "#FFDA71");//darker orange/brown
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.6;
+ ps_code[n][2]=0;
+ n++;
+
+ /*8*/
+ sprintf (html_code[n], "#FFEE85");//mysti rose
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.4;
+ ps_code[n][2]=0;
+ n++;
+
+ /*9*/
+ sprintf (html_code[n], "#FFFF99");
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.2;
+ ps_code[n][2]=0;
+ n++;
+
+ /*9*/
+ sprintf (html_code[n], "#FFFFAD");
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.2;
+ ps_code[n][2]=0;
+ n++;
+
+ /*9*/
+ sprintf (html_code[n], "#FFFFC1");
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.2;
+ ps_code[n][2]=0;
+ n++;
+
+
+ }
+ else if (!color_file && new_scheme==1 )
+ {
+ n=0;
+ /*0*/
+ sprintf (html_code[n], "#7AD1FF");//blue
+ ps_code[n][0]=0.4;
+ ps_code[n][1]=0.4;
+ ps_code[n][2]=1;
+ n++;
+ /*2*/
+ sprintf (html_code[n], "#91FF49");//blue green
+ ps_code[n][0]=0.6;
+ ps_code[n][1]=1;
+ ps_code[n][2]=0;
+ n++;
+ /*2*/
+ sprintf (html_code[n], "#A5FF5D");//Green pea
+ ps_code[n][0]=0.6;
+ ps_code[n][1]=1;
+ ps_code[n][2]=0;
+ n++;
+
+ /*3*/
+ sprintf (html_code[n], "#B9FF71");//lighter pink
+ ps_code[n][0]=0.8;
+ ps_code[n][1]=1;
+ ps_code[n][2]=0;
+ n++;
+
+ /*4*/
+ sprintf (html_code[n], "#FFC5C3");//light pink
+ ps_code[n][0]=1.0;
+ ps_code[n][1]=1.0;
+ ps_code[n][2]=0;
+ n++;
+
+ /*5*/
+ sprintf (html_code[n], "#FAD1B9");//light orange
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.85;
+ ps_code[n][2]=0;
+ n++;
+
+ /*6*/
+ sprintf (html_code[n], "#FAE6B9");//light orange/bown
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.7;
+ ps_code[n][2]=0;
+ n++;
+
+ /*7*/
+ sprintf (html_code[n], "#FAF1B9");//darker orange/brown
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.6;
+ ps_code[n][2]=0;
+ n++;
+
+ /*8*/
+ sprintf (html_code[n], "#F8FAB9");//mysti rose
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.4;
+ ps_code[n][2]=0;
+ n++;
+
+ /*9*/
+ sprintf (html_code[n], "#EDFAB9");
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.2;
+ ps_code[n][2]=0;
+ n++;
+
+ }
+ else if (!color_file && new_scheme==0)//old code
+ {
+ n=0;
+ /*0*/
+ sprintf (html_code[n], "#6666FF");
+ ps_code[n][0]=0.4;
+ ps_code[n][1]=0.4;
+ ps_code[n][2]=1;
+ n++;
+ /*1*/
+ sprintf (html_code[n], "#00FF00");
+ ps_code[n][0]=0.6;
+ ps_code[n][1]=1;
+ ps_code[n][2]=0;
+ n++;
+
+ /*2*/
+ sprintf (html_code[n], "#66FF00");
+ ps_code[n][0]=0.8;
+ ps_code[n][1]=1;
+ ps_code[n][2]=0;
+ n++;
+
+ /*3*/
+ sprintf (html_code[n], "#CCFF00");
+ ps_code[n][0]=1.0;
+ ps_code[n][1]=1.0;
+ ps_code[n][2]=0;
+ n++;
+
+ /*4*/
+ sprintf (html_code[n], "#FFFF00");
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.85;
+ ps_code[n][2]=0;
+ n++;
+
+ /*5*/
+ sprintf (html_code[n], "#FFCC00");
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.7;
+ ps_code[n][2]=0;
+ n++;
+
+ /*6*/
+ sprintf (html_code[n], "#FF9900");
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.6;
+ ps_code[n][2]=0;
+ n++;
+
+ /*7*/
+ sprintf (html_code[n], "#FF6600");
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.4;
+ ps_code[n][2]=0;
+ n++;
+
+ /*8*/
+ sprintf (html_code[n], "#FF3300");
+ ps_code[n][0]=1;
+ ps_code[n][1]=0.2;
+ ps_code[n][2]=0;
+ n++;
+
+
+ /*9*/
+ sprintf (html_code[n], "#FF2000");
+ ps_code[n][0]=1;
+ ps_code[n][1]=0;
+ ps_code[n][2]=0;
+ n++;
+ }
+ else if (color_file)
+ {
+ fp=vfopen( COLOR_FILE, "r");
+
+ while ((c=fgetc(fp))!='*');
+ while ((c=fgetc(fp))!='\n');
+
+ c=0;
+ while ((c=fgetc(fp))!=EOF)
+ {
+ ungetc(c, fp);
+ if ( fscanf (fp, "%d", &classC)==0)break;
+ fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]);
+ while ((c=fgetc(fp))!='\n' && c!=EOF);
+ if ( c==EOF)ungetc(c, fp);
+ }
+ vfclose(fp);
+ }
+
+ for (a=0; a<n; a++)
+ {
+ for (b=0; b<3; b++)
+ if (ps_code[a][b]>1){rgb255=1;b=3;a=n;}
+ }
+ if (rgb255)
+ for (a=0; a<n; a++)
+ {
+ for (b=0; b<3; b++)
+ ps_code[a][b]/=255;
+ }
+ }
+
+
+
+
+ /*Conversions*/
+ if ( val==10)val--;
+
+ r=&C->r;
+ g=&C->g;
+ b=&C->b;
+
+ if ( val==10)val--;
+ sprintf ( C->html_color_class, "value%d",val);
+
+
+ if (val<=9 && val>=0)
+ {
+
+ sprintf ( C->html_color, "%s", html_code[val]);
+ r[0]=ps_code[val][0];
+ g[0]=ps_code[val][1];
+ b[0]=ps_code[val][2];
+ }
+
+ else if (val==DEFAULT_COLOR || val==NO_COLOR_RESIDUE || val==NO_COLOR_GAP || (val>'A' && val<'z'))
+ {
+ C->html_color[0]='\0';
+ sprintf ( C->html_color_class, "valuedefault");
+ r[0]=1.;
+ g[0]=1;
+ b[0]=1;
+
+ }
+ else if (val==GAP_COLOR)
+ {
+ C->html_color[0]='\0';
+ sprintf ( C->html_color_class, "valuegap");
+ r[0]=1.;
+ g[0]=1;
+ b[0]=1;
+ }
+ else if (val==INK_COLOR )
+ {
+ sprintf ( C->html_color, "000000");
+ sprintf ( C->html_color_class, "valueink");
+ r[0]=0.;
+ g[0]=0;
+ b[0]=0;
+ }
+ return;
+
+
+ }
+
+// 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*),\
+FILE_format *(*print_format_char) ( int ,Color *, Color *, FILE_format*),\
+void (*get_rgb_values_format) ( int ,Color *),\
+FILE_format* (*vfclose_format) ( FILE_format *))
+ {
+ int a, b, c;
+ int max_name_len=15;
+ int max_len=0;
+ char *buf2, *buf3;
+
+ static char *buf;
+ int s;
+ int *n_residues;
+ static FILE_format *fps;
+ Color *ink;
+ Color *box_c;
+ Color *white;
+ Alignment *S;
+
+
+ S=copy_aln (B, NULL);
+
+ buf2=(char*)vcalloc (Sin->len_aln+1, sizeof (char));
+ buf3=(char*)vcalloc ( B->len_aln+1, sizeof (char));
+ for ( a=0; a<B->nseq; a++)
+ {
+ int i,n, r;
+
+ i=name_is_in_list ( B->name[a], Sin->name, Sin->nseq, -1);
+ if (i==-1)continue;
+ sprintf (buf2, "%s", Sin->seq_al[i]);ungap(buf2);
+ sprintf (buf3, "%s", S->seq_al[a]);ungap(buf3);
+
+
+
+ if (strlen (buf2) !=strlen(buf3))
+ {
+ for (b=0; b<strlen (buf2); b++)HERE ("%d", buf2[b]);
+ fprintf ( stderr, "\nERROR: Incompatible cache ON sEQ: %s\n", S->name[a]);
+ fprintf ( stderr, "\n%s\n%s", buf2, buf3);
+ fprintf ( stderr, "\n\n%s\n%s", Sin->seq_al[i],S->seq_al[a]); exit (EXIT_FAILURE);
+ }
+
+ for (n=0,b=0;b<B->len_aln; b++)
+ {
+ r=S->seq_al[a][b];
+ if (!is_gap(r))
+ {
+ S->seq_al[a][b]=buf2[n++];
+ }
+ }
+ }
+
+ S=aln2number(S);
+ vfree (buf2);
+
+ box_c=(Color*)vcalloc ( 1, sizeof (Color));
+ get_rgb_values_format (DEFAULT_COLOR, (white=(Color*)vcalloc ( 1, sizeof (Color))));
+ get_rgb_values_format (INK_COLOR, (ink =(Color*)vcalloc ( 1, sizeof (Color))));
+
+ n_residues=(int*)vcalloc ( B->nseq+1, sizeof (int));
+ for ( a=0; a<B->nseq; a++)n_residues[a]=B->order[a][1];
+
+ fps=vfopen_format( name);
+ if ( buf==NULL)
+ {
+ buf=(char*)vcalloc (10000, sizeof (int));
+ }
+
+ if ( max_len==0)
+ {
+ for ( a=0; a< B->nseq; a++)
+ {if ( strlen (B->name[a])>max_len)
+ max_len= strlen ( (B->name[a]));
+ }
+ }
+ if ( max_len>max_name_len)max_len=max_name_len;
+
+ sprintf (buf, "\n%s, %s (%s)\n%s\n",PROGRAM,VERSION,BUILD_INFO, 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;
+ fps->line=fps->line-fps->line%3;
+
+
+
+
+ for (a=0; a<B->len_aln; a+=fps->line)
+ {
+
+ if ( (fps->n_line+(B->nseq+4))>fps->max_line_ppage && !((B->nseq+4)>fps->max_line_ppage))
+ {
+ fps=print_format_char ( fps->eop,white, ink, fps);
+ }
+
+ for (b=0; b<=B->nseq; b++)
+ {
+ sprintf (buf,"%-*.*s ",max_len+2, max_len,(b==B->nseq)?"":S->name[b]);
+ fps=print_format_string ( buf,white, ink, fps);
+ if(B->output_res_num)
+ {
+ sprintf (buf, " %4d ", n_residues[b]+1);
+ fps=print_format_string ( buf,white, ink, fps);
+ }
+
+ for (fps->in_seq=1,c=a;c<a+fps->line && c<B->len_aln;c++)
+ {
+ if (b==B->nseq)
+ {
+ n_residues[b]++;
+ get_rgb_values_format (DEFAULT_COLOR,box_c);
+ s=analyse_aln_column ( B, c);
+ }
+ else
+ {
+ n_residues[b]+=!is_gap(B->seq_al[b][c]);
+ s=B->seq_al[b][c];
+ if (!is_gap(s) && S->seq_al[b][c]!=NO_COLOR_RESIDUE )
+ {
+ get_rgb_values_format ( S->seq_al[b][c], box_c);
+ }
+ else
+ {
+ get_rgb_values_format (GAP_COLOR, box_c);
+ }
+ }
+ fps=print_format_char ( s,box_c, ink,fps);
+ }
+ fps->in_seq=0;
+
+ if(B->output_res_num)
+ {
+ sprintf (buf, " %4d ", n_residues[b]);
+ fps=print_format_string ( buf,white, ink, fps);
+ }
+
+ fps=print_format_char ( '\n', white, ink, fps);
+
+ }
+ fps=print_format_string ( "\n\n",white, ink, fps);
+ }
+ fps=print_format_string ( "\n\n\n",white, ink,fps);
+
+
+ vfclose_format( fps);
+ free_aln (S);
+ vfree (n_residues);
+ return 1;
+
+ }
+
+int output_raw_score (Alignment *A, Alignment *B, char *name)
+{
+ FILE *fp;
+ int a, b,pos;
+ int *ngap;
+ int *len;
+
+ if (!A)return NULL;
+ ngap=(int*)vcalloc (A->len_aln, sizeof (int));
+ len=(int*)vcalloc (A->len_aln,sizeof (int));
+ for (b=0; b<A->len_aln; b++)
+ for (a=0; a<A->nseq; a++)
+ {
+ int g=is_gap(A->seq_al[a][b]);
+ ngap[b]+=g;
+ len[a]+=1-g;
+ }
+
+ fp=vfopen (name, "w");
+ fprintf ( fp, "#ALN nseq: %d len: %d score: %d\n", A->nseq, A->len_aln, (B)?B->score:0);
+ for (b=0; b<A->len_aln; b++)
+ fprintf (fp, "#COLUMN pos: %d ngap: %d score: %d\n", b+1,ngap[b],(B)?B->seq_al[B->nseq][b]-'0':0);
+ for (a=0; a<A->nseq; a++)
+ fprintf ( fp, "#SEQUENCE name: %s len: %d score: %d\n", A->name[a], len[a], (B)?B->score_seq[a]:0);
+ for (a=0; a<A->nseq; a++)
+ for (pos=0,b=0; b<A->len_aln; b++)
+ {
+ int r=A->seq_al[a][b];
+ int s=(B)?B->seq_al[a][b]:0;
+ int g=is_gap(r);
+ pos+=1-g;
+ if (!g && s!=NO_COLOR_RESIDUE)
+ {
+ int s=B->seq_al[a][b];
+ if (s>='0')s-='0';
+ fprintf (fp, "#RESIDUE seq: %s pos: %d res: %c score: %d\n", A->name[a],pos, r,s);
+ }
+ }
+ vfclose (fp);
+ vfree (ngap);
+ vfree(len);
+ return 1;
+}
+
+
+
+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 a, b, c,l;
+ int max_name_len=15;
+ int max_len=0;
+ static char *buf,*buf2;
+ int s;
+ static FILE_format *fps;
+ Color *ink;
+ Color *box_c;
+ Color *white;
+ int *n_residues;
+
+
+ box_c=(Color*)vcalloc ( 1, sizeof (Color));
+ get_rgb_values_format (DEFAULT_COLOR, (white=(Color*)vcalloc ( 1, sizeof (Color))));
+ get_rgb_values_format (INK_COLOR, (ink =(Color*)vcalloc ( 1, sizeof (Color))));
+
+ n_residues=(int*)vcalloc ( B->nseq+1, sizeof (int));
+ for ( a=0; a<B->nseq; a++)n_residues[a]=B->order[a][1];
+
+
+ fps=vfopen_format( name);
+ if ( buf==NULL)
+ {
+ buf=(char*)vcalloc (10000, sizeof (int));
+ buf2=(char*)vcalloc (10000, sizeof (int));
+ }
+
+ if ( max_len==0)
+ {
+ for ( a=0; a< B->nseq; a++)
+ {if ( strlen (B->name[a])>max_len)
+ max_len= strlen ( (B->name[a]));
+ }
+ }
+
+ if ( vfopen_format==vfopen_ascii)
+ {
+ fps->line+= max_len;
+ }
+ else if ( max_len>max_name_len)max_len=max_name_len;
+
+
+
+ sprintf (buf, "%s, %s (%s)\n%s\nCPU TIME:%d sec.\n%s",PROGRAM,VERSION,BUILD_INFO, AUTHOR, (B->cpu+get_time())/1000, (S->generic_comment)?S->generic_comment:"");
+ fps=print_format_string ( buf,white, ink, fps);
+ sprintf (buf, "SCORE=%d\n*\n", S->score_aln);
+ fps=print_format_string ( buf,white, ink, fps);
+
+ sprintf ( buf2, " BAD AVG GOOD");
+ l=strlen(buf2);
+ get_rgb_values_format ( DEFAULT_COLOR, box_c);
+ fps=print_format_char ( buf2[0],box_c, ink, fps);
+ for ( a=1; a<l-1; a++)
+ {
+ get_rgb_values_format ( MIN(9,a-1), box_c);
+ fps=print_format_char ( buf2[a],box_c,ink,fps);
+ }
+ fps=print_format_char ( buf2[a], box_c, ink, fps);
+
+
+ fps=print_format_string ( "\n*\n",white,ink, fps);
+ for ( a=0;S->score_seq && a< B->nseq; a++)
+ {
+ get_rgb_values_format (S->score_seq[a]/10, box_c);
+ sprintf ( buf, "%-*.*s ", max_len+2,max_len, S->name[a]);
+ fps=print_format_string ( buf,box_c, ink,fps);
+ sprintf ( buf, ": %3d\n", S->score_seq[a]);
+ fps=print_format_string ( buf,white, ink,fps);
+ }
+ //Print the Consensus score
+ get_rgb_values_format (S->score_aln/10, box_c);
+ sprintf ( buf, "%-*.*s ", max_len+2,max_len, S->name[S->nseq]);
+ fps=print_format_string ( buf,box_c, ink,fps);
+ sprintf ( buf, ": %3d\n", S->score_aln/10);
+ fps=print_format_string ( buf,white, ink,fps);
+
+ fps=print_format_string ( "\n",white, ink,fps);
+
+
+
+ fps->line-=max_len;
+ fps->line=fps->line-(fps->line%3);
+
+ for (a=0; a<B->len_aln; a+=fps->line)
+ {
+
+ if ( (fps->n_line+(B->nseq+4))>fps->max_line_ppage && !((B->nseq+4)>fps->max_line_ppage))
+ {
+ fps=print_format_char ( fps->eop,white, ink, fps);
+ }
+
+ for (b=0; b<=S->nseq; b++)
+ {
+ if ( b==S->nseq && print_format_string !=print_ascii_string) fps=print_format_string ( "\n",white, ink, fps);
+ sprintf (buf,"%-*.*s ",max_len+2,max_len,S->name[b]);
+ fps=print_format_string ( buf,white, ink, fps);
+ if(B->output_res_num)
+ {
+ sprintf (buf, " %4d ", n_residues[b]+1);
+ fps=print_format_string ( buf,white, ink, fps);
+ }
+
+ for (fps->in_seq=1,c=a;c<a+fps->line && c<B->len_aln;c++)
+ {
+ if (b==S->nseq)
+ {
+
+ if (S->score_seq)
+ {
+ int s;
+ s=S->seq_al[b][c];
+ if ( s>='0' && s<='9')s-='0';
+ get_rgb_values_format (s,box_c);
+ }
+ else get_rgb_values_format (DEFAULT_COLOR,box_c);
+ n_residues[b]++;
+ s=analyse_aln_column ( B, c);
+ }
+ else
+ {
+ n_residues[b]+=!is_gap(B->seq_al[b][c]);
+ //s=toupper(B->seq_al[b][c]);
+ s=GET_CASE(B->residue_case, B->seq_al[b][c]);
+
+ if (!is_gap(s) && S->seq_al[b][c]!=NO_COLOR_RESIDUE )
+ {
+ get_rgb_values_format ( S->seq_al[b][c], box_c);
+
+ }
+ else
+ {
+ get_rgb_values_format (GAP_COLOR, box_c);
+
+ }
+
+ }
+ fps=print_format_char ( s,box_c, ink,fps);
+ }
+ fps->in_seq=0;
+
+ if(B->output_res_num)
+ {
+ sprintf (buf, " %4d ",n_residues[b]);
+ fps=print_format_string ( buf,white, ink, fps);
+ }
+
+ fps=print_format_char ( '\n', white, ink, fps);
+
+ }
+ fps=print_format_string ( "\n\n",white, ink, fps);
+ }
+ fps=print_format_string ( "\n\n\n",white, ink,fps);
+ vfclose_format( fps);
+ return 1;
+
+ }
+
+int output_reliability_format_fasta ( 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 a, b, c,l;
+ int max_name_len=15;
+ int max_len=0;
+ static char *buf,*buf2;
+ int s;
+ static FILE_format *fps;
+ Color *ink;
+ Color *box_c;
+ Color *white;
+ int *n_residues;
+
+
+ box_c=(Color*)vcalloc ( 1, sizeof (Color));
+ get_rgb_values_format (DEFAULT_COLOR, (white=(Color*)vcalloc ( 1, sizeof (Color))));
+ get_rgb_values_format (INK_COLOR, (ink =(Color*)vcalloc ( 1, sizeof (Color))));
+
+ n_residues=(int*)vcalloc ( B->nseq+1, sizeof (int));
+ for ( a=0; a<B->nseq; a++)n_residues[a]=B->order[a][1];
+
+
+ fps=vfopen_format( name);
+ if ( buf==NULL)
+ {
+ buf=(char*)vcalloc (10000, sizeof (int));
+ buf2=(char*)vcalloc (10000, sizeof (int));
+ }
+
+ if ( max_len==0)
+ {
+ for ( a=0; a< B->nseq; a++)
+ {if ( strlen (B->name[a])>max_len)
+ max_len= strlen ( (B->name[a]));
+ }
+ }
+
+ if ( vfopen_format==vfopen_ascii)
+ {
+ fps->line+= max_len;
+ }
+ else if ( max_len>max_name_len)max_len=max_name_len;
+
+ fps->line-=max_len;
+ fps->line=fps->line-(fps->line%3);
+
+ for (b=0; b<S->nseq; b++)
+ {
+ sprintf (buf,">%-*.*s \n",max_len+2,max_len,S->name[b]);
+ fps=print_format_string ( buf,white, ink, fps);
+ for (fps->in_seq=1,c=0;c<B->len_aln;c++)
+ {
+ n_residues[b]+=!is_gap(B->seq_al[b][c]);
+ s=B->seq_al[b][c];
+ if (!is_gap(s) && S->seq_al[b][c]!=NO_COLOR_RESIDUE )
+ {
+ get_rgb_values_format ( S->seq_al[b][c], box_c);
+ }
+ else
+ {
+ get_rgb_values_format (GAP_COLOR, box_c);
+ }
+
+ fps=print_format_char ( s,box_c, ink,fps);
+ }
+ fps->in_seq=0;
+ fps=print_format_char ( '\n', white, ink, fps);
+ }
+ vfclose_format( fps);
+ return 1;
+ }
+
+/*****************************************************************************/
+/* PDF FUNCTIONS */
+/* */
+/*****************************************************************************/
+int output_color_pdf ( Alignment *B,Alignment *S, char *name)
+ {
+ char *tmp_name;
+ char command[LONG_STRING];
+
+
+#ifndef PS2PDF
+ fprintf (stderr, "\nPDF FORMAT IS NOT SUPPORTED: INSTALL THE PROGRAM PS2PDF\n");
+ myexit (EXIT_FAILURE);
+#else
+ tmp_name=vtmpnam(NULL);
+
+ output_color_ps (B, S, tmp_name);
+ sprintf ( command, "%s %s %s", PS2PDF, tmp_name, name);
+ my_system ( command);
+ vremove ( tmp_name);
+#endif
+
+
+ return 1;
+ }
+int output_reliability_pdf ( Alignment *B,Alignment *S, char *name)
+ {
+ char *tmp_name;
+ char command[LONG_STRING];
+
+
+
+#ifndef PS2PDF
+ fprintf (stderr, "\nPDF FORMAT IS NOT SUPPORTED: INSTALL THE PROGRAM PS2PDF\n");
+ myexit (EXIT_FAILURE);
+#else
+ tmp_name=vtmpnam(NULL);
+
+ output_reliability_ps (B, S, tmp_name);
+ sprintf ( command, "%s %s %s", PS2PDF, tmp_name, name);
+ my_system ( command);
+ vremove ( tmp_name);
+#endif
+
+
+ return 1;
+ }
+/*****************************************************************************/
+/* POST SCRIPT FUNCTIONS */
+/* */
+/*****************************************************************************/
+int output_color_ps ( Alignment *B,Alignment *S, char *name)
+ {
+ output_color_format (B, S, name, vfopen_ps,print_ps_string,print_ps_char,get_rgb_values_ps, vfclose_ps);
+ return 1;
+ }
+int output_reliability_ps ( Alignment *B,Alignment *S, char *name)
+ {
+ output_reliability_format (B, S, name, vfopen_ps,print_ps_string,print_ps_char,get_rgb_values_ps, vfclose_ps);
+ return 1;
+ }
+FILE_format *print_ps_string( char *s, Color *box, Color *ink, FILE_format *fps)
+ {
+ int l;
+ int a;
+
+ l=strlen (s);
+
+ for ( a=0; a< l; a++)
+ {
+ fps=print_ps_char (s[a], box, ink, fps);
+ }
+ return fps;
+ }
+
+
+FILE_format * print_ps_char ( int c, Color *box, Color *ink, FILE_format *f)
+ {
+
+ int ch;
+ int cw;
+
+ ch=f->font+3;
+ cw=f->font-2;
+
+ if ( c=='(' || c==')')return f;
+ else if (c!='\n' && c!=f->eop)
+ {
+ fprintf(f->fp,"%d %d moveto\n", f->x,f->y);
+ fprintf(f->fp,"0 %d rlineto\n%d 0 rlineto\n0 -%d rlineto\nclosepath\n",ch,cw,ch );
+ fprintf(f->fp,"%3.1f %3.1f %3.1f setrgbcolor\nfill\n%3.1f %3.1f %3.1f setrgbcolor\n", box->r,box->g,box->b, ink->r, ink->g, ink->b);
+ fprintf(f->fp,"%d %d moveto\n(%c) show\n", f->x+1,f->y+3, c);
+
+ f->x+=cw;
+ }
+ else
+ {
+ f->n_line++;
+ if ( f->n_line==f->max_line_ppage || c==f->eop)
+ {
+
+ f->n_line=0;
+ f->x=f->x0;
+ f->y=f->y0;
+ fprintf(f->fp,"showpage\n");
+ f->n_pages++;
+ fprintf ( f->fp, "%c%cPage: %d %d\n",'%', '%', f->n_pages, f->n_pages);
+ }
+ else
+ {
+ f->x=f->x0;
+ f->y-=ch;
+ }
+ }
+ return f;
+ }
+FILE_format* print_ps_line (int len, Color *c, FILE_format *f)
+{
+ static int x=0;
+ static int y=0;
+ int pix=1;
+ int xs=0;
+ static int width;
+
+ if (!width)
+ {
+ width=1;
+ fprintf (f->fp, "%d setlinewidth\n", pix);
+ }
+
+ if (len==-1)
+ {
+ y-=pix;
+ x=xs;
+ }
+ else
+ {
+ fprintf (f->fp, "newpath\n");
+ fprintf (f->fp, "%d %d moveto\n",x, y);
+ fprintf(f->fp,"%3.1f %3.1f %3.1f setrgbcolor\n", c->r,c->g,c->b);
+ x+=len*pix;
+ fprintf (f->fp, "%d %d lineto\n", x, y);
+ fprintf (f->fp, "stroke\n");
+ }
+ return f;
+}
+
+void get_rgb_values_ps ( int val, Color *C)
+ {
+ get_rgb_values ( val, C);
+ }
+
+
+
+FILE_format* vfopen_ps ( char *name)
+ {
+ FILE_format*fps;
+
+ fps=(FILE_format*)vcalloc ( 1, sizeof ( FILE_format));
+ fps->font=9;
+ fps->max_line_ppage=60;
+ fps->line=get_msa_line_length (0, 0);/*N char per line*/
+ fps->x0=15;
+ fps->y0=750;
+ fps->eop='^';
+
+ fps->fp=vfopen ( name, "w");
+ fprintf(fps->fp,"%%!PS-Adobe-2.0\n/Courier findfont\n%d scalefont\nsetfont\n",fps->font);
+ fprintf(fps->fp, "%%%%Pages: (atend)\n");
+ fprintf(fps->fp,"newpath\n");
+ ++(fps->n_pages);
+ fprintf (fps->fp, "%%%%Page: %d %d\n", fps->n_pages, fps->n_pages);
+ fprintf (fps->fp,"%d %d translate\n",fps->x0, fps->y0);
+ return fps;
+ }
+
+FILE_format* vfclose_ps ( FILE_format *fps)
+ {
+
+ fprintf(fps->fp,"showpage\n");
+ fprintf ( fps->fp, "%%%%Pages: %d\n", fps->n_pages);
+ fprintf(fps->fp,"%%%%EOF");
+ fprintf(fps->fp,"%%%%\n");
+ vfclose ( fps->fp);
+ vfree (fps);
+ return NULL;
+ }
+/*****************************************************************************/
+/* HTML FUNCTIONS */
+/* */
+/*****************************************************************************/
+
+/*****************************************************************************/
+//JM_ADD
+/*****************************************************************************/
+void output_hit_matrix(char *fileName, float **ffpHitScoreMatrix, int nl)
+{
+ int i, j;
+ FILE *fp;
+
+ fp=vfopen(fileName, "w");
+ for(i = 0; i < nl; i++)
+ {
+ for(j = 0; j < i; j++)
+ fprintf(fp, "%6.2f ", ffpHitScoreMatrix[j][i-j]);
+ for(j = i; j < nl; j++)
+ fprintf(fp, "%6.2f ", ffpHitScoreMatrix[i][j-i]);
+ fprintf(fp, "\n");
+ }
+ 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);
+ return 1;
+}
+
+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 a, b;
+ int max_name_len=15;
+ int max_len=0;
+
+ static char *buf;
+ static FILE_format *fps;
+ Color *ink;
+ Color *box_c;
+ Color *white;
+
+ box_c=(Color*)vcalloc ( 1, sizeof (Color));
+ get_rgb_values_format (DEFAULT_COLOR, (white=(Color*)vcalloc ( 1, sizeof (Color))));
+ get_rgb_values_format (INK_COLOR, (ink =(Color*)vcalloc ( 1, sizeof (Color))));
+
+ if ( max_len==0)
+ {
+ for ( a=0; a< B->nseq; a++)
+ {
+ if ( strlen (B->name[a])>max_len)
+ max_len= strlen ( (B->name[a]));
+ }
+ }
+ if ( max_len>max_name_len)max_len=max_name_len;
+
+ if ( buf==NULL)
+ buf=(char*)vcalloc (10000, sizeof (int));
+ int iEmptyChr = 32; //SPACE ASCIICODE
+ int iColorValue;
+ fps=vfopen_format(name);
+ for (a=0; a < nl; a++)
+ {
+ sprintf (buf,"%*d ", max_len+2, a);
+ fps=print_format_string ( buf,white, ink, fps);
+ for(b = 0; b < a; b++)
+ {
+ iColorValue = (int)((ffPScoreTable[b][a-b]*9)/100);
+ get_rgb_values_format (iColorValue, box_c);
+ fps=print_format_char (iEmptyChr,box_c, ink,fps);
+ }
+ for(b = a; b < nl; b++)
+ {
+ iColorValue = (int)((ffPScoreTable[a][b-a]*9)/100);
+ get_rgb_values_format (iColorValue, box_c);
+ fps=print_format_char (iEmptyChr,box_c, ink,fps);
+ }
+ fps=print_format_char ('\n', white, ink, fps);
+ }
+ vfclose_format(fps);
+ vfree(buf);
+ vfree(box_c);
+ return 1;
+}
+
+/*****************************************************************************/
+
+int output_color_html ( Alignment *B,Alignment *S, char *name)
+ {
+ output_color_format (B, S, name, vfopen_html,print_html_string,print_html_char,get_rgb_values_html, vfclose_html);
+ return 1;
+ }
+int output_reliability_html ( Alignment *B,Alignment *S, char *name)
+ {
+ output_reliability_format (B, S, name, vfopen_html,print_html_string,print_html_char,get_rgb_values_html, vfclose_html);
+ return 1;
+ }
+FILE_format *print_html_string( char *s, Color *box, Color *ink, FILE_format *fhtml)
+ {
+ int l;
+ int a;
+
+ l=strlen (s);
+
+ for ( a=0; a< l; a++)
+ {
+ fhtml=print_html_char (s[a], box, ink, fhtml);
+ }
+ fhtml=print_html_char (CLOSE_HTML_SPAN,NULL,NULL,fhtml);
+ return fhtml;
+ }
+
+
+FILE_format * print_html_char ( int c, Color *box, Color *ink, FILE_format *f)
+ {
+ char html_color[100];
+ int in_span, new_color;
+ char string[1000];
+
+
+ if (c==CLOSE_HTML_SPAN)
+ {
+ if (f->in_html_span)fprintf ( f->fp, "</span>");
+ f->in_html_span=0;
+ return f;
+ }
+
+
+ in_span=f->in_html_span;
+ new_color=1-(strm (box->html_color_class, f->previous_html_color));
+
+
+
+ sprintf (f->previous_html_color, "%s", box->html_color_class);
+ sprintf ( html_color, "class=%s", box->html_color_class);
+
+
+ if ( c!=' ')sprintf ( string, "%c", c);
+ else sprintf ( string, " ");
+
+ if ( !in_span && c!='\n' && c!=f->eop)
+ {
+ fprintf ( f->fp, "<span %s>%s",html_color,string );
+ f->in_html_span=1;
+ }
+ else if (in_span && !new_color && c!='\n' && c!=f->eop)
+ {
+
+ fprintf ( f->fp, "%s",string);
+ }
+ else if (in_span && new_color && c!='\n' && c!=f->eop)
+ {
+ fprintf ( f->fp, "</span><span %s>%s",html_color,string);
+ }
+ else if ( c=='\n')
+ {
+ if ( f->in_html_span)fprintf ( f->fp, "</span>");
+ fprintf ( f->fp, "<br>");
+ sprintf ( f->previous_html_color, "no_color_set");
+ f->in_html_span=0;
+ f->n_line++;
+ }
+
+
+
+
+
+ return f;
+ }
+
+void get_rgb_values_html ( int val, Color *C)
+ {
+ get_rgb_values ( val, C);
+ }
+
+FILE_format* vfopen_html ( char *name)
+ {
+ FILE_format*fhtml;
+ Color *color;
+ int a;
+
+ color=(Color*)vcalloc ( 1, sizeof (Color));
+
+ fhtml=(FILE_format*)vcalloc ( 1, sizeof ( FILE_format));
+ fhtml->font=11;
+ fhtml->max_line_ppage=100000;
+ fhtml->line=get_msa_line_length (0, 0);/*N char per line*/
+ fhtml->x0=15;
+ fhtml->y0=800;
+ fhtml->eop='^';
+ sprintf ( fhtml->previous_html_color, "no_value_set");
+ fhtml->fp=vfopen ( name, "w");
+
+ fprintf(fhtml->fp,"<html>\n<style>\n");
+
+ fprintf(fhtml->fp,"SPAN { font-family: courier new, courier-new, courier, monospace; font-weight: bold; font-size: %dpt;}\n", fhtml->font);
+ fprintf(fhtml->fp,"SPAN { line-height:100%%}\n");
+ fprintf(fhtml->fp,"SPAN { white-space: pre}\n");
+
+ for ( a=0; a< 10; a++)
+ {
+ get_rgb_values_html ( a, color);
+ if ( !strm (color->html_color, ""))fprintf (fhtml->fp, "SPAN.%s {background: %s}\n", color->html_color_class, color->html_color );
+ else fprintf (fhtml->fp, "SPAN.%s {}\n", color->html_color_class );
+ }
+ get_rgb_values_html (DEFAULT_COLOR, color);
+ if ( !strm (color->html_color, ""))fprintf (fhtml->fp, "SPAN.%s {background: %s}\n", color->html_color_class, color->html_color );
+ else fprintf (fhtml->fp, "SPAN.%s {}\n", color->html_color_class );
+
+ get_rgb_values_html (GAP_COLOR, color);
+ if ( !strm (color->html_color, ""))fprintf (fhtml->fp, "SPAN.%s {background: %s}\n", color->html_color_class, color->html_color );
+ else fprintf (fhtml->fp, "SPAN.%s {}\n", color->html_color_class );
+
+ get_rgb_values_html (INK_COLOR, color);
+ if ( !strm (color->html_color, ""))fprintf (fhtml->fp, "SPAN.%s {background: %s}\n", color->html_color_class, color->html_color );
+ else fprintf (fhtml->fp, "SPAN.%s {}\n", color->html_color_class );
+
+
+
+ fprintf(fhtml->fp,"</style>");
+ fprintf(fhtml->fp,"<body>");
+
+ return fhtml;
+ }
+FILE_format* vfclose_html ( FILE_format *fhtml)
+ {
+ if ( fhtml->in_html_span)fprintf(fhtml->fp,"</span>");
+ fprintf(fhtml->fp,"</body></html>\n");
+ vfclose ( fhtml->fp);
+ vfree (fhtml);
+ return NULL;
+ }
+/*****************************************************************************/
+/* ascii FUNCTIONS */
+/* */
+/*****************************************************************************/
+int output_color_ascii ( Alignment *B,Alignment *S, char *name)
+ {
+
+ output_color_format (B, S, name, vfopen_ascii,print_ascii_string,print_ascii_char,get_rgb_values_ascii, vfclose_ascii);
+ return 1;
+ }
+int output_reliability_ascii ( Alignment *B,Alignment *S, char *name)
+ {
+ output_reliability_format (B, S, name, vfopen_ascii,print_ascii_string,print_ascii_char,get_rgb_values_ascii, vfclose_ascii);
+ return 1;
+ }
+
+int output_reliability_fasta ( Alignment *B,Alignment *S, char *name)
+ {
+ output_reliability_format_fasta (B, S, name, vfopen_ascii,print_ascii_string,print_ascii_char,get_rgb_values_ascii, vfclose_ascii);
+ return 1;
+ }
+
+FILE_format *print_ascii_string( char *s, Color *box, Color *ink, FILE_format *fascii)
+ {
+ int l;
+ int a;
+
+ l=strlen (s);
+
+ for ( a=0; a< l; a++)
+ {
+ fascii=print_ascii_char (s[a], box, ink, fascii);
+ }
+ return fascii;
+ }
+
+
+FILE_format * print_ascii_char ( int c, Color *box, Color *ink, FILE_format *f)
+ {
+ if (box->ascii_value>=0 && f->in_seq)fprintf ( f->fp, "%c", box->ascii_value);
+ else fprintf ( f->fp, "%c",c);
+ return f;
+ }
+
+
+void get_rgb_values_ascii ( int val, Color *C)
+{
+
+
+ if ( val==NO_COLOR_RESIDUE)C->ascii_value='-';
+ else if ( val==NO_COLOR_GAP)C->ascii_value='*';
+ else if ( val>9){C->ascii_value='#'; }
+ else if ( val>=0 && val<=9) C->ascii_value=val+'0';
+ else C->ascii_value=val;
+ }
+
+FILE_format* vfopen_ascii ( char *name)
+ {
+ FILE_format*fascii;
+ fascii=(FILE_format*)vcalloc ( 1, sizeof ( FILE_format));
+ fascii->font=11;
+ fascii->max_line_ppage=100000;
+ fascii->line=get_msa_line_length (0,0);/*N char per line*/
+ fascii->x0=15;
+ fascii->y0=800;
+ fascii->eop='^';
+ fascii->fp=vfopen ( name, "w");
+
+
+ return fascii;
+ }
+FILE_format* vfclose_ascii ( FILE_format *fascii)
+ {
+ vfclose ( fascii->fp);
+ vfree (fascii);
+ return NULL;
+ }
+
+
+/*****************************************************************************/
+/* seq_score output */
+/* */
+/*****************************************************************************/
+
+int output_seq_reliability_ascii ( Alignment *B,Alignment *S, char *name)
+{
+ FILE *fp;
+ int a;
+ int max_len=0;
+ for ( a=0; a< B->nseq; a++)
+ {if ( strlen (B->name[a])>max_len)
+ max_len= strlen ( (B->name[a]));
+ }
+
+
+ fp=vfopen ( name, "w");
+ fprintf ( fp, "ALN_SCORE %d\n", S->score_aln);
+ for ( a=0; a< S->nseq; a++)fprintf (fp, "SEQ_SCORE %*.*s %3d\n", max_len+2,max_len,S->name[a],S->score_seq[a]);
+ vfclose (fp);
+
+ return 1;
+}
+
+int aln2compressed_ps (Alignment *A,char *file)
+{
+ FILE_format *fps;
+ int a, b, cs, cl, ns;
+
+ static Color *C=(Color*)vcalloc ( 1, sizeof (Color));
+ fps=vfopen_ps(file);
+ for (a=0; a<A->nseq; a++)
+ {
+ for (cs=-1,cl=0,b=0; b<A->len_aln; b++)
+ {
+ ns=A->seq_al[a][b]-'0';
+ if (cs==-1){cs=ns;cl=1;}
+ else if (ns==cs){cl++;}
+ else
+ {
+
+ get_rgb_values_ps(cs,C);
+ fps=print_ps_line (cl,C, fps);
+ cl=1;
+ cs=ns;
+ }
+ }
+ get_rgb_values_ps(cs,C);
+ fps=print_ps_line (cl, C, fps);
+ fps=print_ps_line (-1, NULL, fps);
+ }
+ vfclose_ps (fps);
+}
+int aln2compressed_pdf ( Alignment *A,char *name)
+ {
+ char *tmp_name;
+ char command[LONG_STRING];
+
+
+#ifndef PS2PDF
+ fprintf (stderr, "\nPDF FORMAT IS NOT SUPPORTED: INSTALL THE PROGRAM PS2PDF\n");
+ myexit (EXIT_FAILURE);
+#else
+ tmp_name=vtmpnam(NULL);
+
+ aln2compressed_ps (A, tmp_name);
+ sprintf ( command, "%s %s %s", PS2PDF, tmp_name, name);
+ my_system ( command);
+ vremove ( tmp_name);
+#endif
+
+
+ return 1;
+ }
git://source.jalview.org / jabaws.git / blobdiff