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#include "seaview.h"
#include <ctype.h>
#include <FL/Fl_Multiline_Input.H>
#define ISSEQCHAR(c) (isalpha(c) || c=='-' || c=='*' )
typedef struct {
SEA_VIEW *view;
Fl_Input *seq_name_field;
Fl_Input *seq_field;
} view_name_struct;
/* included prototypes */
void clear_callback(Fl_Widget *ob, void *data);
void refresh_callback(Fl_Widget *ob, void *data);
void remove_gaps_callback(Fl_Widget *ob, void *data);
void remove_numbers_callback(Fl_Widget *ob, void *data);
void to_upcase_callback(Fl_Widget *ob, void *data);
void load_seq_callback(void *data);
void load_seq_dialog(SEA_VIEW *view);
char complement_base(char old);
void edit_comments_dialog(SEA_VIEW *view);
void edit_sequence_dialog(SEA_VIEW *view);
int load_sequence_for_edit(struct editseq *editdata);
char *renumber_seq(char *seq);
void renumber_callback(Fl_Widget *ob, void *data);
void edit_sequence_callback(struct editseq *editdata);
void update_comments_callback(void *data);
int load_comments(SEA_VIEW *view, Fl_Input *input, Fl_Widget *name);
char *cre_consensus(SEA_VIEW *view, char *newname);
Fl_Widget *cre_adjusted_button(int x, int y, int *w, int h,
const char *label);
/* external prototypes */
extern void hide_window_callback(Fl_Widget *ob, void *data);
extern void allonge_seqs(char **seq, int totseqs, int maxlen, int *eachlength,
int tot_comment_lines, char **comment_line, char **pregion_line);
extern int compute_wid_names(SEA_VIEW *view, int totseqs);
extern int compute_size_params(SEA_VIEW *view, int force_recompute);
extern int calc_max_seq_length(int seq_length, int tot_seqs);
void clear_callback(Fl_Widget *ob, void *data)
{
Fl_Input *seq_input, *seq_name_input;
seq_name_input = ((view_name_struct *)data)->seq_name_field;
seq_input = ((view_name_struct *)data)->seq_field;
seq_input->value("");
if(seq_name_input != NULL) seq_name_input->value("");
}
void refresh_callback(Fl_Widget *ob, void *data)
{
Fl_Input *seq_input;
seq_input = ((view_name_struct *)data)->seq_field;
seq_input->redraw();
}
void remove_gaps_callback(Fl_Widget *ob, void *data)
{
Fl_Input *seq_input;
char *old_seq, *new_seq, *p, *q;
size_t lseq;
seq_input = (Fl_Input *)data;
old_seq = (char *)seq_input->value();
lseq = strlen(old_seq);
new_seq = (char *)malloc(lseq+1);
if(new_seq == NULL) return;
p = old_seq; q = new_seq;
while(*p != 0) {
if(*p != '-' ) *(q++) = *p;
p++;
}
*q = 0;
seq_input->value(new_seq);
}
void remove_numbers_callback(Fl_Widget *ob, void *data)
{
Fl_Input *seq_input;
char *old_seq, *new_seq, *p, *q;
size_t lseq;
seq_input = (Fl_Input *)data;
old_seq = (char *)seq_input->value();
lseq = strlen(old_seq);
new_seq = (char *)malloc(lseq+1);
if(new_seq == NULL) return;
p = old_seq; q = new_seq;
while(*p != 0) {
if( ! isdigit(*p) ) *(q++) = *p;
p++;
}
*q = 0;
seq_input->value(new_seq);
}
void to_upcase_callback(Fl_Widget *ob, void *data)
{
Fl_Input *seq_input = (Fl_Input *)data;
char *old_seq = (char *)seq_input->value();
int lseq = strlen(old_seq);
char *new_seq = (char *)malloc(lseq+1);
if(new_seq == NULL) return;
char *p = old_seq;
char *q = new_seq - 1;
do *(++q) = toupper(*(p++)); while(*q != 0);
seq_input->value(new_seq);
}
void load_seq_callback(void *data)
{
Fl_Input *seq_name_input, *seq_input;
SEA_VIEW *view;
char *name, *newseq, *tmp, *p, *q;
int lenseq;
seq_name_input = ((view_name_struct *)data)->seq_name_field;
view = ((view_name_struct *)data)->view;
seq_input = ((view_name_struct *)data)->seq_field;
name = (char *)seq_name_input->value();
if(strlen(name) == 0) {
fl_alert(
"`Seq. name' field is empty\nPlease enter a sequence name");
return;
}
tmp = (char *)seq_input->value();
lenseq = (int)strlen(tmp);
newseq = (char *)malloc(lenseq+1);
if(newseq == NULL) {
fl_alert("Not enough memory");
return;
}
p = tmp; q = newseq; lenseq = 0;
while(*p != 0) {
if(*p != ' ' && *p != '\n' && *p != '\t') {
if(view->allow_lower) *(q++) = (*p);
else *(q++) = toupper(*p);
lenseq++;
}
p++;
}
*q = 0;
add_seq_to_align(view, name, newseq, lenseq);
free(newseq);
}
Fl_Widget *cre_adjusted_button(int x, int y, int *w, int h,
const char *label)
{
Fl_Button *obj;
const int lsize = FL_NORMAL_SIZE;
fl_font(FL_HELVETICA, lsize);
// *w = (int) ( fl_width(label) + 2 * fl_width("R") + 0.5 );
*w = (int) ( fl_width(label) + 10 + 0.5 );
obj = new Fl_Button(x, y, *w, h, label);
obj->labelsize(lsize);
obj->labelfont(FL_HELVETICA);
return (Fl_Widget *)obj;
}
void load_seq_dialog(SEA_VIEW *view)
{
Fl_Window *load_form;
Fl_Input *seq_input, *seq_name_input;
view_name_struct view_name;
Fl_Widget *cancel, *add, *obj;
int fin, width;
load_form = new Fl_Window(490,530);
load_form->box(FL_FLAT_BOX);
load_form->label("Sequence Loading");
int curr_y = 5;
fin = 5;
Fl_Group *top = new Fl_Group(fin,curr_y,load_form->w() - 2 * fin, 25);
static char label[] = "Seq. name:";
fl_font(FL_HELVETICA, FL_NORMAL_SIZE);
width = (int)fl_width(label) + 4 * 2;
Fl_Box *name_box = new Fl_Box(FL_UP_BOX,
fin, top->y(), width, top->h(), label);
name_box->labelsize(FL_NORMAL_SIZE);
name_box->box(FL_NO_BOX);
fin += width + 5;
seq_name_input = new Fl_Input(fin,top->y(),100,top->h(),"");
seq_name_input->type(FL_NORMAL_INPUT);
fin += seq_name_input->w() + 5;
add = cre_adjusted_button(fin,top->y(),&width,top->h(),
"Add to alignment");
fin += width + 5;
cancel = cre_adjusted_button(fin,top->y(),&width,top->h(),
"Cancel");
((Fl_Button *)cancel)->shortcut(FL_COMMAND | 'w');
fin += width;
top->resizable(NULL);
top->size(fin - top->x(), top->h());
top->end();
curr_y += top->h() + 15;
seq_input = new Fl_Input(top->x(), curr_y, load_form->w() - 2 * top->x(), 450,
#if defined(__APPLE__)
""
#elif defined(WIN32)
"Type sequence or paste it with CRTL-V in panel below"
#else
"Type or paste sequence with middle mouse button in panel below"
#endif
);
seq_input->type(FL_MULTILINE_INPUT);
seq_input->align(FL_ALIGN_TOP);
seq_input->textfont(FL_COURIER);
seq_input->textsize(12);
fin = top->x();
curr_y += seq_input->h() + 5;
Fl_Group *bottom = new Fl_Group(fin, curr_y, top->w(), top->h() );
obj = cre_adjusted_button(fin, curr_y, &width, bottom->h(), "Refresh");
obj->callback(refresh_callback, &view_name);
fin += width + 5;
obj = cre_adjusted_button(fin, curr_y, &width, bottom->h(), "Clear");
obj->callback(clear_callback, &view_name);
fin += width + 5;
obj = cre_adjusted_button(fin, curr_y, &width, bottom->h(),
"Remove gaps");
obj->callback(remove_gaps_callback, seq_input);
fin += width + 5;
obj = cre_adjusted_button(fin,curr_y,&width,bottom->h(),
"Remove numbers");
obj->callback(remove_numbers_callback, seq_input);
fin += width + 5;
obj = cre_adjusted_button(fin, curr_y, &width, bottom->h(),
"to UPPER");
obj->callback(to_upcase_callback, seq_input);
fin += width;
bottom->resizable(NULL);
bottom->size(fin - bottom->x(), bottom->h());
bottom->end();
load_form->resizable(seq_input);
view_name.seq_name_field = seq_name_input;
view_name.seq_field = seq_input;
load_form->end();
load_form->position((Fl::w() - load_form->w())/2, (Fl::h() - load_form->h())/2);
seq_name_input->value("");
seq_input->value("");
view_name.view = view;
#if defined(__APPLE__)
seq_input->value("\n\n\n\n\n\nType sequence or paste it with cmd-V\n\n\n");
seq_input->position(seq_input->size(), 0);
#endif
seq_input->take_focus();
load_form->show();
#ifndef MICRO
load_form->hotspot(load_form);
#endif
while (TRUE) {
obj = Fl::readqueue();
if (!obj) Fl::wait();
else if(obj == add || obj == cancel || obj == load_form) {
if (obj == add) {
load_seq_callback(&view_name);
}
delete load_form;
break;
}
}
}
int add_seq_to_align(SEA_VIEW *view, char *newname, char *newseq, int lenseq, bool no_gui)
/* returns 0 if failed or the rank of newly added sequence
*/
{
int num, *newsel, numset;
char **newcol;
static char defname[]="newfile";
char **new_s, **new_n, **new_c;
if(view->tot_seqs == 0) {
view->max_seq_length = lenseq;//the true value is set later in init_dna_scroller
}
num = view->tot_seqs + 1;
if(view->sequence != NULL) new_s = (char **)realloc(view->sequence, num * sizeof(char *));
else new_s = (char **)malloc(num * sizeof(char *));
if(new_s != NULL) view->sequence = new_s;
if(view->comments != NULL) {
new_c = (char **)realloc(view->comments, num * sizeof(char *));
if(new_c != NULL) view->comments = new_c;
else goto nomem;
}
else view->comments = (char **)calloc(num, sizeof(char *));
if(view->seqname != NULL) new_n = (char **)realloc(view->seqname, num * sizeof(char *));
else new_n = (char **)malloc(num * sizeof(char *));
if(new_n != NULL) view->seqname = new_n;
if(new_s == NULL || new_n == NULL) goto nomem;
if(lenseq > view->max_seq_length) {
view->max_seq_length = calc_max_seq_length(lenseq, view->tot_seqs);
allonge_seqs(view->sequence, view->tot_seqs, view->max_seq_length, view->each_length,
view->tot_comment_lines, view->comment_line, &view->region_line);
if (!no_gui) {
for (int i = 0; i < view->tot_seqs; i++) free(view->col_rank[i]);
free(view->col_rank);
view->col_rank = prepcolranks(view->sequence, view->tot_seqs, view->max_seq_length, view->each_length,
( view->protein ? get_color_for_aa : get_color_for_base ),
view->numb_gc, view->allow_lower);
}
}
if( (view->seqname[num-1] = (char *)malloc(strlen(newname)+1)) == NULL)
goto nomem;
strcpy(view->seqname[num-1], newname);
if(view->comments != NULL) {
view->comments[num-1] = NULL;
}
if( (view->sequence[num-1] = (char *)malloc(view->max_seq_length + 1)) == NULL)
goto nomem;
memcpy(view->sequence[num-1], newseq, lenseq+1);
if(view->masename == NULL && !no_gui) {
newname = (char *) fl_input("Name of the new alignment?", "");
if(newname == NULL) newname = defname;
}
else newname = view->masename;
if (view->tot_seqs == 0 && !no_gui) {
init_dna_scroller(view, 1, newname, is_a_protein_seq(newseq), NULL);
set_seaview_modified(view, TRUE);
view->DNA_obj->redraw();
((Fl_Menu_Item*)view->menu_file + SAVE_AS)->activate();
return 1;
}
if( (newsel = (int *)malloc(num*sizeof(int))) == NULL) goto nomem;
memcpy(newsel, view->each_length, (num-1)*sizeof(int) );
free(view->each_length);
view->each_length = newsel;
view->each_length[num-1] = lenseq;
if (lenseq > view->seq_length && !no_gui) {
double x; int l;
view->seq_length = lenseq;
x = ( (double) view->tot_sites ) / ( view->seq_length + 3 );
if(x>1) x=1;
((Fl_Slider*)view->horsli)->slider_size(x);
l = view->seq_length - view->tot_sites+3;
if(l<1) l=1;
((Fl_Slider*)view->horsli)->bounds(1,l);
}
if(view->numb_dnacolors > 1 && !no_gui) {
if( (newcol = (char **)malloc(num*sizeof(char *))) == NULL)
goto nomem;
memcpy(newcol, view->col_rank, (num-1)*sizeof(char *) );
char **tmpcol = prepcolranks(view->sequence+num-1, 1,
view->max_seq_length,
view->each_length+num-1,
( view->protein ? get_color_for_aa : get_color_for_base ),
view->numb_gc, view->allow_lower);
if(tmpcol == NULL) out_of_memory();
newcol[num-1] = tmpcol[0];
free(tmpcol);
free(view->col_rank);
view->col_rank = newcol;
}
if( (newsel = (int *)malloc(num*sizeof(int))) == NULL) goto nomem;
if (!no_gui) {
memcpy(newsel, view->sel_seqs, (num-1)*sizeof(int) );
free(view->sel_seqs);
view->sel_seqs = newsel;
view->sel_seqs[num-1] = FALSE;
}
for(numset = 0; numset < view->numb_species_sets; numset++) {
if( (newsel = (int *)malloc(num*sizeof(int))) == NULL) goto nomem;
memcpy(newsel, view->list_species_sets[numset], (num-1)*sizeof(int) );
free(view->list_species_sets[numset]);
view->list_species_sets[numset] = newsel;
view->list_species_sets[numset][num-1] = FALSE;
}
view->tot_seqs = num;
view->cursor_seq = num;
view->cursor_site = 1;
view->first_site = 1;
if (no_gui) return num;
if(strlen(view->seqname[num - 1]) > (unsigned)view->wid_names) {
view->wid_names = compute_wid_names(view, num);
compute_size_params(view, TRUE);
}
set_seaview_modified(view, TRUE);
((Fl_Slider*)view->horsli)->value(1);
set_tot_lines(view, view->tot_lines);
view->first_seq = FL_max(num - view->tot_lines + 1, 1);
((Fl_Slider*)view->vertsli)->value(view->first_seq);
view->DNA_obj->redraw();
view->vertsli->redraw();
view->horsli->redraw();
return num;
nomem:
void (*alert)(const char *,...) = no_gui ? Fl::fatal : fl_alert;
alert("Not enough memory\nto create the new sequence %s", newname);
return 0;
}
char complement_base(char old)
{
static char bases[] = "ACGTURYMWSKVHDBacgturymwskvhdb";
static char complement[] = "TGCAAYRKWSMBDHVtgcaayrkwsmbdhv";
char *p;
if( (p = strchr(bases, old)) != NULL )
return complement[ p - bases ];
else
return old;
}
void edit_comments_dialog(SEA_VIEW *view)
{
Fl_Window *comments_form;
Fl_Input *comments_input;
Fl_Widget *comments_name;
view_name_struct comments_data;
Fl_Widget *o, *cancel, *apply;
Fl_Widget *obj;
int fin, width;
comments_form = new Fl_Window(490,530);
comments_form->label("Comments Editing");
comments_form->box(FL_FLAT_BOX);
Fl_Group *top_group = new Fl_Group(5,5,comments_form->w() - 10, 25);
fin = 5;
apply = cre_adjusted_button(fin,5,&width,25, "Apply");
fin += width + 5;
cancel = cre_adjusted_button(fin,5,&width,25,"Cancel");
((Fl_Button *)cancel)->shortcut(FL_COMMAND | 'w');
fin += width + 5;
obj = cre_adjusted_button(fin,5,&width,25,"Refresh");
obj->callback(refresh_callback, &comments_data);
fin += width + 5;
comments_name = new Fl_Box(FL_DOWN_BOX, fin, 5,
top_group->x() +top_group->w() - fin, 25, "");
comments_name->align(FL_ALIGN_LEFT | FL_ALIGN_CLIP | FL_ALIGN_INSIDE);
comments_name->labelfont(FL_COURIER);
comments_name->labelsize(FL_NORMAL_SIZE);
top_group->resizable(comments_name);
top_group->end();
comments_input = new Fl_Input(5,35,top_group->w(),
comments_form->h() - 5 - 35, "");
comments_input->type(FL_MULTILINE_INPUT);
comments_input->textfont(FL_COURIER);
comments_input->textsize(12);
comments_data.seq_field = comments_input;
comments_form->resizable(comments_input);
comments_form->end();
comments_form->position( (Fl::w() - comments_form->w())/2,
(Fl::h() - comments_form->h())/2 );
comments_data.view = view;
if(load_comments(view, comments_input, comments_name)) {
delete comments_form;
fl_alert("Not enough memory");
return;
}
comments_input->take_focus();
comments_form->show();
#ifndef MICRO
comments_form->hotspot(comments_form);
#endif
while (TRUE) {
o = Fl::readqueue();
if (!o) Fl::wait();
else if (o == apply || o == cancel || o == comments_form) {
if (o == apply) {
update_comments_callback(&comments_data);
}
delete comments_form;
break;
}
}
}
struct editseq {
Fl_Multiline_Input *input;
Fl_Widget *name;
SEA_VIEW *view;
int seqnum;
};
void edit_sequence_dialog(SEA_VIEW *view)
{
struct editseq *editdata;
int fin, width, num;
Fl_Window *form;
Fl_Widget *obj, *apply, *cancel;
for(num = 0; num <view->tot_seqs; num++) { if(view->sel_seqs[num]) break; }
if(num >= view->tot_seqs) return;
editdata = (struct editseq *)malloc(sizeof(struct editseq));
if(editdata == NULL) return;
editdata->seqnum = num;
editdata->view = view;
form = new Fl_Window(770,530);
form->label("Sequence Editing");
form->box(FL_FLAT_BOX);
form->user_data(editdata);
Fl_Group *top_group = new Fl_Group(5,5,form->w() - 10, 25);
fin = 5;
apply = cre_adjusted_button(fin,5,&width,25, "Apply");
fin += width + 5;
obj = cre_adjusted_button(fin,5,&width,25,"Renumber");
obj->callback(renumber_callback, 0);
fin += width + 5;
cancel = cre_adjusted_button(fin,5,&width,25,"Cancel");
((Fl_Button *)cancel)->shortcut(FL_COMMAND | 'w');
fin += width + 5;
editdata->name = new Fl_Box(FL_DOWN_BOX, fin, 5,
top_group->x() +top_group->w() - fin, 25, "");
editdata->name->align(FL_ALIGN_LEFT | FL_ALIGN_CLIP | FL_ALIGN_INSIDE);
editdata->name->labelfont(FL_COURIER);
editdata->name->labelsize(FL_NORMAL_SIZE);
top_group->resizable(editdata->name);
top_group->end();
editdata->input = new Fl_Multiline_Input(5,35,top_group->w(),
form->h() - 5 - 35, "");
editdata->input->type(FL_MULTILINE_INPUT);
editdata->input->textfont(FL_COURIER);
editdata->input->textsize(12);
form->resizable(editdata->input);
form->end();
form->position( (Fl::w() - form->w())/2,
(Fl::h() - form->h())/2 );
if(load_sequence_for_edit(editdata)) {
free(editdata);
delete form;
fl_alert("Not enough memory");
return;
}
form->show();
#ifndef MICRO
form->hotspot(form);
#endif
editdata->input->take_focus();
while (TRUE) {
obj = Fl::readqueue();
if (!obj) Fl::wait();
else if(obj == apply || obj == cancel || obj == form) {
if (obj == apply) {
edit_sequence_callback(editdata);
}
free(editdata);
delete form;
break;
}
}
}
int load_sequence_for_edit(struct editseq *editdata)
{
char *temp;
editdata->name->label(editdata->view->seqname[editdata->seqnum]);
editdata->name->redraw();
temp = renumber_seq(editdata->view->sequence[editdata->seqnum]);
if(temp == NULL) return TRUE;
editdata->input->value(temp);
free(temp);
editdata->input->position(0);
return FALSE;
}
char *renumber_seq(char *seq)
{
int l, nl, pos;
char *p, *q, *temp;
const int w = 100;
p = seq - 1;
l = 0;
while(*(++p) != 0) {
if(ISSEQCHAR(*p)) l++;
}
nl = l / w + 2;
temp = (char *)malloc(l + 7 * nl + 100);
if(temp == NULL) return NULL;
p = seq - 1;
q = temp;
pos = 0;
while(*(++p) != 0) {
if( ! ISSEQCHAR(*p)) continue;
*q++ = *p; pos++;
if(pos % w == 0) {
sprintf(q, "%6d\n", pos);
q += strlen(q);
}
}
strcpy(q, "\n");
return temp;
}
void renumber_callback(Fl_Widget *ob, void *data)
{
char *temp;
struct editseq *editdata = (struct editseq *)ob->window()->user_data();
temp = renumber_seq((char *)editdata->input->value());
if(temp == NULL) return;
editdata->input->value(temp);
free(temp);
}
void edit_sequence_callback(struct editseq *editdata)
{
char *p, *newseq, *q, **newcolseq;
SEA_VIEW *view;
int num, l;
view = editdata->view;
num = editdata->seqnum;
l = strlen( editdata->input->value() );
newseq = (char *)malloc(l + 1);
if(newseq == NULL) return;
q = newseq;
p = (char *)editdata->input->value() - 1;
while(*(++p) != 0) {
if( ! ISSEQCHAR(*p) ) continue;
*(q++) = *p;
}
*q = 0;
l = strlen(newseq);
if (l > view->max_seq_length) {
view->max_seq_length = calc_max_seq_length(l, view->tot_seqs);
allonge_seqs(view->sequence, view->tot_seqs, view->max_seq_length, view->each_length,
view->tot_comment_lines, view->comment_line, &view->region_line);
for (int i = 0; i < view->tot_seqs; i++) free(view->col_rank[i]);
free(view->col_rank);
view->col_rank = prepcolranks(view->sequence, view->tot_seqs, view->max_seq_length, view->each_length,
( view->protein ? get_color_for_aa : get_color_for_base ),
view->numb_gc, view->allow_lower);
}
if(view->numb_gc > 1) {
newcolseq = prepcolranks(&newseq, 1,
view->max_seq_length, &l,
( view->protein ? get_color_for_aa : get_color_for_base ),
view->numb_gc, view->allow_lower);
if(newcolseq == NULL) return;
free(view->col_rank[num]);
view->col_rank[num] = newcolseq[0];
free(newcolseq);
}
strcpy(view->sequence[num], newseq); free(newseq);
view->each_length[num] = l;
set_seaview_modified(view, TRUE);
if(l > view->seq_length) {
double x;
view->seq_length = l;
x = ( (double) view->tot_sites ) / ( view->seq_length + 3 );
if(x>1) x=1;
((Fl_Slider*)view->horsli)->slider_size(x);
l = view->seq_length - view->tot_sites+3;
if(l<1) l=1;
((Fl_Slider*)view->horsli)->bounds(1,l);
}
else view->mod_seq = num;
view->DNA_obj->redraw();
}
void update_comments_callback(void *data)
{
Fl_Input *comments_input;
SEA_VIEW *view;
int num, l, num_l;
char *temp, *p, *q, *r;
view = ((view_name_struct *)data)->view;
if(view->comments == NULL) {
view->comments = (char **)calloc(view->tot_seqs , sizeof(char *));
if(view->comments == NULL) return;
}
comments_input = ((view_name_struct *)data)->seq_field;
num = comments_input->argument();
num_l = 0;
p = (char *)comments_input->value(); l =strlen(p);
q = p;
while( (q = strchr(q, '\n')) != NULL) {
q++; num_l++;
}
if(p[l - 1] != '\n') num_l++;
temp = (char *)malloc(l + num_l + 1);
if(temp == NULL) {
fl_alert("Not enough memory");
return;
}
r = temp;
do {
q = strchr(p, '\n'); if(q == NULL) q = strchr(p, 0) - 1;
*(r++) = ';';
memcpy(r, p, q - p + 1); r += q - p + 1;
p = q + 1;
}
while( *p != 0);
if( *(r - 1) != '\n') *(r++) = '\n';
*r = 0;
if(view->comments[num] != NULL) free(view->comments[num]);
view->comments[num] = temp;
set_seaview_modified(view, TRUE);
}
int load_comments(SEA_VIEW *view, Fl_Input *input, Fl_Widget *name)
{
int num;
char *temp, *p, *q, *r;
for(num = 0; num <view->tot_seqs; num++)
if(view->sel_seqs[num]) break;
input->argument( num);
name->label(view->seqname[num]);
name->redraw();
if( view->comments == NULL || view->comments[num] == NULL) {
input->value("");
return FALSE;
}
temp = (char *)malloc(strlen(view->comments[num]) + 1);
if( temp == NULL) return TRUE;
r = temp; p = view->comments[num];
do {
q = strchr(p, '\n');
memcpy(r, p + 1, q - p); r += q - p;
p = q + 1;
}
while( *p != 0);
*r = 0;
input->value(temp);
free(temp);
input->position(0);
return FALSE;
}
static int *sort_f_transmit;
static int sort_f(const void *v1, const void *v2) {
int i1 = *(int*)v1;
int i2 = *(int*)v2;
return sort_f_transmit[i2] - sort_f_transmit[i1];
}
char calc_iupac_consensus(int *freqs, float minval) {
// order for freqs[1-16]: ACGTUMRWSYKVHDBN
// code for nucleotide sets: 4 bits representing A,C,G,T=U
// then coded_set[i-1] is the integer value of the set of count freq[i]
static int coded_set[16] = {1,2,4,8,8,3,5,9,6,10,12,7,11,13,14,15};
static char set_to_iupac[18] = {".ACMGRSVTWYHKDBN"};
int sorted_freqs[16];
freqs[16] += freqs[0]; // add count of non-IUPAC characters to count of N
for (int i = 0; i < 16; i++) sorted_freqs[i] = i+1;
sort_f_transmit = freqs;
// sort residue counts in decreasing order
qsort(sorted_freqs, 16, sizeof(int), sort_f);
int cumul = 0;
int set = 0;
// walk through residue counts in decreasing order until cumulated counts exceeds minval
for (int rank = 0; rank < 16; rank++) {
int residue = sorted_freqs[rank]; // the next most frequent residue
cumul += freqs[residue]; // summed frequencies till here
set |= coded_set[residue - 1]; // the set of all counted residues till here
// residues of equal frequencies are pooled together
if (rank < 15 && freqs[residue] == freqs[sorted_freqs[rank+1]]) continue;
if (cumul >= minval ) break;
}
if (set == 8 && sorted_freqs[0] == 5) return 'U';
return set_to_iupac[set];
}
char calc_site_consensus(int *freqs, int dernier, int threshold, char *residues, char unknown, int total,
int protein, int allowgaps, int iupac)
{
char retval;
int maxi = 0, num, kind, last;
maxi = freqs[1];
kind = 1;
if(protein) last = dernier;
else last = 5;
for(num = 2; num < last; num++) {
if(freqs[num] > maxi) {
maxi = freqs[num];
kind = num;
}
}
if (!protein && !iupac) {
total -= freqs[16];//DNA: don't count uninformative N's for frequency calculation
if(total == 0) return 'N';
}
float minval = total * (threshold / 100.);
if (allowgaps) {
num = dernier - 1; // check if '-' has the highest freq
if (freqs[num] > maxi) {
return freqs[num] > minval ? '-' : unknown;
}
}
if (iupac && !protein ) { // for DNA/RNA with IUPAC codes
retval = calc_iupac_consensus(freqs, minval);
}
else {
if( maxi >= minval )
retval = residues[kind - 1];
else
retval = unknown;
}
return retval;
}
char *cre_consensus(SEA_VIEW *view, char *newname)
{
char *newseq, *p, *residues, unknown;
int pos, num, total, kind, dernier, vu;
static char dna_residues[]="ACGTUMRWSYKVHDBN-";
static const char prot_residues[] = "EDQNHRKILMVAPSGTFYWC-";
static int freqs[30];
newseq = (char *)malloc(view->seq_length + 1);
if(newseq == NULL) return NULL;
if(view->protein) {
residues = (char *)prot_residues;
unknown = 'X';
}
else {
residues = (char *)dna_residues;
unknown = 'N';
}
dernier = strlen(residues) + 1;
for (pos = 0; pos < view->seq_length; pos++) {
vu = total = 0; memset(freqs, 0, dernier * sizeof(int));
for(num = 0; num < view->tot_seqs; num++) {
if( !view->sel_seqs[num] ) continue;
if(pos >= view->each_length[num]) continue;
vu++;
if(view->sequence[num][pos] == '-' && ! view->consensus_allowgaps) continue;
total++;
p = strchr(residues, toupper(view->sequence[num][pos]));
if(p == NULL) kind = 0;
else kind = p - residues + 1;
++(freqs[kind]);
}
if(vu == 0) break;
if(total == 0)
newseq[pos] = '-';
else {
newseq[pos] = calc_site_consensus(freqs, dernier, view->consensus_threshold, residues, unknown,
total, view->protein, view->consensus_allowgaps, view->consensus_allowiupac);
}
newseq[pos + 1] = 0;
}
sprintf(newname, "Consensus%d", view->consensus_threshold);
return newseq;
}
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