void print_hsp(gpointer key,gpointer value,gpointer user_data)
{
Sequence * query;
HSPset * set;
btCanvas * btc;
btPasteArea * btp;
int i,j;
char q,t;
query = (Sequence *)user_data;
set = (HSPset *) value;
btc = new_Ascii_btCanvas(stdout,12,50,5,3);
for(i=0;i<set->len;i++) {
for(j=0;j<set->hsp[i]->length;) {
btp = get_reserved_left_btCanvas(btc);
paste_string_btPasteArea(btp,0,0,query->name,BC_RIGHT,0);
paste_string_btPasteArea(btp,0,2,set->hsp[i]->target->name,BC_RIGHT,0);
free_btPasteArea(btp);
for(;j<set->hsp[i]->length && can_get_paste_area_btCanvas(btc,1) == TRUE;j++) {
btp = get_paste_area_btCanvas(btc,1);
q = query->seq[set->hsp[i]->query_start+j];
t = set->hsp[i]->target->seq[set->hsp[i]->target_start+j];
paste_char_btPasteArea(btp,0,0,q,0);
paste_char_btPasteArea(btp,0,2,t,0);
if( q == t ) {
paste_char_btPasteArea(btp,0,1,t,0);
}
free_btPasteArea(btp);
}
advance_line_btCanvas(btc);
}
advance_line_btCanvas(btc);
}
free_btCanvas(btc);
}
boolean write_alignment_separator(btCanvas * btc,int aln,int score)
{
char buffer[64];
btPasteArea * btp;
sprintf(buffer,"Alignment %d Score %4.2f (Bits)",aln,Score2Bits(score));
btp = get_paste_area_btCanvas(btc,strlen(buffer));
paste_string_btPasteArea(btp,0,5,buffer,BC_RIGHT,0);
free_btPasteArea(btp);
advance_line_btCanvas(btc);
return TRUE;
}
boolean write_name_start_stuff(btCanvas * btc,char * protname,int protoff,char * dnaname,Sequence * dna,int name_len,AlnColumn * alc)
{
char buffer[64];
btPasteArea * btp;
btp = get_reserved_left_btCanvas(btc);
paste_string_btPasteArea(btp,0,0,protname,BC_RIGHT,0);
paste_string_btPasteArea(btp,0,3,dnaname,BC_RIGHT,0);
sprintf(buffer,"%d",alc->alu[0]->start+1+protoff);
paste_string_btPasteArea(btp,name_len+5-strlen(buffer),0,buffer,BC_RIGHT,0);
if( dna->offset < dna->end )
sprintf(buffer,"%d",alc->alu[1]->start+1+dna->offset);
else
sprintf(buffer,"-%d",dna->offset - (alc->alu[1]->start+1));
paste_string_btPasteArea(btp,name_len+5-strlen(buffer),3,buffer,BC_RIGHT,0);
free_btPasteArea(btp);
return TRUE;
}
boolean protdna_btc_display(AlnBlock * alb,char * protsequence,char * protname_in,int protoff,Sequence * dna,CodonTable * ct,int name,int main,btCanvas * btc,char (*match_central_line)(char,int,char),boolean multalign)
{
AlnColumn * alc;
AlnColumn * alc_temp,*alc_endscore;
int a_phase, d_phase;
int intron_number = 1;
int aln_score;
int aln_num = 1;
btPasteArea * btp;
char tempbuf[2];
char protname[60];
char dnaname[60];
char dnatemp[4];
char protc;
char transc;
boolean is_reversed = FALSE;
boolean issplit;
if( strlen(protname_in) > name ) {
info("Name %s is longer than allowed name block (%d). Truncating\n",protname_in,name);
strncpy(protname,protname_in,name);
protname[name] = '\0';
} else {
strcpy(protname,protname_in);
}
if( strlen(dna->name) > name ) {
info("Name %s is longer than allowed name block (%d). Truncating\n",dna->name,name);
strncpy(dnaname,dna->name,name);
dnaname[name] = '\0';
} else {
strcpy(dnaname,dna->name);
}
if( dna->offset > dna->end ) {
is_reversed = TRUE;
}
for(alc=alb->start;alc != NULL;) {
if ( strcmp(alc->alu[1]->text_label,"END") == 0 )
break; /* end of alignment */
for(;alc != NULL && is_random_AlnColumn_genewise(alc) == TRUE;alc = alc->next)
;
if( alc == NULL)
break; /* end of alignment */
if( multalign == TRUE ) {
/* get the end score */
for(aln_score = 0,alc_endscore=alc;alc_endscore->next != NULL;alc_endscore = alc_endscore->next) {
if( is_random_AlnColumn_genewise(alc_endscore) == TRUE)
break;
aln_score += alc_endscore->alu[0]->score[0];
}
/*aln_score += alc_endscore->alu[0]->score[0];*/
write_alignment_separator(btc,aln_num++,aln_score);
}
while( alc != NULL ) {
write_name_start_stuff(btc,protname,protoff,dnaname,dna,name,alc);
for(; alc != NULL;alc=alc->next ) {
if( is_random_AlnColumn_genewise(alc) == TRUE )
break;
if( strcmp(alc->alu[1]->text_label,"INSERT") == 0 ) {
if( can_get_paste_area_btCanvas(btc,1) == FALSE)
break; /* back to upper for, to place names and starts */
btp = get_paste_area_btCanvas(btc,1);
paste_char_btPasteArea(btp,0,0,protsequence[alc->alu[0]->start+1],0);
paste_char_btPasteArea(btp,0,2,'-',0);
free_btPasteArea(btp);
} else if ( strcmp(alc->alu[1]->text_label,"SEQUENCE_INSERTION") == 0 ||
strcmp(alc->alu[1]->text_label,"SEQUENCE_DELETION") == 0 ) {
if( can_get_paste_area_btCanvas(btc,1) == FALSE)
break; /* back to upper for, to place names and starts */
btp = get_paste_area_btCanvas(btc,1);
if( strcmp(alc->alu[0]->text_label,"INSERT_STATE")== 0 ) {
paste_char_btPasteArea(btp,0,0,'-',0);
}
else {
paste_char_btPasteArea(btp,0,0,protsequence[alc->alu[0]->end],0);
}
sprintf(tempbuf,"%d",alc->alu[1]->end - alc->alu[1]->start);
paste_char_btPasteArea(btp,0,3,tempbuf[0],0);
paste_char_btPasteArea(btp,0,2,'!',0);
free_btPasteArea(btp);
} else if (strcmp(alc->alu[1]->text_label,"END") == 0 && strcmp(alc->alu[0]->text_label,"END") == 0) {
break; /* end of alignment */
} else if ( strcmp(alc->alu[1]->text_label,"RANDOM_SEQUENCE") == 0 ) {
break;
} else if( strcmp(alc->alu[1]->text_label,"CODON") == 0 ) {
if( can_get_paste_area_btCanvas(btc,1) == FALSE)
break; /* back to upper for, to place names and starts */
btp = get_paste_area_btCanvas(btc,1);
if( strcmp(alc->alu[0]->text_label,"INSERT_STATE")== 0 ) {
write_codon_match(btp,'-',' ',alc->alu[1]->start+1,aminoacid_from_seq(ct,dna->seq+alc->alu[1]->start+1),dna->seq+alc->alu[1]->start+1);
}
else {
write_codon_match(btp,protsequence[alc->alu[0]->end],(*match_central_line)(protsequence[alc->alu[0]->end],alc->alu[0]->score[0],aminoacid_from_seq(ct,dna->seq+alc->alu[1]->start+1)),alc->alu[1]->start+1,aminoacid_from_seq(ct,dna->seq+alc->alu[1]->start+1),dna->seq+alc->alu[1]->start+1);
}
free_btPasteArea(btp);
continue;
} else if ( strstartcmp(alc->alu[1]->text_label,"5SS") == 0 ) {
/*
* intron stuff. Figure out the start and end,
* then place the 5'SS Central and End.
*
* If we can't fit in the intron, loop over
* in this region before returning to higher loop.
*
*/
if( strcmp(alc->alu[1]->text_label,"5SS_PHASE_0") == 0 ) {
d_phase = 0;
} else if ( strcmp(alc->alu[1]->text_label,"5SS_PHASE_1") == 0 ) {
d_phase = 1;
} else if ( strcmp(alc->alu[1]->text_label,"5SS_PHASE_2") == 0 ) {
d_phase = 2;
} else {
warn("No no no. You have a non 0,1,2 phase intron (god knows how!). Not displaying it %s",alc->alu[1]->text_label);
advance_line_btCanvas(btc);
return FALSE;
}
alc_temp = alc->next;
if( strcmp(alc_temp->alu[1]->text_label,"CENTRAL_INTRON") != 0 ) {
warn("Bad news. I have found a 5SS in your alignment, but it is not followed by a central intron node. Don't like it!");
advance_line_btCanvas(btc);
return FALSE;
}
for(alc_temp = alc_temp->next ;alc_temp != NULL && strstartcmp(alc_temp->alu[1]->text_label,"3SS") != 0;alc_temp = alc_temp->next)
;
if( alc_temp == NULL ) {
warn("Got to the end of the alignment in the middle of an intron from %s. Weird!",alc->alu[1]->text_label);
advance_line_btCanvas(btc);
return FALSE;
}
if( strcmp(alc_temp->alu[1]->text_label,"3SS_PHASE_0") == 0 ) {
a_phase = 0;
} else if ( strcmp(alc_temp->alu[1]->text_label,"3SS_PHASE_1") == 0 ) {
a_phase = 1;
} else if ( strcmp(alc_temp->alu[1]->text_label,"3SS_PHASE_2") == 0 ) {
a_phase = 2;
} else {
warn("No no no. You have a non 0,1,2 phase intron (god knows how!). Not displaying it %s",alc_temp->alu[1]->text_label);
advance_line_btCanvas(btc);
return FALSE;
}
/*
* At this point we have alc on 5SS alc_temp on 3SS.
*
* Check to see if we can place 5SS and Central intron piece
* on the line, if not advance.
*
*/
if( can_get_paste_area_btCanvas(btc,d_phase+7+13) == FALSE) {
advance_line_btCanvas(btc);
write_name_start_stuff(btc,protname,protoff,dnaname,dna,name,alc);
}
/*** ok, if we can't get it now then we are f****d ***/
if( can_get_paste_area_btCanvas(btc,d_phase+7+13) == FALSE) {
warn("You have specified a length of your main canvas too small. I need at least 23 characters long.");
advance_line_btCanvas(btc);
return FALSE;
}
btp = get_paste_area_btCanvas(btc,d_phase+7);
/* ? split phase */
if( a_phase == 0 || (a_phase != d_phase ) ) {
protc = ' ';
transc = ' ';
dnatemp[0]= '\0';
issplit = FALSE;
} else {
if( strcmp(alc_temp->alu[0]->text_label,"INSERT_STATE")== 0 ) {
protc = '-';
} else {
protc = protsequence[alc->alu[0]->start+1];
}
dnatemp[0] = tolower((int)dna->seq[alc->alu[1]->start+1]);
if( d_phase == 2) {
dnatemp[1] = tolower((int)dna->seq[alc->alu[1]->start+2]);
} else {
dnatemp[1] = tolower((int)dna->seq[alc_temp->alu[1]->end-1]);
}
dnatemp[2] = tolower((int)dna->seq[alc_temp->alu[1]->end]);
dnatemp[3] = '\0';
transc = aminoacid_from_seq(ct,dnatemp);
issplit = TRUE;
}
write_5intron_match(btp,d_phase,7,dna->seq+alc->alu[1]->start+1);
free_btPasteArea(btp);
btp = get_paste_area_btCanvas(btc,13);
if( is_reversed == FALSE )
write_intron_desc(btp,alc->alu[1]->start+1+d_phase+dna->offset,alc_temp->alu[1]->start+3+dna->offset,intron_number++,issplit,protc,transc,dnatemp);
else
write_intron_desc(btp,dna->offset - (alc->alu[1]->start+d_phase+1),dna->offset - (alc_temp->alu[1]->start+3),intron_number++,issplit,protc,transc,dnatemp);
free_btPasteArea(btp);
/*
* written the start of the intron, now to deal with the
* acceptor. We need to loop here, because we might go over the
* line length.
*/
alc = alc->next->next; /*** move alc forward two columns ***/
while( alc != alc_temp ) {
for(; alc != alc_temp;alc = alc->next) { /** alc_temp is 3SS **/
if( strcmp(alc->alu[1]->text_label,"PYRIMIDINE_TRACT") == 0 ) {
if( can_get_paste_area_btCanvas(btc,1) == FALSE )
break;
btp = get_paste_area_btCanvas(btc,1);
paste_char_btPasteArea(btp,0,3,dna->seq[alc->alu[1]->start+1],0);
paste_char_btPasteArea(btp,0,4,'+',0);
free_btPasteArea(btp);
} else if( strcmp(alc->alu[1]->text_label,"SPACER") == 0 ) {
if( can_get_paste_area_btCanvas(btc,1) == FALSE )
break;
btp = get_paste_area_btCanvas(btc,1);
paste_char_btPasteArea(btp,0,3,dna->seq[alc->alu[1]->start+1],0);
free_btPasteArea(btp);
} else {
warn("Sorry, don't know how to print %s. Skipping...",alc->alu[1]->text_label);
}
}
/** end for for loop **/
if ( alc == alc_temp ) {
break;
}
/*** run out of space ***/
advance_line_btCanvas(btc);
write_name_start_stuff(btc,protname,protoff,dnaname,dna,name,alc);
} /** end of while still in central->3SS **/
/*
* Now do 3SS
*
*/
if( can_get_paste_area_btCanvas(btc,a_phase == 0 ? 3 : 3- a_phase + 3) == FALSE ) {
advance_line_btCanvas(btc);
write_name_start_stuff(btc,protname,protoff,dnaname,dna,name,alc);
}
if( a_phase != 0 ) {
btp = get_paste_area_btCanvas(btc,3 - a_phase + 3);
write_3intron_match(btp,a_phase,3,dna->seq + alc->alu[1]->start+1);
free_btPasteArea(btp);
} else {
btp = get_paste_area_btCanvas(btc,3);
write_3intron_match(btp,a_phase,3,dna->seq + alc->alu[1]->start+1);
free_btPasteArea(btp);
}
/*
* Finished with intron !!!
*/
} else {
warn("Sorry, could not print the alignment %s:%s column",alc->alu[0]->text_label,alc->alu[1]->text_label);
}
} /*** in this loop ***/
advance_line_btCanvas(btc);
if( alc == NULL)
break;
if ( is_random_AlnColumn_genewise(alc) == TRUE)
break;
} /* end of while over alignments */
} /* end of foreach alignment */
/*** end of print ! **/
return TRUE;
}
boolean write_pretty_str_align_btc(AlnBlock * alb,char * qname,char * query,char * tname,char * target,btCanvas * btc)
{
AlnColumn * alc;
AlnUnit * q;
AlnUnit * t;
char buffer[14];
int number_position;
btPasteArea * btp;
number_position = strlen(qname);
if( strlen(tname) > number_position ) {
number_position = strlen(tname);
}
for(alc=alb->start;alc != NULL;) {
/** put names in **/
btp = get_reserved_left_btCanvas(btc);
paste_string_btPasteArea(btp,0,0,qname,BC_RIGHT,0);
paste_string_btPasteArea(btp,0,2,tname,BC_RIGHT,0);
sprintf(buffer,"%d",alc->alu[0]->start+1+1);
paste_string_btPasteArea(btp,number_position+2,0,buffer,BC_RIGHT,0);
sprintf(buffer,"%d",alc->alu[1]->start+1+1);
paste_string_btPasteArea(btp,number_position+2,2,buffer,BC_RIGHT,0);
free_btPasteArea(btp);
/** now loop over this block **/
for(;alc != NULL && can_get_paste_area_btCanvas(btc,1) == TRUE;alc=alc->next) {
q = alc->alu[0];
t = alc->alu[1];
/*
* at the end, break
*/
if( strcmp(q->text_label,"END") == 0 ) {
alc = NULL;
break;
}
if( strcmp(t->text_label,"LOOP") == 0 ) {
btp = get_paste_area_btCanvas(btc,1);
paste_char_btPasteArea(btp,0,0,'L',0);
paste_char_btPasteArea(btp,0,1,'$',0);
paste_char_btPasteArea(btp,0,2,'L',0);
free_btPasteArea(btp);
advance_line_btCanvas(btc);
for(;alc != NULL && strcmp(alc->alu[1]->text_label,"LOOP") == 0;alc = alc->next) {
;
}
break;
}
/*
* Get the paste area, length 1, depth will be 3
*/
btp = get_paste_area_btCanvas(btc,1);
/*
* Write in the query sequence
*
*/
if( strcmp(q->text_label,"SEQUENCE") == 0 || strstr(q->text_label,"BOUND") != NULL ) {
paste_char_btPasteArea(btp,0,0,((int)query[q->start+1]),0);
} else if( strcmp(q->text_label,"UNMATCHED_SEQUENCE") == 0 ) {
paste_char_btPasteArea(btp,0,0,tolower((int)query[q->start+1]),0);
} else {
/** is insert- we could check **/
if( strcmp(q->text_label,"INSERT") != 0 ) {
warn("Got an uninterpretable label, %s",q->text_label);
paste_char_btPasteArea(btp,0,0,'?',0);
} else {
paste_char_btPasteArea(btp,0,0,'-',0);
}
}
/*
* Write in the target sequence
*
*/
if( strcmp(t->text_label,"SEQUENCE") == 0 ) {
paste_char_btPasteArea(btp,0,2,toupper((int)target[t->start+1]),0);
} else if( strcmp(t->text_label,"UNMATCHED_SEQUENCE") == 0 ) {
paste_char_btPasteArea(btp,0,2,tolower((int)target[t->start+1]),0);
} else {
/** is insert- we could check **/
if( strcmp(t->text_label,"INSERT") != 0 ) {
warn("Got an uninterpretable label, %s",t->text_label);
paste_char_btPasteArea(btp,0,2,'?',0);
} else {
paste_char_btPasteArea(btp,0,2,'-',0);
}
}
/*
* Match line
*/
if( strcmp(q->text_label,"SEQUENCE") == 0 && strcmp(t->text_label,"SEQUENCE") == 0 ) {
if( q->score[0] > 0 ) {
if( query[q->start+1] == target[t->start+1] ) {
paste_char_btPasteArea(btp,0,1,target[t->start+1],0);
} else {
paste_char_btPasteArea(btp,0,1,'+',0);
}
}
} else
paste_char_btPasteArea(btp,0,1,' ',0);
free_btPasteArea(btp);
} /* end of for this block */
advance_line_btCanvas(btc);
} /* end of for the alignment */
return TRUE; /* we never returned false. Ooops! */
}
