void make_consensus_DnaHmmProb(DnaHmmProb * dhp)
{
int i;
int j;
double prob_max;
int base;
dhp->consensus = calloc(dhp->len+1,sizeof(char));
for(i=0;i<dhp->len;i++) {
prob_max = -1.0;
for(j=0;j<4;j++) {
if( dhp->unit[i]->match[j] > prob_max ) {
prob_max = dhp->unit[i]->match[j];
base = j;
}
}
if( prob_max > 0.5 ) {
dhp->consensus[i] = char_from_base(base);
} else if ( prob_max > 0.3 ) {
dhp->consensus[i] = tolower(char_from_base(base));
} else {
dhp->consensus[i] = '.';
}
}
dhp->consensus[i] = '\0';
}
void show_single_codon_emission(double no,int base4codon,FILE * ofp)
{
codon c;
base one;
base two;
base three;
c = codon_from_base4_codon(base4codon);
all_bases_from_codon(c,&one,&two,&three);
fprintf(ofp,"%c%c%c %.2f\n",char_from_base(one),char_from_base(two),char_from_base(three),no);
}
void show_RandomModelDNAScore(RandomModelDNAScore * rds,FILE * ofp)
{
register int i;
for(i=0;i<5;i++) {
fprintf(ofp,"Base %d[%c], Score %d [prob %.2f]\n",i,char_from_base(i),rds->base[i],Score2Probability(rds->base[i]));
}
}
char char_for_base(int base)
{
if( base < 5 ) {
return char_from_base(base);
}
if( base == BASE_GAP ) {
return '-';
} else {
return ' ';
}
}
void show_base_emission(double * base,FILE * ofp)
{
register int i;
fprintf(ofp,"begin consensus\n");
for(i=0;i<4;i++)
fprintf(ofp,"%c %.2f\n",char_from_base(i),base[i]);
fprintf(ofp,"end consensus\n");
}
char draw_random_base_RandomModelDNA(RandomModelDNA * rm)
{
double draw,tot;
int i;
draw = random_0_to_1();
for(tot=rm->base[0],i=0;draw > tot && i<4;tot += rm->base[++i])
;
if( i >= 26 ) {
warn("Weird - got a draw %f which outside of random model total %f\n",draw,tot);
return '?';
}
return char_from_base(i);
}
char first_char_from_dnanumber(int dnanumber,int nmer_size,int flipped)
{
int base = 1;
int basepair;
int power;
int i;
if( flipped == 1 ) {
/* first number is therefore lowest bit */
basepair = dnanumber % 4;
/* fprintf(stderr,"Going to use %d as number\n",basepair);*/
basepair = complement_base(basepair);
return char_from_base(basepair);
} else {
for(i=0;i<nmer_size-1;i++)
base *= 4;
basepair = (int) (dnanumber / base);
return char_from_base(basepair);
}
}
char char_complement_base(char c)
{
return char_from_base(complement_base(base_from_char(c)));
}
