/* RECONSTRUCT GENOME OF AN ISOLATE */
struct pathogen * reconstruct_genome(struct pathogen *in){
int i;
struct lineage *line = get_lineage(in);
struct vec_int ** listSnpVec, *temp, *genome;
struct pathogen *out = (struct pathogen *) malloc(sizeof(struct pathogen));
if(out == NULL){
fprintf(stderr, "\n[in: pathogen.c->reconstruct_genome]\nNo memory left to reconstruct pathogen genome. Exiting.\n");
exit(1);
}
/* get all snps in the lineage */
listSnpVec = (struct vec_int **) malloc(line->n * sizeof(struct vec_int *));
for(i=0;i<line->n;i++){
listSnpVec[i] = get_snps_vec(line->pathogens[i]);
}
/* merge snps */
temp = merge_vec_int(listSnpVec, line->n);
/* remove reverse mutations */
genome = keep_odd_int(temp);
/* create output and fill it in */
out->age = in->age;
out->ances = in->ances;
out->snps = genome;
/* free temporary allocation & return */
free_lineage(line);
free(listSnpVec);
free_vec_int(temp);
return out;
}
static Boolean WhatOrg (Int4 taxid, CharPtr taxon)
{
OrgRefPtr orp;
CharPtr lineage;
CharPtr nodes[] = {"Archaea", "Viruses", "Eukaryotae", "Eubacteria"};
Int4 i;
Boolean flagTaxHit;
/*
orp pointers only; mem doesn't have to be free'd
*/
if ((orp = tax1_getOrgRef (taxid, NULL, NULL, NULL)) != NULL)
{
if (orp->taxname != NULL)
{
flagTaxHit = FALSE;
if ((lineage = get_lineage (orp->taxname)) != NULL)
{
for (i = 0; i < 4; i++)
{
if (StrStr (lineage, nodes[i]))
{
switch (i)
{
case 0:
taxon[0] = 'A';
flagTaxHit = TRUE;
break;
case 1:
taxon[1] = 'B';
taxon[4] = 'V';
flagTaxHit = TRUE;
break;
case 2:
taxon[2] = 'E';
flagTaxHit = TRUE;
break;
case 3:
taxon[3] = 'P';
flagTaxHit = TRUE;
break;
}
}
}
MemFree (lineage);
return flagTaxHit;
}
}
}
return FALSE;
}
