species create_new_herb_species(ptrdiff_t seed) {
species result = create_herb_species();
herb_species* hsp = get_herb_species(result);
determine_new_plant_materials(&(hsp->materials), seed);
seed = prng(seed);
determine_new_herb_appearance(&(hsp->appearance), seed);
seed = prng(seed);
hsp->growth.seed_growth.grammar = BIO_CG_SPROUT_IN_SOIL;
hsp->growth.seed_growth.sprout_time = (
posmod(prng(seed + 1771), 5)
+ posmod(prng(seed + 311), 8)
);
seed = prng(seed);
// TODO: Real values here...
hsp->growth.seed_growth_resist = 5;
hsp->growth.growth_resist = 10;
hsp->growth.growth_strength = 8;
determine_new_herb_core_growth(&(hsp->growth.core_growth), seed);
return result;
}
cg_expansion* pick_expansion(
cell_grammar *cg,
chunk_neighborhood* nbh,
block_index base,
ptrdiff_t seed
) {
size_t i;
int success;
cg_expansion *exp;
list *options = create_list();
block root_block = *nb_block(nbh, base);
for (i = 0; i < l_get_length(cg->expansions); ++i) {
exp = (cg_expansion*) l_get_item(cg->expansions, i);
success = check_expansion(exp, nbh, base, root_block);
if (success) {
l_append_element(options, (void*) exp);
}
}
if (l_is_empty(options)) {
cleanup_list(options);
return NULL;
}
// Choose an option based on our seed:
i = posmod(prng(seed + 819991), l_get_length(options));
exp = (cg_expansion*) l_get_item(options, i);
cleanup_list(options);
return exp;
}
double ThreePeriodicMarkovChain::scoreSubsequence(const Sequence &seq,
const BOOM::String &str,
int begin,int length,
int seqPhase)
{
// ### This is quick and dirty -- will be optimizing this class next week
// to use a suffix-tree-like data structure so that each base is
// read only once
double score=0;
int end=begin+length;
switch(getStrand())
{
case FORWARD_STRAND:
for(int pos=begin ; pos<end ; ++pos)
score+=chains[(seqPhase+pos-begin)%3]->
scoreSingleBase(seq,str,pos,seq[pos],str[pos]);
break;
case REVERSE_STRAND:
for(int pos=begin ; pos<end ; ++pos)
score+=chains[posmod(seqPhase-(pos-begin))]->
scoreSingleBase(seq,str,pos,seq[pos],str[pos]);
break;
}
return score;
}
int Edge::propagateBackward(int phase)
{
if(isIntergenic()) return (left->getStrand()==FORWARD_STRAND ? 0 : 2);
if(!isCoding()) return phase;
int length=getFeatureEnd()-getFeatureBegin();
switch(getStrand())
{
case FORWARD_STRAND:
return posmod(phase-length);
case REVERSE_STRAND:
return (phase+length)%3;
}
}
/* Ensure that the contributing source sample is
* within bounds. If not, reflect, clamp, or wrap.
*/
int Resampler::reflect(const int j, const int src_x, const Boundary_Op boundary_op)
{
int n;
if (j < 0)
{
if (boundary_op == BOUNDARY_REFLECT)
{
n = -j;
if (n >= src_x)
n = src_x - 1;
}
else if (boundary_op == BOUNDARY_WRAP)
n = posmod(j, src_x);
else
n = 0;
}
else if (j >= src_x)
{
if (boundary_op == BOUNDARY_REFLECT)
{
n = (src_x - j) + (src_x - 1);
if (n < 0)
n = 0;
}
else if (boundary_op == BOUNDARY_WRAP)
n = posmod(j, src_x);
else
n = src_x - 1;
}
else
n = j;
return n;
}
void grow_block(chunk_neighborhood *nbh, block_index idx, ptrdiff_t t) {
global_pos cell_position;
chunk *c = nbh->members[NBH_CENTER];
block *b = c_block(c, idx);
cidx__glpos(c, &idx, &cell_position);
ptrdiff_t growth_rate = get_growth_rate(*b);
ptrdiff_t growth_offset = posmod(cell_hash(&cell_position), growth_rate);
if (
(gri_vitality(*b) != GR_VITALITY_DEAD)
&& ((t - growth_offset) % growth_rate == 0)
) {
if (bi_gcore(*b)) {
grow_from_core(nbh, idx);
} else if (bi_gsite(*b)) {
grow_at_site(nbh, idx);
}
}
}
