void MicrotubuleProcess::connectNwSw(unsigned int i)
{
unsigned int a(startCoord+i);
Voxel& aVoxel((*theLattice)[a]);
unsigned int b(startCoord+(Protofilaments-1)*theDimerSize+(i-1));
Voxel& adjoin((*theLattice)[b]);
aVoxel.adjoiningCoords[aVoxel.adjoiningSize++] = b;
adjoin.adjoiningCoords[adjoin.adjoiningSize++] = a;
}
void MicrotubuleProcess::connectEastWest(unsigned int i, unsigned int j)
{
unsigned int a(startCoord+j*theDimerSize+i);
Voxel& aVoxel((*theLattice)[a]);
unsigned int b(startCoord+(j-1)*theDimerSize+i);
Voxel& adjoin((*theLattice)[b]);
aVoxel.adjoiningCoords[aVoxel.adjoiningSize++] = b;
adjoin.adjoiningCoords[adjoin.adjoiningSize++] = a;
}
void MicrotubuleProcess::connectNorthSouth(unsigned int i, unsigned int j)
{
unsigned int a(startCoord+j*theDimerSize+(i-1));
Voxel& aVoxel((*theLattice)[a]);
unsigned int b(startCoord+j*theDimerSize+i);
Voxel& adjoin((*theLattice)[b]);
aVoxel.adjoiningCoords[NORTH] = b;
adjoin.adjoiningCoords[SOUTH] = a;
aVoxel.adjoiningSize = 2;
adjoin.adjoiningSize = 2;
}
void MicrotubuleProcess::connectPeriodic(unsigned int j)
{
unsigned int a(startCoord+j*theDimerSize+theDimerSize-1);
Voxel& aVoxel((*theLattice)[a]);
unsigned int b(startCoord+j*theDimerSize);
Voxel& adjoin((*theLattice)[b]);
aVoxel.adjoiningCoords[NORTH] = b;
adjoin.adjoiningCoords[SOUTH] = a;
aVoxel.adjoiningSize = 2;
adjoin.adjoiningSize = 2;
}
void MicrotubuleProcess::addIndirect(Voxel& offVoxel, unsigned a,
Voxel& latVoxel, unsigned b)
{
Point aPoint(*offVoxel.point);
for(unsigned int i(0); i != theAdjoiningCoordSize; ++i)
{
unsigned int aCoord(latVoxel.adjoiningCoords[i]);
Voxel& adjoin((*theLattice)[aCoord]);
if(adjoin.id == theComp->vacantSpecies->getID() || adjoin.id == tempID)
{
Point adPoint(theSpatiocyteStepper->coord2point(aCoord));
double dist(getDistance(&aPoint, &adPoint));
if(dist <= offLatticeRadius && inMTCylinder(adPoint))
{
offVoxel.adjoiningCoords[offVoxel.adjoiningSize++] = b;
initAdjoins(latVoxel);
updateAdjoinSize(latVoxel);
latVoxel.initAdjoins[latVoxel.adjoiningSize++] = a;
}
}
}
}
int dm_table_add_target(struct dm_table *t, const char *type,
sector_t start, sector_t len, char *params)
{
int r = -EINVAL, argc;
char **argv;
struct dm_target *tgt;
if ((r = check_space(t)))
return r;
tgt = t->targets + t->num_targets;
memset(tgt, 0, sizeof(*tgt));
if (!len) {
DMERR("%s: zero-length target", dm_device_name(t->md));
return -EINVAL;
}
tgt->type = dm_get_target_type(type);
if (!tgt->type) {
DMERR("%s: %s: unknown target type", dm_device_name(t->md),
type);
return -EINVAL;
}
tgt->table = t;
tgt->begin = start;
tgt->len = len;
tgt->error = "Unknown error";
/*
* Does this target adjoin the previous one ?
*/
if (!adjoin(t, tgt)) {
tgt->error = "Gap in table";
r = -EINVAL;
goto bad;
}
r = dm_split_args(&argc, &argv, params);
if (r) {
tgt->error = "couldn't split parameters (insufficient memory)";
goto bad;
}
r = tgt->type->ctr(tgt, argc, argv);
kfree(argv);
if (r)
goto bad;
t->highs[t->num_targets++] = tgt->begin + tgt->len - 1;
/* FIXME: the plan is to combine high here and then have
* the merge fn apply the target level restrictions. */
combine_restrictions_low(&t->limits, &tgt->limits);
return 0;
bad:
DMERR("%s: %s: %s", dm_device_name(t->md), type, tgt->error);
dm_put_target_type(tgt->type);
return r;
}
void MicrotubuleProcess::enlistLatticeVoxels()
{
for(unsigned int n(startCoord); n != endCoord; ++n)
{
Voxel& offVoxel((*theLattice)[n]);
offVoxel.diffuseSize = offVoxel.adjoiningSize;
double rA(theSpatiocyteStepper->getMinLatticeSpace());
if(rA < offLatticeRadius)
{
rA = offLatticeRadius;
}
Point center(*offVoxel.point);
unsigned int aCoord(theSpatiocyteStepper->point2coord(center));
Point cl(theSpatiocyteStepper->coord2point(aCoord));
//theSpecies[3]->addMolecule(aVoxel.coord);
Point bottomLeft(*offVoxel.point);
Point topRight(*offVoxel.point);
bottomLeft.x -= rA+center.x-cl.x+theSpatiocyteStepper->getColLength();
bottomLeft.y -= rA+center.y-cl.y+theSpatiocyteStepper->getLayerLength();
bottomLeft.z -= rA+center.z-cl.z+theSpatiocyteStepper->getRowLength();
topRight.x += rA+cl.x-center.x+theSpatiocyteStepper->getColLength()*1.5;
topRight.y += rA+cl.y-center.y+theSpatiocyteStepper->getLayerLength()*1.5;
topRight.z += rA+cl.z-center.z+theSpatiocyteStepper->getRowLength()*1.5;
unsigned int blRow(0);
unsigned int blLayer(0);
unsigned int blCol(0);
theSpatiocyteStepper->point2global(bottomLeft, blRow, blLayer, blCol);
unsigned int trRow(0);
unsigned int trLayer(0);
unsigned int trCol(0);
theSpatiocyteStepper->point2global(topRight, trRow, trLayer, trCol);
std::vector<unsigned int> checkedAdjoins;
for(unsigned int i(blRow); i < trRow; ++i)
{
for(unsigned int j(blLayer); j < trLayer; ++j)
{
for(unsigned int k(blCol); k < trCol; ++k)
{
unsigned int lat(theSpatiocyteStepper->global2coord(i, j, k));
Voxel& latVoxel((*theLattice)[lat]);
if(latVoxel.id != theSpatiocyteStepper->getNullID())
{
//theSpecies[3]->addMolecule(latVoxel);
Point aPoint(theSpatiocyteStepper->coord2point(lat));
if(inMTCylinder(aPoint))
{
for(unsigned int l(0); l != theAdjoiningCoordSize;
++l)
{
unsigned adj(latVoxel.adjoiningCoords[l]);
Voxel& adjoin((*theLattice)[adj]);
if(adjoin.id == theComp->vacantSpecies->getID())
{
checkedAdjoins.push_back(adj);
addDirect(offVoxel, n, adjoin, adj);
}
}
}
}
}
}
}
for(unsigned int i(0); i != checkedAdjoins.size(); ++i)
{
(*theLattice)[checkedAdjoins[i]].id = theComp->vacantSpecies->getID();
}
}
for(unsigned int i(0); i != occCoords.size(); ++i)
{
Voxel& aVoxel((*theLattice)[occCoords[i]]);
unsigned int* temp = aVoxel.initAdjoins;
aVoxel.initAdjoins = aVoxel.adjoiningCoords;
aVoxel.adjoiningCoords = temp;
aVoxel.diffuseSize = aVoxel.adjoiningSize;
}
for(unsigned int i(0); i != occCoords.size(); ++i)
{
Voxel& aVoxel((*theLattice)[occCoords[i]]);
for(unsigned int i(0); i != aVoxel.adjoiningSize; ++i)
{
unsigned int aCoord(aVoxel.adjoiningCoords[i]);
Voxel& adjoin((*theLattice)[aCoord]);
if(adjoin.id == theComp->vacantSpecies->getID())
{
Point adPoint(theSpatiocyteStepper->coord2point(aCoord));
if(inMTCylinder(adPoint))
{
std::cout << "error in MT Process" << std::endl;
}
}
else if(adjoin.id != theVacantSpecies->getID() &&
adjoin.id != theMinusSpecies->getID() &&
adjoin.id != thePlusSpecies->getID() &&
adjoin.id != theSpatiocyteStepper->getNullID())
{
std::cout << "species error in MT Process" << std::endl;
}
}
}
}
