bool
ChemistryMulti::check (const Scope& scope, const Geometry& geo,
const Soil& soil, const SoilWater& soil_water,
const SoilHeat& soil_heat, const Chemistry& chemistry,
Treelog& msg) const
{
bool ok = true;
for (size_t c = 0; c < combine.size (); c++)
{
Treelog::Open nest (msg, "Chemistry: '" + combine[c]->objid + "'");
if (!combine[c]->check (scope, geo, soil, soil_water, soil_heat,
chemistry, msg))
ok = false;
}
// Check for duplicate chemicals.
std::map<symbol, size_t> found;
for (size_t i = 0; i < chemicals.size (); i++)
{
const symbol type = chemicals[i]->objid;
std::map<symbol, size_t>::const_iterator f = found.find (type);
if (f != found.end ())
{
std::ostringstream tmp;
tmp << "Chemical '" << type << "' definded in multiple chemistries:";
for (size_t j = 0; j < combine.size (); j++)
if (combine[j]->know (type))
tmp << " '" << combine[j]->objid << "'";
msg.error (tmp.str ());
ok = false;
}
found[type] = i;
}
return ok;
}
bool has_attribute (const symbol name) const
{
bool missing = false;
for (size_t i = 0; i < layers.size (); i++)
if (!layers[i]->horizon->has_attribute (name))
missing = true;
for (size_t i = 0; i < zones.size (); i++)
if (!zones[i]->horizon->has_attribute (name))
missing = true;
return !missing;
}
void
ChemistryMulti::mass_balance (const Geometry& geo,
const SoilWater& soil_water) const
{
for (size_t c = 0; c < combine.size (); c++)
combine[c]->mass_balance (geo, soil_water);
}
void ErrorEstimatorImpl::output(std::ostream& os) const
{
os << "[ErrorEstimator] iterations:" << iterationCount_ <<
" error:" << error_ << endl;
for (int i=0; i<(int)massSpreads_.size(); i++)
os << " " << *massSpreads_[i] << endl;
}
const MassSpread* ErrorEstimatorImpl::massSpread(int index) const
{
if (index < 0 || index >= (int)massSpreads_.size())
throw out_of_range("[ErrorEstimatorImpl::massSpread] Index out of range.");
return massSpreads_[index];
}
void paintColumns()
{
for(size_t i=0;i< columns.size();++i)
{
}
}
void
ChemistryMulti::tick_top (const Units& units, const Geometry& geo,
const Soil& soil, const SoilWater& soil_water,
const SoilHeat& soil_heat,
const double tillage_age /* [d] */,
const Surface& surface,
const double snow_leak_rate, // [h^-1]
const double canopy_cover, // [],
const double canopy_leak_rate, // [h^-1]
const double litter_cover, // [],
const double litter_leak_rate, // [h^-1]
const double surface_runoff_rate /* [h^-1] */,
const double surface_water /* [mm] */,
const double total_rain /* [mm/h] */,
const double direct_rain, // [mm/h]
const double canopy_drip /* [mm/h] */,
const double h_veg /* [m] */,
Chemistry& chemistry,
const double dt, // [h]
Treelog& msg)
{
for (size_t c = 0; c < combine.size (); c++)
combine[c]->tick_top (units, geo, soil, soil_water, soil_heat,
tillage_age, surface,
snow_leak_rate, canopy_cover, canopy_leak_rate,
litter_cover, litter_leak_rate,
surface_runoff_rate, surface_water,
total_rain, direct_rain, canopy_drip, h_veg,
chemistry, dt, msg);
}
void
ChemistryMulti::mix (const Geometry& geo, const Soil& soil,
const SoilWater& soil_water,
const double from, const double to,
const double penetration)
{
for (size_t c = 0; c < combine.size (); c++)
combine[c]->mix (geo, soil, soil_water, from, to, penetration);
}
void
ChemistryMulti::swap (const Geometry& geo,
const Soil& soil, const SoilWater& soil_water,
const double from, const double middle,
const double to)
{
for (size_t c = 0; c < combine.size (); c++)
combine[c]->swap (geo, soil, soil_water, from, middle, to);
}
void
ChemistryMulti::sorption_table (const Soil& soil, const size_t cell,
const double Theta, const double start,
const double factor, const int intervals,
Treelog& msg) const
{
for (size_t c = 0; c < combine.size (); c++)
combine[c]->sorption_table (soil, cell, Theta, start, factor, intervals,
msg);
}
void
Movement1D::initialize_derived (const Soil& soil,
const Groundwater& groundwater,
bool has_macropores, Treelog& msg)
{
TREELOG_MODEL (msg);
for (size_t i = 0; i < matrix_water.size (); i++)
matrix_water[i]->has_macropores (has_macropores);
}
void
ChemistryMulti::tick_source (const Scope& scope, const Geometry& geo,
const Soil& soil, const SoilWater& soil_water,
const SoilHeat& soil_heat,
const OrganicMatter& organic,
const Chemistry& chemistry, Treelog& msg)
{
for (size_t c = 0; c < combine.size (); c++)
combine[c]->tick_source (scope, geo, soil, soil_water, soil_heat,
organic, chemistry, msg);
}
bool has_attribute (const symbol name, Treelog& msg) const
{
bool missing = false;
for (size_t i = 0; i < layers.size (); i++)
if (!layers[i]->horizon->has_attribute (name))
{
msg.error ("Required attribute '"
+ name + "' is missing from the soil horizon '"
+ layers[i]->horizon->objid + "'");
missing = true;
}
for (size_t i = 0; i < zones.size (); i++)
if (!zones[i]->horizon->has_attribute (name))
{
msg.error ("Required attribute '"
+ name + "' is missing from the soil zone '"
+ zones[i]->horizon->objid + "'");
missing = true;
}
return !missing;
}
void
ChemistryMulti::initialize (const Scope& scope,
const Geometry& geo,
const Soil& soil,
const SoilWater& soil_water,
const SoilHeat& soil_heat,
const Surface& surface, Treelog& msg)
{
for (size_t c = 0; c < combine.size (); c++)
combine[c]->initialize (scope, geo, soil, soil_water, soil_heat, surface,
msg);
}
double
ChemistryMulti::suggest_dt () const
{
double dt = 0.0;
for (size_t c = 0; c < combine.size (); c++)
{
const double chem_dt = combine[c]->suggest_dt ();
if (std::isnormal (chem_dt)
&& (!std::isnormal (dt) || chem_dt < dt))
dt = chem_dt;
}
return dt;
}
void
ChemistryMulti::tick_soil (const Scope& scope,
const Geometry& geo, const double ponding,
const double R_mixing,
const Soil& soil, const SoilWater& soil_water,
const SoilHeat& soil_heat, Movement& movement,
const OrganicMatter& organic_matter,
Chemistry& chemistry,
const double dt, Treelog& msg)
{
TREELOG_MODEL (msg);
for (size_t c = 0; c < combine.size (); c++)
combine[c]->tick_soil (scope, geo, ponding, R_mixing,
soil, soil_water, soil_heat, movement,
organic_matter, chemistry, dt, msg);
}
void loop()
{
rows.push_back(new Column);
rows.back()->label.assign("CHROM");
rows.push_back(new Column);
rows.back()->label.assign("POS");
rows.push_back(new Column);
rows.back()->label.assign("ID");
rows.push_back(new Column);
rows.back()->label.assign("REF");
rows.push_back(new Column);
rows.back()->label.assign("ALT");
for(int i=0;i< samples.size();++i)
{
Sample* sample=samples.at(i);
rows.push_back(new Column);
rows.back()->label.assign(sample->name).append(":QUAL");
rows.push_back(new Column);
rows.back()->label.assign(sample->name).append(":FILTER");
rows.push_back(new Column);
rows.back()->label.assign(sample->name).append(":INFO");
rows.push_back(new Column);
rows.back()->label.assign(sample->name).append(":FORMAT");
rows.push_back(new Column);
rows.back()->label.assign(sample->name).append(":CALL");
}
screen=Screen::startup();
screen->border();
screen->refresh();
for(;;)
{
int c=screen->getch();
switch(c)
{
case 'q':
{
break;
}
case
}
}
Screen::shutdown();
}
void
ChemistryMulti::deposit (const symbol chem, const double flux, Treelog& msg)
{
bool found = false;
for (size_t c = 0; c < combine.size (); c++)
if (combine[c]->know (chem))
{
if (found)
msg.error ("Duplicate chemical '" + chem + "' detected");
Chemical& chemical = combine[c]->find (chem);
chemical.deposit (flux);
found = true;
}
if (found)
return;
check_ignore (chem, msg);
}
void
ChemistryMulti::incorporate (const Geometry& geo,
const symbol chem, const double amount,
const Volume& volume,
Treelog& msg)
{
bool found = false;
for (size_t c = 0; c < combine.size (); c++)
if (combine[c]->know (chem))
{
if (found)
msg.error ("Duplicate chemical '" + chem + "' detected");
Chemical& chemical = combine[c]->find (chem);
chemical.incorporate (geo, amount, volume);
found = true;
}
if (found)
return;
check_ignore (chem, msg);
}
void
ChemistryMulti::clear ()
{
for (size_t c = 0; c < combine.size (); c++)
combine[c]->clear ();
}
void
Movement1D::tick_water (const Geometry1D& geo,
const Soil& soil, const SoilHeat& soil_heat,
Surface& surface, Groundwater& groundwater,
const std::vector<double>& S,
std::vector<double>& h_old,
const std::vector<double>& Theta_old,
const std::vector<double>& h_ice,
std::vector<double>& h,
std::vector<double>& Theta,
std::vector<double>& q,
std::vector<double>& q_p,
const double dt,
Treelog& msg)
{
const size_t top_edge = 0U;
const size_t bottom_edge = geo.edge_size () - 1U;
// Limit for groundwater table.
size_t last = soil.size () - 1;
// Limit for ridging.
const size_t first = (surface.top_type (geo, 0U) == Surface::soil)
? surface.last_cell (geo, 0U)
: 0U;
// Calculate matrix flow next.
for (size_t m = 0; m < matrix_water.size (); m++)
{
water_attempt (m);
Treelog::Open nest (msg, matrix_water[m]->name);
try
{
matrix_water[m]->tick (msg, geo, soil, soil_heat,
first, surface, top_edge,
last, groundwater, bottom_edge,
S, h_old, Theta_old, h_ice, h, Theta, 0U, q,
dt);
for (size_t i = last + 2; i <= soil.size (); i++)
{
q[i] = q[i-1];
q_p[i] = q_p[i-1];
}
// Update surface and groundwater reservoirs.
surface.accept_top (q[0] * dt, geo, 0U, dt, msg);
surface.update_pond_average (geo);
const double q_down = q[soil.size ()] + q_p[soil.size ()];
groundwater.accept_bottom (q_down * dt, geo, soil.size ());
if (m > 0)
msg.debug ("Reserve model succeeded");
return;
}
catch (const char* error)
{
msg.debug (std::string ("UZ problem: ") + error);
}
catch (const std::string& error)
{
msg.debug (std::string ("UZ trouble: ") + error);
}
water_failure (m);
}
throw "Water matrix transport failed";
}
int main(int argc,char** argv)
{
const char* exonFile=0;
int optind=1;
char* faidxfile=NULL;
while(optind < argc)
{
if(strcmp(argv[optind],"-h")==0)
{
this->usage(cerr,argc,argv);
return(EXIT_FAILURE);
}
else if(strcmp(argv[optind],"-f")==0 && optind+1< argc)
{
faidxfile = argv[++optind];
}
else if(strcmp(argv[optind],"-g")==0 && optind+1< argc)
{
exonFile=argv[++optind];
}
else if(strcmp(argv[optind],"--")==0)
{
++optind;
break;
}
else if(argv[optind][0]=='-')
{
cerr << "unknown option '" << argv[optind]<< "'" << endl;
this->usage(cerr,argc,argv);
return EXIT_FAILURE;
}
else
{
break;
}
++optind;
}
if(faidxfile==0)
{
cerr << "no fasta genome defined." << endl;
this->usage(cerr,argc,argv);
return EXIT_FAILURE;
}
this->faidx.reset(new IndexedFasta(faidxfile));
if(exonFile==0)
{
cerr << "no bed for exons defined." << endl;
this->usage(cerr,argc,argv);
return EXIT_FAILURE;
}
if(optind==argc)
{
cerr << "BAM files missing"<< endl;
return EXIT_FAILURE;
}
else
{
while(optind< argc)
{
char* bamfile=argv[optind++];
WHERE("Open "<< bamfile);
BamFile2* bam=new BamFile2(bamfile);
this->bamFiles.push_back(bam);
bam->open(true);
}
}
//open exon file
igzstreambuf buf(exonFile);
istream in(&buf);
this->readExons(in);
buf.close();
if(exons.empty())
{
cerr << "No exon.\n";
return EXIT_FAILURE;
}
run();
for(size_t i=0;i< bamFiles.size();++i)
{
bamFiles[i]->close();
}
return EXIT_SUCCESS;
}
void
ChemistryMulti::update_C (const Soil& soil, const SoilWater& soil_water)
{
for (size_t c = 0; c < combine.size (); c++)
combine[c]->update_C (soil, soil_water);
}
void
ChemistryMulti::harvest (const double removed, const double surface)
{
for (size_t c = 0; c < combine.size (); c++)
combine[c]->harvest (removed, surface);
}
