#include "stock.h"
#include "keeper.h"
#include "areatime.h"
#include "naturalm.h"
#include "grower.h"
#include "stockprey.h"
#include "stockpredator.h"
#include "initialcond.h"
#include "migration.h"
#include "readfunc.h"
#include "errorhandler.h"
#include "maturity.h"
#include "renewal.h"
#include "transition.h"
#include "spawner.h"
#include "stray.h"
#include "readword.h"
#include "readaggregation.h"
#include "gadget.h"
#include "global.h"
Stock::Stock(CommentStream& infile, const char* givenname,
const AreaClass* const Area, const TimeClass* const TimeInfo, Keeper* const keeper)
: BaseClass(givenname), stray(0), spawner(0), renewal(0), maturity(0), transition(0),
migration(0), prey(0), predator(0), initial(0), LgrpDiv(0), grower(0), naturalm(0) {
doesgrow = doeseat = iseaten = doesmigrate = istagged = 0;
doesmove = doesrenew = doesmature = doesspawn = doesstray = 0;
int i, tmpint = 0;
char c;
char text[MaxStrLength];
strncpy(text, "", MaxStrLength);
char filename[MaxStrLength];
strncpy(filename, "", MaxStrLength);
IntVector tmpareas;
ifstream datafile;
CommentStream subdata(datafile);
keeper->setString(this->getName());
//read the area data
infile >> text >> ws;
if (strcasecmp(text, "livesonareas") != 0)
handle.logFileUnexpected(LOGFAIL, "livesonareas", text);
c = infile.peek();
while (isdigit(c) && !infile.eof()) {
infile >> tmpint >> ws;
tmpareas.resize(1, Area->getInnerArea(tmpint));
c = infile.peek();
}
this->storeAreas(tmpareas);
//read the stock age and length data
int minage, maxage, numage;
double minlength, maxlength, dl;
readWordAndVariable(infile, "minage", minage);
readWordAndVariable(infile, "maxage", maxage);
numage = maxage - minage + 1;
if (minage < 0)
handle.logMessage(LOGFAIL, "Error in stock - stock age must be positive");
if (numage < 1)
handle.logMessage(LOGFAIL, "Error in stock - failed to create age groups");
readWordAndVariable(infile, "minlength", minlength);
readWordAndVariable(infile, "maxlength", maxlength);
readWordAndVariable(infile, "dl", dl);
if (minlength < 0.0)
handle.logMessage(LOGFAIL, "Error in stock - stock length must be positive");
LgrpDiv = new LengthGroupDivision(minlength, maxlength, dl);
if (LgrpDiv->Error() || isZero(dl))
handle.logMessage(LOGFAIL, "Error in stock - failed to create length group");
//JMB need to read the location of the reference weights file
char refweight[MaxStrLength];
strncpy(refweight, "", MaxStrLength);
readWordAndValue(infile, "refweightfile", refweight);
//JMB need to set the lowerlgrp and size vectors to a default
//value to allow the whole range of lengths to be calculated
IntVector lower(numage, 0);
IntVector agesize(numage, LgrpDiv->numLengthGroups());
Alkeys.resize(areas.Size(), minage, lower, agesize);
for (i = 0; i < Alkeys.Size(); i++)
Alkeys[i].setToZero();
//read the growth length group data
DoubleVector grlengths;
CharPtrVector grlenindex;
readWordAndValue(infile, "growthandeatlengths", filename);
datafile.open(filename, ios::in);
handle.checkIfFailure(datafile, filename);
handle.Open(filename);
i = readLengthAggregation(subdata, grlengths, grlenindex);
handle.Close();
datafile.close();
datafile.clear();
LengthGroupDivision* GrowLgrpDiv = new LengthGroupDivision(grlengths);
if (GrowLgrpDiv->Error())
handle.logMessage(LOGFAIL, "Error in stock - failed to create growth length group for", this->getName());
//Check the growth length groups cover the stock length groups
if (!checkLengthGroupStructure(LgrpDiv, GrowLgrpDiv))
handle.logMessage(LOGFAIL, "Error in stock - invalid length group structure for growth of", this->getName());
if (LgrpDiv->minLength() < GrowLgrpDiv->minLength())
handle.logMessage(LOGFAIL, "Error in stock - invalid minimum length group for growth of", this->getName());
if (!isSmall(LgrpDiv->minLength() - GrowLgrpDiv->minLength()))
handle.logMessage(LOGWARN, "Warning in stock - minimum lengths don't match for growth of", this->getName());
if (LgrpDiv->maxLength() > GrowLgrpDiv->maxLength())
handle.logMessage(LOGFAIL, "Error in stock - invalid maximum length group for growth of", this->getName());
if (!isSmall(LgrpDiv->maxLength() - GrowLgrpDiv->maxLength()))
handle.logMessage(LOGWARN, "Warning in stock - maximum lengths don't match for growth of", this->getName());
//JMB check that the growth is defined on evenly spaced length groups
if (isZero(GrowLgrpDiv->dl()))
handle.logMessage(LOGWARN, "Warning in stock - growth length structure not evenly spaced for", this->getName());
handle.logMessage(LOGMESSAGE, "Read basic stock data for stock", this->getName());
//read the growth function data
PopInfo nullpop;
tmpPopulation.AddRows(areas.Size(), LgrpDiv->numLengthGroups(), nullpop);
readWordAndVariable(infile, "doesgrow", doesgrow);
if (doesgrow) {
grower = new Grower(infile, LgrpDiv, GrowLgrpDiv, areas, TimeInfo, keeper, refweight, this->getName(), Area, grlenindex);
} else
grower = 0;
handle.logMessage(LOGMESSAGE, "Read growth data for stock", this->getName());
//read the natural mortality data
infile >> text;
if (strcasecmp(text, "naturalmortality") != 0)
handle.logFileUnexpected(LOGFAIL, "naturalmortality", text);
naturalm = new NaturalMortality(infile, minage, numage, this->getName(), areas, TimeInfo, keeper);
handle.logMessage(LOGMESSAGE, "Read natural mortality data for stock", this->getName());
//read the prey data
readWordAndVariable(infile, "iseaten", iseaten);
if (iseaten) {
prey = new StockPrey(infile, areas, this->getName(), minage, numage, TimeInfo, keeper);
} else
prey = 0;
handle.logMessage(LOGMESSAGE, "Read prey data for stock", this->getName());
//read the predator data
readWordAndVariable(infile, "doeseat", doeseat);
if (doeseat) {
predator = new StockPredator(infile, this->getName(), areas, LgrpDiv,
GrowLgrpDiv, minage, numage, TimeInfo, keeper);
} else
predator = 0;
handle.logMessage(LOGMESSAGE, "Read predator data for stock", this->getName());
//read the initial conditions
infile >> text;
if (strcasecmp(text, "initialconditions") != 0)
handle.logFileUnexpected(LOGFAIL, "initialconditions", text);
initial = new InitialCond(infile, areas, keeper, refweight, this->getName(), Area, dl);
handle.logMessage(LOGMESSAGE, "Read initial conditions data for stock", this->getName());
//read the migration data
readWordAndVariable(infile, "doesmigrate", doesmigrate);
if (doesmigrate) {
tmpMigrate.resizeBlank(areas.Size());
infile >> ws;
c = infile.peek();
if ((c == 'y') || (c == 'Y')) {
//about to read the word yearstepfile
migration = new MigrationNumbers(infile, areas, Area, TimeInfo, this->getName(), keeper);
} else if ((c == 'd') || (c == 'D')) {
//about to read the word diffusion
migration = new MigrationFunction(infile, areas, Area, TimeInfo, this->getName(), keeper);
} else {
infile >> text >> ws;
handle.logFileUnexpected(LOGFAIL, "migrationnumbers or migrationfunction", text);
}
} else
migration = 0;
handle.logMessage(LOGMESSAGE, "Read migration data for stock", this->getName());
//read the maturation data
readWordAndVariable(infile, "doesmature", doesmature);
if (doesmature) {
readWordAndValue(infile, "maturityfunction", text);
readWordAndValue(infile, "maturityfile", filename);
ifstream subfile;
subfile.open(filename, ios::in);
CommentStream subcomment(subfile);
handle.checkIfFailure(subfile, filename);
handle.Open(filename);
if (strcasecmp(text, "continuous") == 0) {
maturity = new MaturityA(subcomment, TimeInfo, keeper, minage, numage, areas, this->getName(), LgrpDiv);
} else if (strcasecmp(text, "fixedlength") == 0) {
maturity = new MaturityB(subcomment, TimeInfo, keeper, minage, numage, areas, this->getName(), LgrpDiv);
} else if (strcasecmp(text, "newconstant") == 0) {
maturity = new MaturityC(subcomment, TimeInfo, keeper, minage, numage, areas, this->getName(), LgrpDiv, 4);
} else if (strcasecmp(text, "newconstantweight") == 0) {
maturity = new MaturityD(subcomment, TimeInfo, keeper, minage, numage, areas, this->getName(), LgrpDiv, 6, refweight);
} else if (strcasecmp(text, "ageandlength") == 0) {
handle.logMessage(LOGFAIL, "\nThe ageandlength maturity function is no longer supported");
} else if (strcasecmp(text, "constant") == 0) {
handle.logMessage(LOGFAIL, "\nThe constant maturity function is no longer supported\nUse the newconstant maturity function instead\nNote that this function has had a factor of 4 removed from the source code");
} else if (strcasecmp(text, "constantweight") == 0) {
handle.logMessage(LOGFAIL, "\nThe constantweight maturity function is no longer supported\nUse the newconstantweight maturity function instead\nNote that this function has had a factor of 4 removed from the source code");
} else
handle.logMessage(LOGFAIL, "unrecognised maturity function", text);
handle.Close();
subfile.close();
subfile.clear();
if (!doesgrow)
handle.logMessage(LOGFAIL, "Error in stock - maturation without growth is not implemented");
} else
maturity = 0;
handle.logMessage(LOGMESSAGE, "Read maturity data for stock", this->getName());
//read the movement data
readWordAndVariable(infile, "doesmove", doesmove);
if (doesmove) {
//transition handles the movements of the age group maxage
transition = new Transition(infile, areas, maxage, LgrpDiv, this->getName(), TimeInfo, keeper);
} else
transition = 0;
handle.logMessage(LOGMESSAGE, "Read transition data for stock", this->getName());
//read the renewal data
readWordAndVariable(infile, "doesrenew", doesrenew);
if (doesrenew) {
renewal = new RenewalData(infile, areas, Area, TimeInfo, keeper, refweight, this->getName(), minage, maxage, dl);
} else
renewal = 0;
handle.logMessage(LOGMESSAGE, "Read renewal data for stock", this->getName());
//read the spawning data
readWordAndVariable(infile, "doesspawn", doesspawn);
if (doesspawn) {
readWordAndValue(infile, "spawnfile", filename);
ifstream subfile;
subfile.open(filename, ios::in);
CommentStream subcomment(subfile);
handle.checkIfFailure(subfile, filename);
handle.Open(filename);
spawner = new SpawnData(subcomment, maxage, LgrpDiv, areas, Area, this->getName(), TimeInfo, keeper);
handle.Close();
subfile.close();
subfile.clear();
} else
spawner = 0;
handle.logMessage(LOGMESSAGE, "Read spawning data for stock", this->getName());
infile >> ws;
if (!infile.eof()) {
//read the optional straying data
readWordAndVariable(infile, "doesstray", doesstray);
if (doesstray) {
readWordAndValue(infile, "strayfile", filename);
ifstream subfile;
subfile.open(filename, ios::in);
CommentStream subcomment(subfile);
handle.checkIfFailure(subfile, filename);
handle.Open(filename);
stray = new StrayData(subcomment, LgrpDiv, areas, Area, this->getName(), TimeInfo, keeper);
handle.Close();
subfile.close();
subfile.clear();
} else
stray = 0;
handle.logMessage(LOGMESSAGE, "Read straying data for stock", this->getName());
}
//set the birthday for the stock
birthdate = TimeInfo->numSteps();
//finished reading from infile
delete GrowLgrpDiv;
for (i = 0; i < grlenindex.Size(); i++)
delete[] grlenindex[i];
keeper->clearAll();
}
Stock::Stock(const char* givenname)
: BaseClass(givenname), stray(0), spawner(0), renewal(0), maturity(0), transition(0),
migration(0), prey(0), predator(0), initial(0), LgrpDiv(0), grower(0), naturalm(0) {
doesgrow = doeseat = iseaten = doesmigrate = istagged = 0;
doesmove = doesrenew = doesmature = doesspawn = doesstray = 0;
}
Stock::~Stock() {
if (migration != 0)
delete migration;
if (prey != 0)
delete prey;
if (predator != 0)
delete predator;
if (initial != 0)
delete initial;
if (LgrpDiv != 0)
delete LgrpDiv;
if (grower != 0)
delete grower;
if (naturalm != 0)
delete naturalm;
if (transition != 0)
delete transition;
if (renewal != 0)
delete renewal;
if (maturity != 0)
delete maturity;
if (spawner != 0)
delete spawner;
if (stray != 0)
delete stray;
}
void Stock::Reset(const TimeClass* const TimeInfo) {
naturalm->Reset(TimeInfo);
if (doeseat)
predator->Reset(TimeInfo);
if (doesmature)
maturity->Reset(TimeInfo);
if (doesspawn)
spawner->Reset(TimeInfo);
if (doesstray)
stray->Reset(TimeInfo);
if (iseaten)
prey->Reset(TimeInfo);
if (TimeInfo->getTime() == 1) {
initial->Initialise(Alkeys);
if (doesrenew)
renewal->Reset();
if (doesgrow)
grower->Reset();
if (doesmigrate)
migration->Reset();
if (doesmove)
transition->Reset();
}
if (handle.getLogLevel() >= LOGMESSAGE)
handle.logMessage(LOGMESSAGE, "Reset stock data for stock", this->getName());
}
void Stock::setStock(StockPtrVector& stockvec) {
initial->setCI(LgrpDiv);
if (iseaten)
prey->setCI(LgrpDiv);
if (doesrenew)
renewal->setCI(LgrpDiv);
//JMB for the stock variable stuff to work we need to initialise the population
//very early in the simulation so we do it here and then do it again in the
//reset() function that gets called later (as part of the optimisation runs)
initial->Initialise(Alkeys);
int i;
StockPtrVector tmpStockVector;
if (doesmature) {
maturity->setStock(stockvec);
tmpStockVector = maturity->getMatureStocks();
for (i = 0; i < tmpStockVector.Size(); i++)
if (strcasecmp(tmpStockVector[i]->getName(), this->getName()) == 0)
handle.logMessage(LOGWARN, "Warning in stock - stock maturing into itself", this->getName());
}
if (doesmove) {
transition->setStock(stockvec);
tmpStockVector = transition->getTransitionStocks();
for (i = 0; i < tmpStockVector.Size(); i++)
if (strcasecmp(tmpStockVector[i]->getName(), this->getName()) == 0)
handle.logMessage(LOGWARN, "Warning in stock - stock moving into itself", this->getName());
}
if (doesstray) {
stray->setStock(stockvec);
tmpStockVector = stray->getStrayStocks();
for (i = 0; i < tmpStockVector.Size(); i++)
if (strcasecmp(tmpStockVector[i]->getName(), this->getName()) == 0)
handle.logMessage(LOGWARN, "Warning in stock - stock straying into itself", this->getName());
}
if (doesspawn)
spawner->setStock(stockvec);
}
void Stock::setTagged() {
//resize tagAlkeys to be the same size as Alkeys
int i, minage, maxage;
minage = Alkeys[0].minAge();
maxage = Alkeys[0].maxAge();
IntVector lower(maxage - minage + 1, 0);
IntVector size(maxage - minage + 1, LgrpDiv->numLengthGroups());
tagAlkeys.resize(areas.Size(), minage, lower, size);
for (i = 0; i < tagAlkeys.Size(); i++)
tagAlkeys[i].setToZero();
if (doesmature)
maturity->setTagged();
if (doesmove)
transition->setTagged();
if (doesstray)
stray->setTagged();
}
void Stock::Print(ofstream& outfile) const {
outfile << "\nStock\nName " << this->getName() << "\nLives on internal areas";
int i;
for (i = 0; i < areas.Size(); i++)
outfile << sep << areas[i];
outfile << endl;
outfile << "\ndoes grow " << doesgrow << "\nis eaten " << iseaten
<< "\ndoes eat " << doeseat << "\ndoes migrate " << doesmigrate
<< "\ndoes mature " << doesmature << "\ndoes move " << doesmove
<< "\ndoes renew " << doesrenew << "\ndoes spawn " << doesspawn
<< "\ndoes stray " << doesstray << "\nis tagged " << istagged << endl << endl;
LgrpDiv->Print(outfile);
initial->Print(outfile);
naturalm->Print(outfile);
if (doesmature)
maturity->Print(outfile);
if (iseaten)
prey->Print(outfile);
if (doeseat)
predator->Print(outfile);
if (doesmove)
transition->Print(outfile);
if (doesrenew)
renewal->Print(outfile);
if (doesgrow)
grower->Print(outfile);
if (doesmigrate)
migration->Print(outfile);
if (doesspawn)
spawner->Print(outfile);
if (doesstray)
stray->Print(outfile);
outfile << "\nAge length keys\n";
for (i = 0; i < areas.Size(); i++) {
outfile << "\tInternal area " << areas[i] << "\n\tNumber\n";
Alkeys[i].printNumbers(outfile);
outfile << "\tMean weight\n";
Alkeys[i].printWeights(outfile);
}
}
int Stock::isBirthday(const TimeClass* const TimeInfo) const {
return (TimeInfo->getStep() == birthdate);
}
StockPrey* Stock::getPrey() const {
if (!iseaten)
handle.logMessage(LOGFAIL, "Error in stock - no prey defined for", this->getName());
return prey;
}
Migration* Stock::getMigration() const {
if (!doesmigrate)
handle.logMessage(LOGFAIL, "Error in stock - no migration defined for", this->getName());
return migration;
}
PopPredator* Stock::getPredator() const {
if (!doeseat)
handle.logMessage(LOGFAIL, "Error in stock - no predator defined for", this->getName());
return predator;
}
const StockPtrVector& Stock::getMatureStocks() {
if (!doesmature)
handle.logMessage(LOGFAIL, "Error in stock - no mature stocks defined for", this->getName());
return maturity->getMatureStocks();
}
const StockPtrVector& Stock::getTransitionStocks() {
if (!doesmove)
handle.logMessage(LOGFAIL, "Error in stock - no transition stocks defined for", this->getName());
return transition->getTransitionStocks();
}
const StockPtrVector& Stock::getStrayStocks() {
if (!doesstray)
handle.logMessage(LOGFAIL, "Error in stock - no straying stocks defined for", this->getName());
return stray->getStrayStocks();
}
AgeBandMatrix& Stock::getConsumptionALK(int area) {
// if (!iseaten)
// handle.logMessage(LOGWARN, "Error in stock - no prey for", this->getName());
// return prey->getConsumptionALK(area);
return Alkeys[this->areaNum(area)];
}