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agomez |
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#include "ecosystem.h" |
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#include "errorhandler.h" |
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#include "predator.h" |
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#include "prey.h" |
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#include "lengthprey.h" |
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#include "stockprey.h" |
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#include "preyptrvector.h" |
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#include "predatorptrvector.h" |
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#include "stockprinter.h" |
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#include "stockstdprinter.h" |
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#include "stockpreyprinter.h" |
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#include "predatorprinter.h" |
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#include "predatorpreyprinter.h" |
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#include "predatoroverprinter.h" |
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#include "preyoverprinter.h" |
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#include "stockpreyfullprinter.h" |
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#include "stockfullprinter.h" |
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#include "likelihoodprinter.h" |
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#include "summaryprinter.h" |
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#include "surveyindices.h" |
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#include "understocking.h" |
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#include "catchdistribution.h" |
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#include "catchstatistics.h" |
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#include "recstatistics.h" |
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#include "stomachcontent.h" |
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#include "recapture.h" |
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#include "stockpredator.h" |
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#include "lengthpredator.h" |
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#include "stockdistribution.h" |
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#include "surveydistribution.h" |
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#include "migrationpenalty.h" |
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#include "migrationproportion.h" |
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#include "catchinkilos.h" |
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#include "global.h" |
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void Ecosystem::Initialise() {
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PreyPtrVector preyvec;
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PredatorPtrVector predvec;
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int i, j, count;
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//first check that the names of the components are unique
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for (i = 0; i < fleetvec.Size(); i++)
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for (j = 0; j < fleetvec.Size(); j++)
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if ((strcasecmp(fleetvec[i]->getName(), fleetvec[j]->getName()) == 0) && (i != j))
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handle.logMessage(LOGFAIL, "Error in input files - repeated fleet", fleetvec[i]->getName());
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for (i = 0; i < tagvec.Size(); i++)
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for (j = 0; j < tagvec.Size(); j++)
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if ((strcasecmp(tagvec[i]->getName(), tagvec[j]->getName()) == 0) && (i != j))
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handle.logMessage(LOGFAIL, "Error in input files - repeated tagging experiment", tagvec[i]->getName());
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for (i = 0; i < otherfoodvec.Size(); i++)
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for (j = 0; j < otherfoodvec.Size(); j++)
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if ((strcasecmp(otherfoodvec[i]->getName(), otherfoodvec[j]->getName()) == 0) && (i != j))
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handle.logMessage(LOGFAIL, "Error in input files - repeated other food", otherfoodvec[i]->getName());
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for (i = 0; i < stockvec.Size(); i++)
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for (j = 0; j < stockvec.Size(); j++)
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if ((strcasecmp(stockvec[i]->getName(), stockvec[j]->getName()) == 0) && (i != j))
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handle.logMessage(LOGFAIL, "Error in input files - repeated stock", stockvec[i]->getName());
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for (i = 0; i < likevec.Size(); i++)
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for (j = 0; j < likevec.Size(); j++)
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if ((strcasecmp(likevec[i]->getName(), likevec[j]->getName()) == 0) && (i != j))
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handle.logMessage(LOGFAIL, "Error in input files - repeated likelihood component", likevec[i]->getName());
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for (i = 0; i < printvec.Size(); i++)
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for (j = 0; j < printvec.Size(); j++)
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if ((strcasecmp(printvec[i]->getFileName(), printvec[j]->getFileName()) == 0) && (i != j))
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handle.logMessage(LOGFAIL, "Error in input files - repeated print file", printvec[i]->getFileName());
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//OK, next create a list of all the predators and all the preys
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for (i = 0; i < stockvec.Size(); i++) {
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if (stockvec[i]->isEaten())
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preyvec.resize(stockvec[i]->getPrey());
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if (stockvec[i]->doesEat())
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predvec.resize(stockvec[i]->getPredator());
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}
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for (i = 0; i < otherfoodvec.Size(); i++)
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preyvec.resize(otherfoodvec[i]->getPrey());
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for (i = 0; i < fleetvec.Size(); i++)
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predvec.resize(fleetvec[i]->getPredator());
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//Now we can start initialising things
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handle.logMessage(LOGMESSAGE, ""); //write blank line to log file
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for (i = 0; i < stockvec.Size(); i++) {
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handle.logMessage(LOGMESSAGE, "Initialising stock", stockvec[i]->getName());
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stockvec[i]->setStock(stockvec);
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}
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for (i = 0; i < predvec.Size(); i++) {
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handle.logMessage(LOGMESSAGE, "Initialising predator", predvec[i]->getName());
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((PopPredator*)predvec[i])->setPrey(preyvec, keeper);
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}
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for (i = 0; i < tagvec.Size(); i++) {
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handle.logMessage(LOGMESSAGE, "Initialising tagging experiment", tagvec[i]->getName());
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tagvec[i]->setStock(stockvec);
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}
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//If there are any tagging experiments we need to resize objects to store them
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//This has to take place last, since some tagged stocks might not be set explicitly
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if (tagvec.Size() != 0)
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for (i = 0; i < stockvec.Size(); i++)
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if (stockvec[i]->isTagged())
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stockvec[i]->setTagged();
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for (i = 0; i < stockvec.Size(); i++)
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basevec.resize(stockvec[i]);
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for (i = 0; i < otherfoodvec.Size(); i++)
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basevec.resize(otherfoodvec[i]);
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for (i = 0; i < fleetvec.Size(); i++)
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basevec.resize(fleetvec[i]);
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//Next we initialise the likelihood classes
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count = 0; //JMB count the number of understocking classes
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for (i = 0; i < likevec.Size(); i++) {
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handle.logMessage(LOGMESSAGE, "Initialising likelihood component", likevec[i]->getName());
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switch (likevec[i]->getType()) {
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case SURVEYINDICESLIKELIHOOD:
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((SurveyIndices*)likevec[i])->setFleetsAndStocks(fleetvec, stockvec);
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break;
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case UNDERSTOCKINGLIKELIHOOD:
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((UnderStocking*)likevec[i])->setPredatorsAndPreys(predvec, preyvec, Area);
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count++;
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break;
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case CATCHDISTRIBUTIONLIKELIHOOD:
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((CatchDistribution*)likevec[i])->setFleetsAndStocks(fleetvec, stockvec);
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break;
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case CATCHSTATISTICSLIKELIHOOD:
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((CatchStatistics*)likevec[i])->setFleetsAndStocks(fleetvec, stockvec);
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break;
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case STOMACHCONTENTLIKELIHOOD:
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((StomachContent*)likevec[i])->setPredatorsAndPreys(predvec, preyvec);
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break;
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case TAGLIKELIHOOD:
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((Recaptures*)likevec[i])->setFleetsAndStocks(fleetvec, stockvec);
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break;
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case STOCKDISTRIBUTIONLIKELIHOOD:
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((StockDistribution*)likevec[i])->setFleetsAndStocks(fleetvec, stockvec);
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break;
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case MIGRATIONPENALTYLIKELIHOOD:
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((MigrationPenalty*)likevec[i])->setFleetsAndStocks(fleetvec, stockvec);
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break;
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case CATCHINKILOSLIKELIHOOD:
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((CatchInKilos*)likevec[i])->setFleetsAndStocks(fleetvec, stockvec);
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break;
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case RECSTATISTICSLIKELIHOOD:
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((RecStatistics*)likevec[i])->setFleetsAndStocks(fleetvec, stockvec);
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break;
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case SURVEYDISTRIBUTIONLIKELIHOOD:
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((SurveyDistribution*)likevec[i])->setFleetsAndStocks(fleetvec, stockvec);
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break;
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case MIGRATIONPROPORTIONLIKELIHOOD:
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((MigrationProportion*)likevec[i])->setFleetsAndStocks(fleetvec, stockvec);
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break;
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case BOUNDLIKELIHOOD:
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break;
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default:
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handle.logMessage(LOGFAIL, "Error when initialising model - unrecognised likelihood type", likevec[i]->getType());
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break;
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}
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}
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if (count == 0)
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handle.logMessage(LOGWARN, "Warning in input files - no understocking likelihood component found");
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if (count > 1)
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handle.logMessage(LOGWARN, "Warning in input files - repeated understocking components found");
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//Finally we initialise the printer classes
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for (i = 0; i < printvec.Size(); i++) {
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handle.logMessage(LOGMESSAGE, "Initialising printer for output file", printvec[i]->getFileName());
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switch (printvec[i]->getType()) {
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case STOCKSTDPRINTER:
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((StockStdPrinter*)printvec[i])->setStock(stockvec, Area);
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break;
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case STOCKPRINTER:
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((StockPrinter*)printvec[i])->setStock(stockvec, Area);
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break;
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case PREDATORPRINTER:
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((PredatorPrinter*)printvec[i])->setPredAndPrey(predvec, preyvec, Area);
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break;
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case PREDATOROVERPRINTER:
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((PredatorOverPrinter*)printvec[i])->setPredator(predvec, Area);
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break;
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case PREYOVERPRINTER:
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((PreyOverPrinter*)printvec[i])->setPrey(preyvec, Area);
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break;
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case STOCKPREYPRINTER:
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((StockPreyPrinter*)printvec[i])->setPrey(preyvec, Area);
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break;
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case STOCKPREYFULLPRINTER:
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((StockPreyFullPrinter*)printvec[i])->setPrey(preyvec, Area);
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break;
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case PREDATORPREYPRINTER:
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((PredatorPreyPrinter*)printvec[i])->setPredAndPrey(predvec, preyvec, Area);
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break;
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case STOCKFULLPRINTER:
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((StockFullPrinter*)printvec[i])->setStock(stockvec, Area);
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break;
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case LIKELIHOODPRINTER:
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((LikelihoodPrinter*)printvec[i])->setLikelihood(likevec);
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break;
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case LIKELIHOODSUMMARYPRINTER:
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((SummaryPrinter*)printvec[i])->setLikelihood(likevec);
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break;
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default:
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handle.logMessage(LOGFAIL, "Error when initialising model - unrecognised printer type", printvec[i]->getType());
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break;
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}
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}
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}
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