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agomez |
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#include "surveyindices.h" |
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#include "readfunc.h" |
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#include "readword.h" |
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#include "readaggregation.h" |
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#include "areatime.h" |
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#include "errorhandler.h" |
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#include "stock.h" |
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#include "sibylengthonstep.h" |
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#include "sibyageonstep.h" |
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#include "sibyfleetonstep.h" |
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#include "sibyeffortonstep.h" |
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#include "sibyacousticonstep.h" |
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#include "gadget.h" |
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#include "global.h" |
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SurveyIndices::SurveyIndices(CommentStream& infile, const AreaClass* const Area,
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const TimeClass* const TimeInfo, double weight, const char* name)
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: Likelihood(SURVEYINDICESLIKELIHOOD, weight, name) {
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char text[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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int i, j, biomass;
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IntMatrix ages;
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DoubleVector lengths;
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CharPtrVector charindex, areaindex;
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char datafilename[MaxStrLength];
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char aggfilename[MaxStrLength];
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char sitype[MaxStrLength];
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strncpy(datafilename, "", MaxStrLength);
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strncpy(aggfilename, "", MaxStrLength);
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strncpy(sitype, "", MaxStrLength);
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ifstream datafile;
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CommentStream subdata(datafile);
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readWordAndValue(infile, "datafile", datafilename);
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readWordAndValue(infile, "sitype", sitype);
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//JMB - added the optional reading of the biomass flag
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infile >> ws;
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char c = infile.peek();
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biomass = 0;
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if ((c == 'b') || (c == 'B'))
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readWordAndVariable(infile, "biomass", biomass);
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if (biomass != 0 && biomass != 1)
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handle.logFileMessage(LOGFAIL, "\nError in surveyindex - biomass must be 0 or 1");
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//read in area aggregation from file
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readWordAndValue(infile, "areaaggfile", aggfilename);
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datafile.open(aggfilename, ios::in);
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handle.checkIfFailure(datafile, aggfilename);
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handle.Open(aggfilename);
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i = readAggregation(subdata, areas, areaindex);
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handle.Close();
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datafile.close();
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datafile.clear();
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//Must change from outer areas to inner areas.
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for (i = 0; i < areas.Nrow(); i++)
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for (j = 0; j < areas.Ncol(i); j++)
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areas[i][j] = Area->getInnerArea(areas[i][j]);
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if ((strcasecmp(sitype, "lengths") == 0) || (strcasecmp(sitype, "length") == 0)) {
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readWordAndValue(infile, "lenaggfile", aggfilename);
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datafile.open(aggfilename, ios::in);
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handle.checkIfFailure(datafile, aggfilename);
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handle.Open(aggfilename);
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i = readLengthAggregation(subdata, lengths, charindex);
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handle.Close();
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datafile.close();
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datafile.clear();
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//read the word 'stocknames'
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infile >> text >> ws;
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} else if ((strcasecmp(sitype, "ages") == 0) || (strcasecmp(sitype, "age") == 0)) {
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readWordAndValue(infile, "ageaggfile", aggfilename);
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datafile.open(aggfilename, ios::in);
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handle.checkIfFailure(datafile, aggfilename);
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handle.Open(aggfilename);
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i = readAggregation(subdata, ages, charindex);
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handle.Close();
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datafile.close();
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datafile.clear();
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//read the word 'stocknames'
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infile >> text >> ws;
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} else if ((strcasecmp(sitype, "fleets") == 0) || (strcasecmp(sitype, "fleet") == 0)) {
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readWordAndValue(infile, "lenaggfile", aggfilename);
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datafile.open(aggfilename, ios::in);
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handle.checkIfFailure(datafile, aggfilename);
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handle.Open(aggfilename);
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i = readLengthAggregation(subdata, lengths, charindex);
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handle.Close();
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datafile.close();
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datafile.clear();
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//read in the fleetnames
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i = 0;
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infile >> text >> ws;
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if (strcasecmp(text, "fleetnames") != 0)
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handle.logFileUnexpected(LOGFAIL, "fleetnames", text);
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infile >> text;
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while (!infile.eof() && (strcasecmp(text, "stocknames") != 0)) {
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fleetnames.resize(new char[strlen(text) + 1]);
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strcpy(fleetnames[i++], text);
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infile >> text >> ws;
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}
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if (fleetnames.Size() == 0)
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handle.logFileMessage(LOGFAIL, "\nError in surveyindex - failed to read fleets");
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handle.logMessage(LOGMESSAGE, "Read fleet data - number of fleets", fleetnames.Size());
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} else if ((strcasecmp(sitype, "effort") == 0) || (strcasecmp(sitype, "cpue") == 0)) {
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//read in the fleetnames
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i = 0;
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infile >> text >> ws;
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if (strcasecmp(text, "fleetnames") != 0)
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handle.logFileUnexpected(LOGFAIL, "fleetnames", text);
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infile >> text;
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while (!infile.eof() && (strcasecmp(text, "stocknames") != 0)) {
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fleetnames.resize(new char[strlen(text) + 1]);
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strcpy(fleetnames[i++], text);
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infile >> text >> ws;
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}
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if (fleetnames.Size() == 0)
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handle.logFileMessage(LOGFAIL, "\nError in surveyindex - failed to read fleets");
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handle.logMessage(LOGMESSAGE, "Read fleet data - number of fleets", fleetnames.Size());
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if (biomass) //JMB the biomass flag is probably not needed for effort index
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handle.logMessage(LOGWARN, "Warning in surveyindex - biomass flag specified for effort index");
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} else if (strcasecmp(sitype, "acoustic") == 0) {
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//read in the fleetnames
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i = 0;
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infile >> text >> ws;
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if (strcasecmp(text, "surveynames") != 0)
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handle.logFileUnexpected(LOGFAIL, "surveynames", text);
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infile >> text;
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while (!infile.eof() && (strcasecmp(text, "stocknames") != 0)) {
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charindex.resize(new char[strlen(text) + 1]);
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strcpy(charindex[i++], text);
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infile >> text >> ws;
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}
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if (charindex.Size() == 0)
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handle.logFileMessage(LOGFAIL, "\nError in surveyindex - failed to read acoustic survey names");
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handle.logMessage(LOGMESSAGE, "Read acoustic survey data - number of survey names", charindex.Size());
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if (biomass) //JMB the biomass flag is probably not needed for acoustic index
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handle.logMessage(LOGWARN, "Warning in surveyindex - biomass flag specified for acoustic index");
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} else if (strcasecmp(sitype, "ageandlengths") == 0) {
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handle.logFileMessage(LOGFAIL, "\nThe ageandlengths surveyindex likelihood component is no longer supported\nUse the surveydistribution likelihood component instead");
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} else
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handle.logFileMessage(LOGFAIL, "\nError in surveyindex - unrecognised type", sitype);
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if (strcasecmp(text, "stocknames") != 0)
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handle.logFileUnexpected(LOGFAIL, "stocknames", text);
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i = 0;
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infile >> text;
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//read in the stocknames
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while (!infile.eof() && (strcasecmp(text, "fittype") != 0)) {
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stocknames.resize(new char[strlen(text) + 1]);
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strcpy(stocknames[i++], text);
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infile >> text >> ws;
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}
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if (stocknames.Size() == 0)
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handle.logFileMessage(LOGFAIL, "\nError in surveyindex - failed to read stocks");
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handle.logMessage(LOGMESSAGE, "Read stock data - number of stocks", stocknames.Size());
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//We have now read in all the data from the main likelihood file
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if ((strcasecmp(sitype, "lengths") == 0) || (strcasecmp(sitype, "length") == 0)) {
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SI = new SIByLengthOnStep(infile, areas, lengths, areaindex,
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charindex, TimeInfo, datafilename, this->getName(), biomass);
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} else if ((strcasecmp(sitype, "ages") == 0) || (strcasecmp(sitype, "age") == 0)) {
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SI = new SIByAgeOnStep(infile, areas, ages, areaindex,
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charindex, TimeInfo, datafilename, this->getName(), biomass);
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} else if ((strcasecmp(sitype, "fleets") == 0) || (strcasecmp(sitype, "fleet") == 0)) {
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SI = new SIByFleetOnStep(infile, areas, lengths, areaindex,
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charindex, TimeInfo, datafilename, this->getName(), biomass);
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} else if ((strcasecmp(sitype, "effort") == 0) || (strcasecmp(sitype, "cpue") == 0)) {
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SI = new SIByEffortOnStep(infile, areas, areaindex,
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fleetnames, TimeInfo, datafilename, this->getName(), biomass);
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} else if (strcasecmp(sitype, "acoustic") == 0) {
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SI = new SIByAcousticOnStep(infile, areas, areaindex,
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charindex, TimeInfo, datafilename, this->getName(), biomass);
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} else
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handle.logFileMessage(LOGFAIL, "\nError in surveyindex - unrecognised type", sitype);
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//delete objects that are no longer needed to free memory
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for (i = 0; i < charindex.Size(); i++)
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delete[] charindex[i];
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for (i = 0; i < areaindex.Size(); i++)
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delete[] areaindex[i];
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//prepare for next likelihood component
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infile >> ws;
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if (!infile.eof()) {
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infile >> text >> ws;
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if (strcasecmp(text, "[component]") != 0)
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handle.logFileUnexpected(LOGFAIL, "[component]", text);
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}
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}
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SurveyIndices::~SurveyIndices() {
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int i;
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for (i = 0; i < stocknames.Size(); i++)
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delete[] stocknames[i];
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for (i = 0; i < fleetnames.Size(); i++)
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delete[] fleetnames[i];
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delete SI;
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}
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void SurveyIndices::addLikelihood(const TimeClass* const TimeInfo) {
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SI->Sum(TimeInfo);
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if (TimeInfo->getTime() == TimeInfo->numTotalSteps())
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likelihood += SI->calcSSE();
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}
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void SurveyIndices::setFleetsAndStocks(FleetPtrVector& Fleets, StockPtrVector& Stocks) {
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int i, j, k, found;
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FleetPtrVector f;
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StockPtrVector s;
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for (i = 0; i < fleetnames.Size(); i++) {
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found = 0;
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for (j = 0; j < Fleets.Size(); j++) {
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if (strcasecmp(fleetnames[i], Fleets[j]->getName()) == 0) {
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found++;
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f.resize(Fleets[j]);
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}
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}
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if (found == 0)
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handle.logMessage(LOGFAIL, "Error in surveyindex - failed to match fleet", fleetnames[i]);
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}
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for (i = 0; i < f.Size(); i++)
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for (j = 0; j < f.Size(); j++)
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if ((strcasecmp(f[i]->getName(), f[j]->getName()) == 0) && (i != j))
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| 247 : |
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handle.logMessage(LOGFAIL, "Error in surveyindex - repeated fleet", f[i]->getName());
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| 248 : |
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| 249 : |
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for (i = 0; i < stocknames.Size(); i++) {
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found = 0;
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| 251 : |
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for (j = 0; j < Stocks.Size(); j++) {
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| 252 : |
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if (strcasecmp(stocknames[i], Stocks[j]->getName()) == 0) {
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| 253 : |
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found++;
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| 254 : |
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s.resize(Stocks[j]);
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| 255 : |
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}
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| 256 : |
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}
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| 257 : |
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if (found == 0)
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| 258 : |
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handle.logMessage(LOGFAIL, "Error in surveyindex - failed to match stock", stocknames[i]);
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| 259 : |
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}
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| 260 : |
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for (i = 0; i < s.Size(); i++)
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| 262 : |
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for (j = 0; j < s.Size(); j++)
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| 263 : |
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if ((strcasecmp(s[i]->getName(), s[j]->getName()) == 0) && (i != j))
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| 264 : |
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handle.logMessage(LOGFAIL, "Error in surveyindex - repeated stock", s[i]->getName());
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| 265 : |
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| 266 : |
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//check fleet and stock areas
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| 267 : |
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if (handle.getLogLevel() >= LOGWARN) {
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| 268 : |
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if (fleetnames.Size() > 0) { //JMB might not be any fleets
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| 269 : |
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for (j = 0; j < areas.Nrow(); j++) {
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| 270 : |
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found = 0;
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| 271 : |
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for (i = 0; i < f.Size(); i++)
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| 272 : |
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for (k = 0; k < areas.Ncol(j); k++)
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| 273 : |
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if (f[i]->isInArea(areas[j][k]))
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| 274 : |
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found++;
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| 275 : |
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if (found == 0)
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| 276 : |
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handle.logMessage(LOGWARN, "Warning in surveyindex - fleet not defined on all areas");
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| 277 : |
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}
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| 278 : |
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}
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| 279 : |
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| 280 : |
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for (j = 0; j < areas.Nrow(); j++) {
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| 281 : |
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found = 0;
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| 282 : |
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for (i = 0; i < s.Size(); i++)
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| 283 : |
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for (k = 0; k < areas.Ncol(j); k++)
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| 284 : |
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if (s[i]->isInArea(areas[j][k]))
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| 285 : |
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found++;
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| 286 : |
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if (found == 0)
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| 287 : |
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handle.logMessage(LOGWARN, "Warning in surveyindex - stock not defined on all areas");
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| 288 : |
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}
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| 289 : |
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}
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| 290 : |
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| 291 : |
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SI->setFleetsAndStocks(f, s);
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| 292 : |
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}
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| 293 : |
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| 294 : |
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void SurveyIndices::Reset(const Keeper* const keeper) {
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| 295 : |
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Likelihood::Reset(keeper);
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| 296 : |
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SI->Reset();
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| 297 : |
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if (handle.getLogLevel() >= LOGMESSAGE)
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| 298 : |
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handle.logMessage(LOGMESSAGE, "Reset surveyindex component", this->getName());
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| 299 : |
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}
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| 300 : |
|
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|
| 301 : |
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void SurveyIndices::Print(ofstream& outfile) const {
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| 302 : |
|
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int i;
|
| 303 : |
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outfile << "\nSurvey Indices " << this->getName() << " - likelihood value " << likelihood;
|
| 304 : |
|
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if (stocknames.Size() > 0) {
|
| 305 : |
|
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outfile << "\n\tStock names: ";
|
| 306 : |
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for (i = 0; i < stocknames.Size(); i++)
|
| 307 : |
|
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outfile << stocknames[i] << sep;
|
| 308 : |
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}
|
| 309 : |
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if (fleetnames.Size() > 0) {
|
| 310 : |
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outfile << "\n\tFleet names: ";
|
| 311 : |
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for (i = 0; i < fleetnames.Size(); i++)
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| 312 : |
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outfile << fleetnames[i] << sep;
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| 313 : |
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}
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| 314 : |
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outfile << endl;
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| 315 : |
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SI->Print(outfile);
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| 316 : |
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outfile.flush();
|
| 317 : |
|
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}
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