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agomez |
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#include "tags.h" |
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#include "areatime.h" |
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#include "errorhandler.h" |
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#include "readfunc.h" |
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#include "readword.h" |
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#include "stock.h" |
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#include "stockprey.h" |
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#include "gadget.h" |
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#include "global.h" |
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Tags::Tags(CommentStream& infile, const char* givenname, const AreaClass* const Area,
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const TimeClass* const TimeInfo, Keeper* const keeper, StockPtrVector stockvec)
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: HasName(givenname) {
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taggingstock = 0;
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numtagtimesteps = 0;
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char text[MaxStrLength];
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strncpy(text, "", MaxStrLength);
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ifstream subfile;
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CommentStream subcomment(subfile);
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keeper->addString("tags");
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keeper->addString(givenname);
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//Currently can only have one stock per tagging experiment
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readWordAndValue(infile, "stock", text);
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stocknames.resize(new char[strlen(text) + 1]);
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strcpy(stocknames[0], text);
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//Currently can only have one area per tagging experiment
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readWordAndVariable(infile, "tagarea", tagarea);
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tagarea = Area->getInnerArea(tagarea);
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infile >> ws;
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char c = infile.peek();
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if ((c == 'e') || (c == 'E'))
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readWordAndVariable(infile, "endyear", endyear);
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else
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endyear = TimeInfo->getLastYear();
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int i, found = 0;
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for (i = 0; i < stockvec.Size(); i++) {
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if (strcasecmp(stockvec[i]->getName(), stocknames[0]) == 0) {
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if (found == 0) {
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taggingstock = stockvec[i];
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LgrpDiv = new LengthGroupDivision(*(taggingstock->getLengthGroupDiv()));
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if (LgrpDiv->Error())
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handle.logMessage(LOGFAIL, "Error in tags - failed to create length group");
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tagStocks.resize(taggingstock);
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taggingstock->setTaggedStock();
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}
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found++;
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}
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}
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if (found == 0)
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handle.logMessage(LOGFAIL, "Error in tags - failed to match stock", stocknames[0]);
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if (found > 1)
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handle.logMessage(LOGFAIL, "Error in tags - repeated stock", stocknames[0]);
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//Now read in the tagloss information
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readWordAndVariable(infile, "tagloss", tagloss);
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tagloss.Inform(keeper);
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//read in the numbers format: tagid - length - number
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readWordAndValue(infile, "numbers", text);
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subfile.open(text, ios::in);
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handle.checkIfFailure(subfile, text);
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handle.Open(text);
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readNumbers(subcomment, givenname, TimeInfo);
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handle.Close();
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subfile.close();
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subfile.clear();
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keeper->clearLast();
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keeper->clearLast();
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}
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void Tags::readNumbers(CommentStream& infile, const char* tagname, const TimeClass* const TimeInfo) {
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int year, step, count, reject;
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int i, lenid, keepdata, timeid;
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int numlen = LgrpDiv->numLengthGroups();
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double tmplength, tmpnumber;
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char tmpname[MaxStrLength];
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strncpy(tmpname, "", MaxStrLength);
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infile >> ws;
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//Check the number of columns in the inputfile
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if (countColumns(infile) != 5)
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handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 5");
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year = step = count = reject = 0;
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while (!infile.eof()) {
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keepdata = 1;
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infile >> tmpname >> year >> step >> tmplength >> tmpnumber >> ws;
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//only keep the data if tmpname matches tagname
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if (strcasecmp(tagname, tmpname) != 0)
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keepdata = 0;
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//only keep the data if the length is valid
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lenid = -1;
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for (i = 0; i < numlen; i++)
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if (isEqual(tmplength, LgrpDiv->minLength(i)))
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lenid = i;
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//OK the length doesnt match a minimum length so find the length group it is in
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if ((lenid == -1) && (tmplength > LgrpDiv->minLength()) && (tmplength < LgrpDiv->maxLength())) {
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for (i = 1; i < numlen; i++) {
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if (tmplength < LgrpDiv->minLength(i)) {
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lenid = i - 1;
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break;
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}
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}
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if (lenid == -1)
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lenid = numlen - 1; //then this must be the last length group
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}
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if (lenid == -1)
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keepdata = 0;
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//only keep the data if the number is positive
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if (tmpnumber < 0.0) {
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handle.logMessage(LOGWARN, "Warning in tags - found negative number of tags", tmpnumber);
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keepdata = 0;
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}
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timeid = -1;
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if ((TimeInfo->isWithinPeriod(year, step)) && (keepdata == 1)) {
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for (i = 0; i < Years.Size(); i++)
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if ((Years[i] == year) && (Steps[i] == step))
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timeid = i;
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if (timeid == -1) {
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Years.resize(1, year);
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Steps.resize(1, step);
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timeid = Years.Size() - 1;
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NumberByLength.resize(new DoubleMatrix(1, numlen, 0.0));
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}
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} else
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keepdata = 0;
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if (keepdata == 1) {
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count++;
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(*NumberByLength[timeid])[0][lenid] += tmpnumber;
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} else
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reject++; //count number of rejected data points read from file
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}
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if (count == 0)
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handle.logMessage(LOGWARN, "Warning in tags - found no data in the data file for", tagname);
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if (reject != 0)
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handle.logMessage(LOGMESSAGE, "Discarded invalid tags data - number of invalid entries", reject);
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handle.logMessage(LOGMESSAGE, "Read tags data file - number of entries", count);
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tagyear = 9999;
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tagstep = 9999;
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for (i = 0; i < Years.Size(); i++)
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if ((Years[i] < tagyear) || (Years[i] == tagyear && Steps[i] < tagstep)) {
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tagyear = Years[i];
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tagstep = Steps[i];
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}
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timeid = -1;
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for (i = 0; i < Years.Size(); i++)
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if ((Years[i] == tagyear) && (Steps[i] == tagstep))
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timeid = i;
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if (timeid == -1)
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handle.logMessage(LOGFAIL, "Error in tags - calculated invalid timestep");
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numtagtimesteps = (TimeInfo->numSteps() * (endyear - tagyear)) - tagstep + 1;
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if (endyear == TimeInfo->getLastYear())
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numtagtimesteps += TimeInfo->getLastStep();
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else
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numtagtimesteps += TimeInfo->numSteps();
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}
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Tags::~Tags() {
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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 < NumberByLength.Size(); i++)
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delete NumberByLength[i];
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for (i = 0; i < CI.Size(); i++)
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delete CI[i];
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while (AgeLengthStock.Nrow() > 0)
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AgeLengthStock.Delete(0);
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while (NumBeforeEating.Nrow() > 0)
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NumBeforeEating.Delete(0);
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delete LgrpDiv;
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}
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void Tags::Reset() {
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int i;
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while (AgeLengthStock.Nrow() > 0)
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AgeLengthStock.Delete(0);
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while (NumBeforeEating.Nrow() > 0)
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NumBeforeEating.Delete(0);
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while (CI.Size() > 0) {
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delete CI[0];
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CI.Delete(0);
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}
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for (i = 0; i < preyindex.Size(); i++)
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preyindex[i] = -1;
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for (i = 0; i < updated.Size(); i++)
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updated[i] = 0;
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}
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void Tags::setStock(StockPtrVector& Stocks) {
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int i, j, found;
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StockPtrVector tmpStockVector;
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char* stockname;
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preyindex.resize(1, -1);
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updated.resize(1, 0);
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if (!(taggingstock->isInArea(tagarea)))
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handle.logMessage(LOGFAIL, "Error in tags - stock isnt defined on tagging area");
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if (taggingstock->doesMove()) {
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tmpStockVector = taggingstock->getTransitionStocks();
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for (i = 0; i < tmpStockVector.Size(); i++) {
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transitionStocks.resize(tmpStockVector[i]);
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preyindex.resize(1, -1);
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updated.resize(1, 0);
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tagStocks.resize(tmpStockVector[i]);
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tmpStockVector[i]->setTaggedStock();
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}
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}
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if (taggingstock->doesMature()) {
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tmpStockVector = taggingstock->getMatureStocks();
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for (i = 0; i < tmpStockVector.Size(); i++) {
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matureStocks.resize(tmpStockVector[i]);
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found = 0;
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for (j = 0; j < transitionStocks.Size(); j++)
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if (strcasecmp(transitionStocks[j]->getName(), tmpStockVector[i]->getName()) != 0)
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found++;
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if (found == 0) {
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preyindex.resize(1, -1);
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updated.resize(1, 0);
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tagStocks.resize(tmpStockVector[i]);
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tmpStockVector[i]->setTaggedStock();
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}
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}
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}
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if (taggingstock->doesStray()) {
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tmpStockVector = taggingstock->getStrayStocks();
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for (i = 0; i < tmpStockVector.Size(); i++) {
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strayStocks.resize(tmpStockVector[i]);
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found = 0;
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for (j = 0; j < transitionStocks.Size(); j++)
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if (strcasecmp(transitionStocks[j]->getName(), tmpStockVector[i]->getName()) != 0)
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found++;
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for (j = 0; j < matureStocks.Size(); j++)
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if (strcasecmp(matureStocks[j]->getName(), tmpStockVector[i]->getName()) != 0)
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found++;
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if (found == 0) {
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preyindex.resize(1, -1);
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updated.resize(1, 0);
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tagStocks.resize(tmpStockVector[i]);
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tmpStockVector[i]->setTaggedStock();
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}
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}
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}
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for (i = 1; i < tagStocks.Size(); i++) {
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stockname = new char[strlen(tagStocks[i]->getName()) + 1];
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| 273 : |
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strcpy(stockname, tagStocks[i]->getName());
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| 274 : |
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stocknames.resize(stockname);
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}
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}
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| 277 : |
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//Must have set stocks according to stocknames using setStock before calling Update()
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| 279 : |
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//Now we need to distribute the tagged fish to the same age/length groups as the tagged stock.
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| 280 : |
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void Tags::Update(int timeid) {
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| 281 : |
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int i, j;
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| 282 : |
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PopInfoVector NumberInArea;
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| 283 : |
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NumberInArea.resizeBlank(LgrpDiv->numLengthGroups());
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| 284 : |
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| 285 : |
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const AgeBandMatrix* stockPopInArea;
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| 286 : |
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const LengthGroupDivision* tmpLgrpDiv;
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| 287 : |
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| 288 : |
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stockPopInArea = &(taggingstock->getCurrentALK(tagarea));
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| 289 : |
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stockPopInArea->sumColumns(NumberInArea);
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| 290 : |
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| 291 : |
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//Now we have total number of stock per length in tagarea, N(., l) (NumberInArea) and
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| 292 : |
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//number of stock per age/length, N(a, l) (stockPopInArea) so we must initialise
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| 293 : |
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//AgeLengthStock so that it can hold all information of number of tagged stock
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| 294 : |
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//per area/age/length after endtime. We must make AgeBandMatrixPtrVector same size as
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| 295 : |
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//the one in stock even though have only one area entry at the beginning
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| 296 : |
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IntVector stockareas = taggingstock->getAreas();
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| 297 : |
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int numareas = stockareas.Size();
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| 298 : |
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int tagareaindex = -1;
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| 299 : |
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j = 0;
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| 300 : |
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while (j <= numareas && tagareaindex == -1) {
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| 301 : |
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if (tagarea == stockareas[j])
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| 302 : |
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tagareaindex = j;
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| 303 : |
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j++;
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| 304 : |
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}
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| 305 : |
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if (tagareaindex == -1)
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| 306 : |
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handle.logMessage(LOGFAIL, "Error in tags - invalid area for tagged stock");
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| 307 : |
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| 308 : |
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int maxage = stockPopInArea->maxAge();
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| 309 : |
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int minage = stockPopInArea->minAge();
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| 310 : |
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int numberofagegroups = maxage - minage + 1;
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| 311 : |
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int upperlgrp, minl, maxl, age, length, stockid;
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| 312 : |
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double numfishinarea, numstockinarea;
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| 313 : |
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IntVector lgrpsize(numberofagegroups, 0);
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| 314 : |
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IntVector lgrpmin(numberofagegroups, 0);
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| 315 : |
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| 316 : |
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for (i = 0; i < numberofagegroups; i++) {
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| 317 : |
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lgrpmin[i]= stockPopInArea->minLength(i + minage);
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| 318 : |
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|
upperlgrp = stockPopInArea->maxLength(i + minage);
|
| 319 : |
|
|
lgrpsize[i] = upperlgrp - lgrpmin[i];
|
| 320 : |
|
|
}
|
| 321 : |
|
|
|
| 322 : |
|
|
AgeLengthStock.resize(new AgeBandMatrixPtrVector(numareas, minage, lgrpmin, lgrpsize));
|
| 323 : |
|
|
for (age = minage; age <= maxage; age++) {
|
| 324 : |
|
|
minl = stockPopInArea->minLength(age);
|
| 325 : |
|
|
maxl = stockPopInArea->maxLength(age);
|
| 326 : |
|
|
for (length = minl; length < maxl; length++) {
|
| 327 : |
|
|
numfishinarea = NumberInArea[length].N;
|
| 328 : |
|
|
numstockinarea = (*stockPopInArea)[age][length].N;
|
| 329 : |
|
|
if (numfishinarea > verysmall && numstockinarea > verysmall)
|
| 330 : |
|
|
(*AgeLengthStock[0])[tagareaindex][age][length].N = (*NumberByLength[timeid])[0][length - minl] * numstockinarea / numfishinarea;
|
| 331 : |
|
|
else
|
| 332 : |
|
|
(*AgeLengthStock[0])[tagareaindex][age][length].N = 0.0;
|
| 333 : |
|
|
}
|
| 334 : |
|
|
}
|
| 335 : |
|
|
taggingstock->addTags(AgeLengthStock[0], this, exp(-tagloss));
|
| 336 : |
|
|
updated[0] = 1;
|
| 337 : |
|
|
|
| 338 : |
|
|
if (taggingstock->isEaten()) {
|
| 339 : |
|
|
tmpLgrpDiv = taggingstock->getPrey()->getLengthGroupDiv();
|
| 340 : |
|
|
lgrpmin.Reset();
|
| 341 : |
|
|
lgrpsize.Reset();
|
| 342 : |
|
|
lgrpmin.resize(numberofagegroups, 0);
|
| 343 : |
|
|
lgrpsize.resize(numberofagegroups, tmpLgrpDiv->numLengthGroups());
|
| 344 : |
|
|
NumBeforeEating.resize(new AgeBandMatrixPtrVector(numareas, minage, lgrpmin, lgrpsize));
|
| 345 : |
|
|
CI.resize(new ConversionIndex(LgrpDiv, tmpLgrpDiv));
|
| 346 : |
|
|
if (CI[CI.Size() - 1]->Error())
|
| 347 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - error when checking length structure");
|
| 348 : |
|
|
|
| 349 : |
|
|
stockid = stockIndex(taggingstock->getName());
|
| 350 : |
|
|
if (stockid < 0 || stockid >= preyindex.Size())
|
| 351 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid stock identifier");
|
| 352 : |
|
|
|
| 353 : |
|
|
preyindex[stockid] = NumBeforeEating.Nrow() - 1;
|
| 354 : |
|
|
}
|
| 355 : |
|
|
|
| 356 : |
|
|
for (i = 1; i < tagStocks.Size(); i++) {
|
| 357 : |
|
|
stockPopInArea = &tagStocks[i]->getCurrentALK(tagarea);
|
| 358 : |
|
|
stockareas = tagStocks[i]->getAreas();
|
| 359 : |
|
|
numareas = stockareas.Size();
|
| 360 : |
|
|
maxage = stockPopInArea->maxAge();
|
| 361 : |
|
|
minage = stockPopInArea->minAge();
|
| 362 : |
|
|
numberofagegroups = maxage - minage + 1;
|
| 363 : |
|
|
lgrpmin.Reset();
|
| 364 : |
|
|
lgrpsize.Reset();
|
| 365 : |
|
|
lgrpmin.resize(numberofagegroups, 0);
|
| 366 : |
|
|
lgrpsize.resize(numberofagegroups, 0);
|
| 367 : |
|
|
for (j = 0; j < numberofagegroups; j++) {
|
| 368 : |
|
|
lgrpmin[j] = stockPopInArea->minLength(j + minage);
|
| 369 : |
|
|
upperlgrp = stockPopInArea->maxLength(j + minage);
|
| 370 : |
|
|
lgrpsize[j] = upperlgrp - lgrpmin[j];
|
| 371 : |
|
|
}
|
| 372 : |
|
|
|
| 373 : |
|
|
AgeLengthStock.resize(new AgeBandMatrixPtrVector(numareas, minage, lgrpmin, lgrpsize));
|
| 374 : |
|
|
if (tagStocks[i]->isEaten()) {
|
| 375 : |
|
|
tmpLgrpDiv = tagStocks[i]->getPrey()->getLengthGroupDiv();
|
| 376 : |
|
|
lgrpmin.Reset();
|
| 377 : |
|
|
lgrpsize.Reset();
|
| 378 : |
|
|
lgrpmin.resize(numberofagegroups, 0);
|
| 379 : |
|
|
lgrpsize.resize(numberofagegroups, tmpLgrpDiv->numLengthGroups());
|
| 380 : |
|
|
NumBeforeEating.resize(new AgeBandMatrixPtrVector(numareas, minage, lgrpmin, lgrpsize));
|
| 381 : |
|
|
CI.resize(new ConversionIndex(LgrpDiv, tmpLgrpDiv));
|
| 382 : |
|
|
if (CI[CI.Size() - 1]->Error())
|
| 383 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - error when checking length structure");
|
| 384 : |
|
|
|
| 385 : |
|
|
stockid = stockIndex(tagStocks[i]->getName());
|
| 386 : |
|
|
if (stockid < 0 || stockid >= preyindex.Size())
|
| 387 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid stock identifier");
|
| 388 : |
|
|
|
| 389 : |
|
|
preyindex[stockid] = NumBeforeEating.Nrow() - 1;
|
| 390 : |
|
|
}
|
| 391 : |
|
|
}
|
| 392 : |
|
|
}
|
| 393 : |
|
|
|
| 394 : |
|
|
void Tags::updateTags(int year, int step) {
|
| 395 : |
|
|
int i, timeid;
|
| 396 : |
|
|
|
| 397 : |
|
|
timeid = -1;
|
| 398 : |
|
|
for (i = 0; i < Years.Size(); i++)
|
| 399 : |
|
|
if (Years[i] == year && Steps[i] == step)
|
| 400 : |
|
|
timeid = i;
|
| 401 : |
|
|
|
| 402 : |
|
|
if (timeid != -1) {
|
| 403 : |
|
|
if (tagyear == year && tagstep == step)
|
| 404 : |
|
|
this->Update(timeid);
|
| 405 : |
|
|
else
|
| 406 : |
|
|
this->addToTagStock(timeid);
|
| 407 : |
|
|
}
|
| 408 : |
|
|
}
|
| 409 : |
|
|
|
| 410 : |
|
|
void Tags::deleteStockTags() {
|
| 411 : |
|
|
int i;
|
| 412 : |
|
|
for (i = 0; i < tagStocks.Size(); i++) {
|
| 413 : |
|
|
if (updated[i] == 1) {
|
| 414 : |
|
|
tagStocks[i]->deleteTags(this->getName());
|
| 415 : |
|
|
updated[i] = 2;
|
| 416 : |
|
|
}
|
| 417 : |
|
|
}
|
| 418 : |
|
|
}
|
| 419 : |
|
|
|
| 420 : |
|
|
void Tags::updateMatureStock(const TimeClass* const TimeInfo) {
|
| 421 : |
|
|
int i, id;
|
| 422 : |
|
|
|
| 423 : |
|
|
if (endyear <= TimeInfo->getYear())
|
| 424 : |
|
|
handle.logMessage(LOGWARN, "Warning in tags - tagging experiment has finished");
|
| 425 : |
|
|
else {
|
| 426 : |
|
|
for (i = 0; i < matureStocks.Size(); i++) {
|
| 427 : |
|
|
id = stockIndex(matureStocks[i]->getName());
|
| 428 : |
|
|
if (id < 0 || id >= AgeLengthStock.Nrow())
|
| 429 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid stock identifier");
|
| 430 : |
|
|
|
| 431 : |
|
|
if (updated[id] == 0) {
|
| 432 : |
|
|
matureStocks[i]->addTags(AgeLengthStock[id], this, exp(-tagloss));
|
| 433 : |
|
|
updated[id] = 1;
|
| 434 : |
|
|
}
|
| 435 : |
|
|
}
|
| 436 : |
|
|
}
|
| 437 : |
|
|
}
|
| 438 : |
|
|
|
| 439 : |
|
|
void Tags::updateTransitionStock(const TimeClass* const TimeInfo) {
|
| 440 : |
|
|
int i, id;
|
| 441 : |
|
|
|
| 442 : |
|
|
if (endyear <= TimeInfo->getYear())
|
| 443 : |
|
|
handle.logMessage(LOGWARN, "Warning in tags - tagging experiment has finished");
|
| 444 : |
|
|
else {
|
| 445 : |
|
|
for (i = 0; i < transitionStocks.Size(); i++) {
|
| 446 : |
|
|
id = stockIndex(transitionStocks[i]->getName());
|
| 447 : |
|
|
if (id < 0 || id >= AgeLengthStock.Nrow())
|
| 448 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid stock identifier");
|
| 449 : |
|
|
|
| 450 : |
|
|
if (updated[id] == 0) {
|
| 451 : |
|
|
transitionStocks[i]->addTags(AgeLengthStock[id], this, exp(-tagloss));
|
| 452 : |
|
|
updated[id] = 1;
|
| 453 : |
|
|
}
|
| 454 : |
|
|
}
|
| 455 : |
|
|
}
|
| 456 : |
|
|
}
|
| 457 : |
|
|
|
| 458 : |
|
|
void Tags::updateStrayStock(const TimeClass* const TimeInfo) {
|
| 459 : |
|
|
int i, id;
|
| 460 : |
|
|
|
| 461 : |
|
|
if (endyear <= TimeInfo->getYear())
|
| 462 : |
|
|
handle.logMessage(LOGWARN, "Warning in tags - tagging experiment has finished");
|
| 463 : |
|
|
else {
|
| 464 : |
|
|
for (i = 0; i < strayStocks.Size(); i++) {
|
| 465 : |
|
|
id = stockIndex(strayStocks[i]->getName());
|
| 466 : |
|
|
if (id < 0 || id >= AgeLengthStock.Nrow())
|
| 467 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid stock identifier");
|
| 468 : |
|
|
|
| 469 : |
|
|
if (updated[id] == 0) {
|
| 470 : |
|
|
strayStocks[i]->addTags(AgeLengthStock[id], this, exp(-tagloss));
|
| 471 : |
|
|
updated[id] = 1;
|
| 472 : |
|
|
}
|
| 473 : |
|
|
}
|
| 474 : |
|
|
}
|
| 475 : |
|
|
}
|
| 476 : |
|
|
|
| 477 : |
|
|
int Tags::stockIndex(const char* stockname) {
|
| 478 : |
|
|
int i;
|
| 479 : |
|
|
for (i = 0; i < tagStocks.Size(); i++)
|
| 480 : |
|
|
if (strcasecmp(stockname, tagStocks[i]->getName()) == 0)
|
| 481 : |
|
|
return i;
|
| 482 : |
|
|
|
| 483 : |
|
|
return -1;
|
| 484 : |
|
|
}
|
| 485 : |
|
|
|
| 486 : |
|
|
int Tags::areaIndex(const char* stockname, int area) {
|
| 487 : |
|
|
int i, j;
|
| 488 : |
|
|
for (i = 0; i < tagStocks.Size(); i++) {
|
| 489 : |
|
|
if (strcasecmp(stockname, tagStocks[i]->getName()) == 0) {
|
| 490 : |
|
|
IntVector stockareas = tagStocks[i]->getAreas();
|
| 491 : |
|
|
for (j = 0; j < stockareas.Size(); j++)
|
| 492 : |
|
|
if (stockareas[j] == area)
|
| 493 : |
|
|
return j;
|
| 494 : |
|
|
return -1;
|
| 495 : |
|
|
}
|
| 496 : |
|
|
}
|
| 497 : |
|
|
return -1;
|
| 498 : |
|
|
}
|
| 499 : |
|
|
|
| 500 : |
|
|
void Tags::storeConsumptionALK(int area, const char* stockname) {
|
| 501 : |
|
|
int stockid, preyid, areaid;
|
| 502 : |
|
|
stockid = stockIndex(stockname);
|
| 503 : |
|
|
if (stockid < 0)
|
| 504 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid stock identifier");
|
| 505 : |
|
|
|
| 506 : |
|
|
preyid = preyindex[stockid];
|
| 507 : |
|
|
if (preyid > NumBeforeEating.Nrow() || preyid < 0)
|
| 508 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid prey identifier");
|
| 509 : |
|
|
|
| 510 : |
|
|
areaid = areaIndex(stockname, area);
|
| 511 : |
|
|
if (areaid < 0)
|
| 512 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid area identifier");
|
| 513 : |
|
|
|
| 514 : |
|
|
(*NumBeforeEating[preyid])[areaid].setToZero();
|
| 515 : |
|
|
(*NumBeforeEating[preyid])[areaid].Add((*AgeLengthStock[stockid])[areaid], *CI[preyid]);
|
| 516 : |
|
|
}
|
| 517 : |
|
|
|
| 518 : |
|
|
const AgeBandMatrix& Tags::getConsumptionALK(int area, const char* stockname) {
|
| 519 : |
|
|
int stockid, preyid, areaid;
|
| 520 : |
|
|
stockid = stockIndex(stockname);
|
| 521 : |
|
|
if (stockid < 0)
|
| 522 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid stock identifier");
|
| 523 : |
|
|
|
| 524 : |
|
|
preyid = preyindex[stockid];
|
| 525 : |
|
|
if (preyid > NumBeforeEating.Nrow() || preyid < 0)
|
| 526 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid prey identifier");
|
| 527 : |
|
|
|
| 528 : |
|
|
areaid = areaIndex(stockname, area);
|
| 529 : |
|
|
if (areaid < 0)
|
| 530 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid area identifier");
|
| 531 : |
|
|
|
| 532 : |
|
|
return (*NumBeforeEating[preyid])[areaid];
|
| 533 : |
|
|
}
|
| 534 : |
|
|
|
| 535 : |
|
|
int Tags::isWithinPeriod(int year, int step) {
|
| 536 : |
|
|
if ((year > tagyear || (year == tagyear && step >= tagstep)) && (year <= endyear))
|
| 537 : |
|
|
return 1;
|
| 538 : |
|
|
return 0;
|
| 539 : |
|
|
}
|
| 540 : |
|
|
|
| 541 : |
|
|
void Tags::addToTagStock(int timeid) {
|
| 542 : |
|
|
int i, tagareaindex;
|
| 543 : |
|
|
PopInfoVector NumberInArea;
|
| 544 : |
|
|
NumberInArea.resizeBlank(LgrpDiv->numLengthGroups());
|
| 545 : |
|
|
const AgeBandMatrix* stockPopInArea;
|
| 546 : |
|
|
stockPopInArea = &(taggingstock->getCurrentALK(tagarea));
|
| 547 : |
|
|
stockPopInArea->sumColumns(NumberInArea);
|
| 548 : |
|
|
|
| 549 : |
|
|
i = 0;
|
| 550 : |
|
|
tagareaindex = -1;
|
| 551 : |
|
|
IntVector stockareas = taggingstock->getAreas();
|
| 552 : |
|
|
while (i <= stockareas.Size() && tagareaindex == -1) {
|
| 553 : |
|
|
if (tagarea == stockareas[i])
|
| 554 : |
|
|
tagareaindex = i;
|
| 555 : |
|
|
i++;
|
| 556 : |
|
|
}
|
| 557 : |
|
|
if (tagareaindex == -1)
|
| 558 : |
|
|
handle.logMessage(LOGFAIL, "Error in tags - invalid area for tagged stock");
|
| 559 : |
|
|
|
| 560 : |
|
|
int maxage = stockPopInArea->maxAge();
|
| 561 : |
|
|
int minage = stockPopInArea->minAge();
|
| 562 : |
|
|
int minl, maxl, age, length;
|
| 563 : |
|
|
double numfishinarea, numstockinarea;
|
| 564 : |
|
|
|
| 565 : |
|
|
for (age = minage; age <= maxage; age++) {
|
| 566 : |
|
|
minl = stockPopInArea->minLength(age);
|
| 567 : |
|
|
maxl = stockPopInArea->maxLength(age);
|
| 568 : |
|
|
for (length = minl; length < maxl; length++) {
|
| 569 : |
|
|
numfishinarea = NumberInArea[length].N;
|
| 570 : |
|
|
numstockinarea = (*stockPopInArea)[age][length].N;
|
| 571 : |
|
|
if (numfishinarea > verysmall && numstockinarea > verysmall)
|
| 572 : |
|
|
(*AgeLengthStock[0])[tagareaindex][age][length].N += (*NumberByLength[timeid])[0][length - minl] * numstockinarea / numfishinarea;
|
| 573 : |
|
|
}
|
| 574 : |
|
|
}
|
| 575 : |
|
|
}
|
| 576 : |
|
|
|
| 577 : |
|
|
void Tags::Print(ofstream& outfile) const {
|
| 578 : |
|
|
// outfile << "\nTag\nName" << sep << this->getName() << endl;
|
| 579 : |
|
|
}
|
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