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agomez |
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#include "maininfo.h" |
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#include "errorhandler.h" |
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#include "gadget.h" |
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#include "runid.h" |
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#include "global.h" |
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void MainInfo::showCorrectUsage(char* error) {
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RUNID.Print(cerr);
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cerr << "\nError in command line value - unrecognised option " << error << endl
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<< "Common options are -l or -s, -i <filename> -o <filename>\n"
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<< "For more information try running Gadget with the -h switch\n";
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exit(EXIT_FAILURE);
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}
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void MainInfo::showUsage() {
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RUNID.Print(cout);
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cout << "\nOptions for running Gadget:\n"
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<< " -l perform a likelihood (optimising) model run\n"
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<< " -s perform a single (simulation) model run\n"
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<< " -n perform a network run (using paramin)\n"
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<< " -v --version display version information and exit\n"
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<< " -h --help display this help screen and exit\n"
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<< "\nOptions for specifying the input to Gadget models:\n"
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<< " -i <filename> read model parameters from <filename>\n"
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<< " -opt <filename> read optimising parameters from <filename>\n"
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<< " -main <filename> read model information from <filename>\n"
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<< " (default filename is 'main')\n"
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<< " -m <filename> read other commandline parameters from <filename>\n"
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<< "\nOptions for specifying the output from Gadget models:\n"
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<< " -p <filename> print final model parameters to <filename>\n"
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<< " (default filename is 'params.out')\n"
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<< " -o <filename> print likelihood output to <filename>\n"
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<< " -print <number> print -o output every <number> iterations\n"
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<< " -precision <number> set the precision to <number> in output files\n"
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<< "\nOptions for debugging Gadget models:\n"
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<< " -log <filename> print logging information to <filename>\n"
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<< " -printinitial <filename> print initial model information to <filename>\n"
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<< " -printfinal <filename> print final model information to <filename>\n"
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<< "\nFor more information see the Gadget web page at http://www.hafro.is/gadget\n\n";
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exit(EXIT_SUCCESS);
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}
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MainInfo::MainInfo()
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: givenOptInfo(0), givenInitialParam(0), runoptimise(0),
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runstochastic(0), runnetwork(0), runprint(1), forceprint(0),
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printInitialInfo(0), printFinalInfo(0), printLogLevel(0), maxratio(0.95) {
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char tmpname[10];
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strncpy(tmpname, "", 10);
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strcpy(tmpname, "main");
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strOptInfoFile = NULL;
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strInitialParamFile = NULL;
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strPrintInitialFile = NULL;
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strPrintFinalFile = NULL;
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strMainGadgetFile = NULL;
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setMainGadgetFile(tmpname);
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}
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MainInfo::~MainInfo() {
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if (strOptInfoFile != NULL) {
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delete[] strOptInfoFile;
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strOptInfoFile = NULL;
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}
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if (strInitialParamFile != NULL) {
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delete[] strInitialParamFile;
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strInitialParamFile = NULL;
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}
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if (strPrintInitialFile != NULL) {
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delete[] strPrintInitialFile;
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strPrintInitialFile = NULL;
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}
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if (strPrintFinalFile != NULL) {
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delete[] strPrintFinalFile;
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strPrintFinalFile = NULL;
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}
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if (strMainGadgetFile != NULL) {
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delete[] strMainGadgetFile;
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strMainGadgetFile = NULL;
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}
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}
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void MainInfo::read(int aNumber, char* const aVector[]) {
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if (aNumber == 1) {
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handle.logMessage(LOGWARN, "Warning - no command line options specified, using default values");
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return;
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}
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int k = 1;
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while (k < aNumber) {
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if (strcasecmp(aVector[k], "-l") == 0) {
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runoptimise = 1;
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} else if (strcasecmp(aVector[k], "-n") == 0) {
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runnetwork = 1;
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#ifndef GADGET_NETWORK
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handle.logMessage(LOGFAIL, "Error - Gadget cannot currently run in network mode for paramin\nGadget must be recompiled to enable the network communication");
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#endif
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} else if (strcasecmp(aVector[k], "-s") == 0) {
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runstochastic = 1;
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} else if (strcasecmp(aVector[k], "-m") == 0) {
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ifstream infile;
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CommentStream incomment(infile);
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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infile.open(aVector[k], ios::in);
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handle.checkIfFailure(infile, aVector[k]);
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if (infile.fail())
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this->showCorrectUsage(aVector[k]);
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this->read(incomment);
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infile.close();
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infile.clear();
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} else if (strcasecmp(aVector[k], "-i") == 0) {
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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this->setInitialParamFile(aVector[k]);
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} else if (strcasecmp(aVector[k], "-o") == 0) {
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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printinfo.setOutputFile(aVector[k]);
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} else if (strcasecmp(aVector[k], "-p") == 0) {
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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printinfo.setParamOutFile(aVector[k]);
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} else if (strcasecmp(aVector[k], "-forceprint") == 0) {
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forceprint = 1;
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} else if (strcasecmp(aVector[k], "-co") == 0) {
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handle.logMessage(LOGFAIL, "The -co switch is no longer supported");
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} else if (strcasecmp(aVector[k], "-printinitial") == 0) {
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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this->setPrintInitialFile(aVector[k]);
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} else if (strcasecmp(aVector[k], "-printfinal") == 0) {
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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this->setPrintFinalFile(aVector[k]);
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} else if (strcasecmp(aVector[k], "-main") == 0) {
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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this->setMainGadgetFile(aVector[k]);
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} else if (strcasecmp(aVector[k], "-opt") == 0) {
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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this->setOptInfoFile(aVector[k]);
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} else if ((strcasecmp(aVector[k], "-printlikelihood") == 0) || (strcasecmp(aVector[k], "-likelihoodprint") == 0)) {
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handle.logMessage(LOGFAIL, "The -printlikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
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} else if (strcasecmp(aVector[k], "-printlikesummary") == 0) {
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handle.logMessage(LOGFAIL, "The -printlikesummary switch is no longer supported\nSpecify a likelihoodsummaryprinter class in the model print file instead");
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} else if (strcasecmp(aVector[k], "-printonelikelihood") == 0) {
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handle.logMessage(LOGFAIL, "The -printonelikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
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} else if ((strcasecmp(aVector[k], "-print") == 0) || (strcasecmp(aVector[k], "-print1") == 0)) {
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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printinfo.setPrintIteration(atoi(aVector[k]));
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} else if (strcasecmp(aVector[k], "-precision") == 0) {
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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printinfo.setPrecision(atoi(aVector[k]));
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} else if ((strcasecmp(aVector[k], "-v") == 0) || (strcasecmp(aVector[k], "--version") == 0)) {
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RUNID.Print(cout);
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exit(EXIT_SUCCESS);
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| 191 : |
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| 192 : |
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} else if ((strcasecmp(aVector[k], "-h") == 0) || (strcasecmp(aVector[k], "--help") == 0)) {
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this->showUsage();
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| 194 : |
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} else if (strcasecmp(aVector[k], "-log") == 0) {
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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handle.setLogFile(aVector[k]);
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printLogLevel = 5;
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} else if (strcasecmp(aVector[k], "-nowarnings") == 0) {
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//handle.logMessage(LOGWARN, "The -nowarnings switch is no longer supported\nSpecify a logging level using the -loglevel <number> instead");
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printLogLevel = 1;
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} else if (strcasecmp(aVector[k], "-loglevel") == 0) {
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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k++;
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| 210 : |
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printLogLevel = atoi(aVector[k]);
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| 211 : |
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} else if (strcasecmp(aVector[k], "-noprint") == 0) {
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| 213 : |
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//JMB disable model printing from the commandline
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| 214 : |
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runprint = 0;
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| 215 : |
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| 216 : |
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} else if (strcasecmp(aVector[k], "-seed") == 0) {
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| 217 : |
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//JMB experimental setting of random number seed from the commandline
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| 218 : |
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//if the "seed" is also specified in the optinfo file then that will override
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| 219 : |
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//any seed that is specified on the commandline
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| 220 : |
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if (k == aNumber - 1)
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| 221 : |
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this->showCorrectUsage(aVector[k]);
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| 222 : |
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k++;
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| 223 : |
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srand(atoi(aVector[k]));
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| 224 : |
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| 225 : |
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} else if (strcasecmp(aVector[k], "-maxratio") == 0) {
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| 226 : |
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//JMB experimental setting of maximum ratio of stock consumed in one timestep
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| 227 : |
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if (k == aNumber - 1)
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this->showCorrectUsage(aVector[k]);
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| 229 : |
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k++;
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| 230 : |
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maxratio = atof(aVector[k]);
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| 231 : |
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| 232 : |
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} else
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| 233 : |
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this->showCorrectUsage(aVector[k]);
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| 234 : |
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| 235 : |
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k++;
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| 236 : |
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}
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| 237 : |
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}
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| 238 : |
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| 239 : |
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void MainInfo::checkUsage(const char* const inputdir, const char* const workingdir) {
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| 240 : |
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int check = 0;
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| 241 : |
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if (runnetwork)
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| 242 : |
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check = max(0, printLogLevel);
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| 243 : |
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else if (runstochastic)
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| 244 : |
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check = max(3, printLogLevel);
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| 245 : |
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else
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| 246 : |
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check = max(2, printLogLevel);
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| 247 : |
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handle.setLogLevel(check);
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| 248 : |
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| 249 : |
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//JMB dont print output if doing a network run
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| 250 : |
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if (!runnetwork)
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| 251 : |
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RUNID.Print(cout);
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| 252 : |
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handle.logMessage(LOGINFO, "Starting Gadget from directory:", workingdir);
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| 253 : |
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handle.logMessage(LOGINFO, "using data from directory:", inputdir);
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| 254 : |
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handle.logMessage(LOGMESSAGE, ""); //write a blank line to the log file
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| 255 : |
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if (strcasecmp(inputdir, workingdir) != 0)
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| 256 : |
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handle.logMessage(LOGWARN, "Warning - working directory different from input directory");
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| 257 : |
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| 258 : |
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if (runnetwork) {
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| 259 : |
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handle.logMessage(LOGINFO, "\n** Gadget running in network mode for Paramin **");
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| 260 : |
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if (printInitialInfo) {
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| 261 : |
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handle.logMessage(LOGINFO, "Warning - cannot print initial model information");
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| 262 : |
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printInitialInfo = 0;
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| 263 : |
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}
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| 264 : |
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if (printFinalInfo) {
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| 265 : |
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handle.logMessage(LOGINFO, "Warning - cannot print final model information");
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| 266 : |
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printFinalInfo = 0;
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| 267 : |
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}
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| 268 : |
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}
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| 269 : |
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| 270 : |
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//JMB check to see if we can actually open required files ...
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| 271 : |
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ifstream tmpin;
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| 272 : |
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if (chdir(inputdir) != 0)
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| 273 : |
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handle.logMessage(LOGFAIL, "Error - failed to change input directory to", inputdir);
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| 274 : |
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if (givenInitialParam) {
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| 275 : |
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//JMB check to see that the input and output filenames are different
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| 276 : |
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//Otherwise Gadget will over-write the inputfile with a blank outputfile ...
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| 277 : |
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if (strcasecmp(strInitialParamFile, printinfo.getParamOutFile()) == 0)
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| 278 : |
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handle.logFileMessage(LOGFAIL, "the parameter input and output filenames are the same");
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| 279 : |
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| 280 : |
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tmpin.open(strInitialParamFile, ios::in);
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| 281 : |
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handle.checkIfFailure(tmpin, strInitialParamFile);
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| 282 : |
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tmpin.close();
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| 283 : |
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tmpin.clear();
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| 284 : |
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}
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| 285 : |
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if (givenOptInfo) {
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| 286 : |
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tmpin.open(strOptInfoFile, ios::in);
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| 287 : |
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handle.checkIfFailure(tmpin, strOptInfoFile);
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| 288 : |
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tmpin.close();
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| 289 : |
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tmpin.clear();
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| 290 : |
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}
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| 291 : |
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ofstream tmpout;
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| 292 : |
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if (chdir(workingdir) != 0)
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| 293 : |
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handle.logMessage(LOGFAIL, "Error - failed to change working directory to", workingdir);
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| 294 : |
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if (printInitialInfo) {
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| 295 : |
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tmpout.open(strPrintInitialFile, ios::out);
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| 296 : |
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handle.checkIfFailure(tmpout, strPrintInitialFile);
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| 297 : |
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tmpout.close();
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| 298 : |
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tmpout.clear();
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| 299 : |
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}
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| 300 : |
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if (printFinalInfo) {
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| 301 : |
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tmpout.open(strPrintFinalFile, ios::out);
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| 302 : |
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handle.checkIfFailure(tmpout, strPrintFinalFile);
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| 303 : |
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tmpout.close();
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| 304 : |
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tmpout.clear();
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| 305 : |
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}
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| 306 : |
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printinfo.checkPrintInfo(runnetwork);
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| 307 : |
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| 308 : |
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//JMB check the value of maxratio
|
| 309 : |
|
|
if ((maxratio < rathersmall) || (maxratio > 1.0)) {
|
| 310 : |
|
|
handle.logMessage(LOGWARN, "Warning - value of maxratio outside bounds", maxratio);
|
| 311 : |
|
|
maxratio = 0.95;
|
| 312 : |
|
|
}
|
| 313 : |
|
|
|
| 314 : |
|
|
if ((!runstochastic) && (runnetwork)) {
|
| 315 : |
|
|
handle.logMessage(LOGWARN, "\nWarning - Gadget for the paramin network should be used with -s option\nGadget will now set the -s switch to perform a simulation run");
|
| 316 : |
|
|
runstochastic = 1;
|
| 317 : |
|
|
}
|
| 318 : |
|
|
|
| 319 : |
|
|
if ((runstochastic) && (runoptimise)) {
|
| 320 : |
|
|
handle.logMessage(LOGWARN, "\nWarning - Gadget has been started with both the -s switch and the -l switch\nHowever, it is not possible to do both a simulation run and a likelihood run!\nGadget will perform only the simulation run (and ignore the -l switch)");
|
| 321 : |
|
|
runoptimise = 0;
|
| 322 : |
|
|
}
|
| 323 : |
|
|
|
| 324 : |
|
|
if ((!runstochastic) && (!runoptimise)) {
|
| 325 : |
|
|
handle.logMessage(LOGWARN, "\nWarning - Gadget has been started without either the -s switch or the -l switch\nGadget will now set the -s switch to perform a simulation run");
|
| 326 : |
|
|
runstochastic = 1;
|
| 327 : |
|
|
}
|
| 328 : |
|
|
|
| 329 : |
|
|
handle.setRunOptimise(runoptimise);
|
| 330 : |
|
|
if ((printLogLevel == 1) && (!runoptimise))
|
| 331 : |
|
|
handle.logMessage(LOGWARN, "\n** Gadget cannot disable warnings for a simulation run **");
|
| 332 : |
|
|
|
| 333 : |
|
|
if ((handle.checkLogFile()) && (runoptimise) && (printLogLevel >= 5))
|
| 334 : |
|
|
handle.logMessage(LOGWARN, "\n** logging model information from a Gadget optimisation is not recommended **");
|
| 335 : |
|
|
|
| 336 : |
|
|
if ((handle.checkLogFile()) && (runnetwork))
|
| 337 : |
|
|
handle.logMessage(LOGWARN, "\n** logging model information from a Gadget network run is not recommended **");
|
| 338 : |
|
|
|
| 339 : |
|
|
//check the printing options
|
| 340 : |
|
|
if (forceprint)
|
| 341 : |
|
|
handle.logMessage(LOGMESSAGE, "\nPrinting model output has been enabled from the command line");
|
| 342 : |
|
|
if (!runprint)
|
| 343 : |
|
|
handle.logMessage(LOGMESSAGE, "\nPrinting model output has been disabled from the command line");
|
| 344 : |
|
|
|
| 345 : |
|
|
check = runprint;
|
| 346 : |
|
|
if (runnetwork)
|
| 347 : |
|
|
check = 0;
|
| 348 : |
|
|
else if ((runoptimise) && (!forceprint))
|
| 349 : |
|
|
check = 0;
|
| 350 : |
|
|
runprint = check;
|
| 351 : |
|
|
|
| 352 : |
|
|
handle.logMessage(LOGMESSAGE, ""); //write blank line to log file
|
| 353 : |
|
|
}
|
| 354 : |
|
|
|
| 355 : |
|
|
void MainInfo::read(CommentStream& infile) {
|
| 356 : |
|
|
int dummy = 0;
|
| 357 : |
|
|
char text[MaxStrLength];
|
| 358 : |
|
|
strncpy(text, "", MaxStrLength);
|
| 359 : |
|
|
infile >> ws;
|
| 360 : |
|
|
while (!infile.eof()) {
|
| 361 : |
|
|
infile >> text >> ws;
|
| 362 : |
|
|
|
| 363 : |
|
|
if (strcasecmp(text, "-i") == 0) {
|
| 364 : |
|
|
infile >> text >> ws;
|
| 365 : |
|
|
this->setInitialParamFile(text);
|
| 366 : |
|
|
} else if (strcasecmp(text, "-o") == 0) {
|
| 367 : |
|
|
infile >> text >> ws;
|
| 368 : |
|
|
printinfo.setOutputFile(text);
|
| 369 : |
|
|
} else if (strcasecmp(text, "-co") == 0) {
|
| 370 : |
|
|
handle.logMessage(LOGFAIL, "The -co switch is no longer supported");
|
| 371 : |
|
|
} else if (strcasecmp(text, "-p") == 0) {
|
| 372 : |
|
|
infile >> text >> ws;
|
| 373 : |
|
|
printinfo.setParamOutFile(text);
|
| 374 : |
|
|
} else if (strcasecmp(text, "-main") == 0) {
|
| 375 : |
|
|
infile >> text >> ws;
|
| 376 : |
|
|
this->setMainGadgetFile(text);
|
| 377 : |
|
|
} else if (strcasecmp(text, "-printinitial") == 0) {
|
| 378 : |
|
|
infile >> text >> ws;
|
| 379 : |
|
|
this->setPrintInitialFile(text);
|
| 380 : |
|
|
} else if (strcasecmp(text, "-printfinal") == 0) {
|
| 381 : |
|
|
infile >> text >> ws;
|
| 382 : |
|
|
this->setPrintFinalFile(text);
|
| 383 : |
|
|
} else if (strcasecmp(text, "-opt") == 0) {
|
| 384 : |
|
|
infile >> text >> ws;
|
| 385 : |
|
|
this->setOptInfoFile(text);
|
| 386 : |
|
|
} else if (strcasecmp(text, "-forceprint") == 0) {
|
| 387 : |
|
|
forceprint = 1;
|
| 388 : |
|
|
} else if (strcasecmp(text, "-noprint") == 0) {
|
| 389 : |
|
|
runprint = 0;
|
| 390 : |
|
|
} else if ((strcasecmp(text, "-print") == 0) || (strcasecmp(text, "-print1") == 0)) {
|
| 391 : |
|
|
infile >> dummy >> ws;
|
| 392 : |
|
|
printinfo.setPrintIteration(dummy);
|
| 393 : |
|
|
} else if (strcasecmp(text, "-precision") == 0) {
|
| 394 : |
|
|
infile >> dummy >> ws;
|
| 395 : |
|
|
printinfo.setPrecision(dummy);
|
| 396 : |
|
|
} else if (strcasecmp(text, "-log") == 0) {
|
| 397 : |
|
|
infile >> text >> ws;
|
| 398 : |
|
|
handle.setLogFile(text);
|
| 399 : |
|
|
printLogLevel = 5;
|
| 400 : |
|
|
} else if (strcasecmp(text, "-nowarnings") == 0) {
|
| 401 : |
|
|
printLogLevel = 1;
|
| 402 : |
|
|
} else if (strcasecmp(text, "-loglevel") == 0) {
|
| 403 : |
|
|
infile >> printLogLevel >> ws;
|
| 404 : |
|
|
} else if (strcasecmp(text, "-seed") == 0) {
|
| 405 : |
|
|
infile >> dummy >> ws;
|
| 406 : |
|
|
srand(dummy);
|
| 407 : |
|
|
} else if (strcasecmp(text, "-maxratio") == 0) {
|
| 408 : |
|
|
infile >> maxratio >> ws;
|
| 409 : |
|
|
} else if (strcasecmp(text, "-printlikesummary") == 0) {
|
| 410 : |
|
|
handle.logMessage(LOGWARN, "The -printlikesummary switch is no longer supported\nSpecify a likelihoodsummaryprinter class in the model print file instead");
|
| 411 : |
|
|
} else if (strcasecmp(text, "-printlikelihood") == 0) {
|
| 412 : |
|
|
handle.logMessage(LOGWARN, "The -printlikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
|
| 413 : |
|
|
} else if (strcasecmp(text, "-printonelikelihood") == 0) {
|
| 414 : |
|
|
handle.logMessage(LOGWARN, "The -printonelikelihood switch is no longer supported\nSpecify a likelihoodprinter class in the model print file instead");
|
| 415 : |
|
|
} else
|
| 416 : |
|
|
this->showCorrectUsage(text);
|
| 417 : |
|
|
}
|
| 418 : |
|
|
}
|
| 419 : |
|
|
|
| 420 : |
|
|
void MainInfo::setPrintInitialFile(char* filename) {
|
| 421 : |
|
|
if (strPrintInitialFile != NULL) {
|
| 422 : |
|
|
delete[] strPrintInitialFile;
|
| 423 : |
|
|
strPrintInitialFile = NULL;
|
| 424 : |
|
|
}
|
| 425 : |
|
|
strPrintInitialFile = new char[strlen(filename) + 1];
|
| 426 : |
|
|
strcpy(strPrintInitialFile, filename);
|
| 427 : |
|
|
printInitialInfo = 1;
|
| 428 : |
|
|
}
|
| 429 : |
|
|
|
| 430 : |
|
|
void MainInfo::setPrintFinalFile(char* filename) {
|
| 431 : |
|
|
if (strPrintFinalFile != NULL) {
|
| 432 : |
|
|
delete[] strPrintFinalFile;
|
| 433 : |
|
|
strPrintFinalFile = NULL;
|
| 434 : |
|
|
}
|
| 435 : |
|
|
strPrintFinalFile = new char[strlen(filename) + 1];
|
| 436 : |
|
|
strcpy(strPrintFinalFile, filename);
|
| 437 : |
|
|
printFinalInfo = 1;
|
| 438 : |
|
|
}
|
| 439 : |
|
|
|
| 440 : |
|
|
void MainInfo::setMainGadgetFile(char* filename) {
|
| 441 : |
|
|
if (strMainGadgetFile != NULL) {
|
| 442 : |
|
|
delete[] strMainGadgetFile;
|
| 443 : |
|
|
strMainGadgetFile = NULL;
|
| 444 : |
|
|
}
|
| 445 : |
|
|
strMainGadgetFile = new char[strlen(filename) + 1];
|
| 446 : |
|
|
strcpy(strMainGadgetFile, filename);
|
| 447 : |
|
|
}
|
| 448 : |
|
|
|
| 449 : |
|
|
void MainInfo::setInitialParamFile(char* filename) {
|
| 450 : |
|
|
if (strInitialParamFile != NULL) {
|
| 451 : |
|
|
delete[] strInitialParamFile;
|
| 452 : |
|
|
strInitialParamFile = NULL;
|
| 453 : |
|
|
}
|
| 454 : |
|
|
strInitialParamFile = new char[strlen(filename) + 1];
|
| 455 : |
|
|
strcpy(strInitialParamFile, filename);
|
| 456 : |
|
|
givenInitialParam = 1;
|
| 457 : |
|
|
}
|
| 458 : |
|
|
|
| 459 : |
|
|
void MainInfo::setOptInfoFile(char* filename) {
|
| 460 : |
|
|
if (strOptInfoFile != NULL) {
|
| 461 : |
|
|
delete[] strOptInfoFile;
|
| 462 : |
|
|
strOptInfoFile = NULL;
|
| 463 : |
|
|
}
|
| 464 : |
|
|
strOptInfoFile = new char[strlen(filename) + 1];
|
| 465 : |
|
|
strcpy(strOptInfoFile, filename);
|
| 466 : |
|
|
givenOptInfo = 1;
|
| 467 : |
|
|
}
|
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