X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=2d29ee3f668ee1817cb71c82189c2a8c6f61cf00;hb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;hp=486316fcdc814307e78e029f9fc7400451cd9393;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git diff --git a/validparameter.cpp b/validparameter.cpp index 486316f..2d29ee3 100644 --- a/validparameter.cpp +++ b/validparameter.cpp @@ -13,16 +13,13 @@ ValidParameters::ValidParameters() { try { + m = MothurOut::getInstance(); initParameterRanges(); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ValidParameters", "ValidParameters"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the ValidParameters class function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /***********************************************************************/ @@ -42,11 +39,11 @@ bool ValidParameters::isValidParameter(string parameter, vector cParams, } } if(!valid) { - cout << "'" << parameter << "' is not a valid parameter." << endl; - cout << "The valid parameters are: "; + m->mothurOut(parameter + " is not a valid parameter."); m->mothurOutEndLine(); + m->mothurOut("The valid parameters are: "); for(int i = 0; i < numParams-1; i++) - cout << cParams.at(i) << ", "; - cout << "and " << cParams.at(numParams-1) << ".\n"; + m->mothurOut(cParams.at(i) + ", "); + m->mothurOut("and " + cParams.at(numParams-1) + ".\n"); return false; } @@ -77,7 +74,7 @@ bool ValidParameters::isValidParameter(string parameter, vector cParams, double logNum = log10((double)pVal); double diff = (double)((int)logNum - logNum); if(diff != 0) { - cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n"; + m->mothurOut("The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n"); return false; } } @@ -103,7 +100,7 @@ bool ValidParameters::isValidParameter(string parameter, vector cParams, else if(range.at(4).compare("only") == 0) c = 1; else { - cout << "The range can only be 'between' or 'only' the bounding numbers.\n"; + m->mothurOut("The range can only be 'between' or 'only' the bounding numbers.\n"); return false; } @@ -112,7 +109,7 @@ bool ValidParameters::isValidParameter(string parameter, vector cParams, else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0) d = 1; else { - cout << "The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n"; + m->mothurOut("The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n"); return false; } @@ -121,7 +118,7 @@ bool ValidParameters::isValidParameter(string parameter, vector cParams, else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0) e = 1; else { - cout << "The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n"; + m->mothurOut("The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n"); return false; } @@ -165,25 +162,25 @@ bool ValidParameters::isValidParameter(string parameter, vector cParams, if(!valid) { - cout << "The '" << parameter << "' parameter needs to be "; + m->mothurOut("The '" + parameter + "' parameter needs to be "); if(c == 1) - cout << "either '" << a << "' or '" << b << "'.\n"; + m->mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n"); else { if(a != piSentinel) { - cout << ">"; + m->mothurOut(">"); if(d != 0) - cout << "="; - cout << " '" << a << "'"; + m->mothurOut("="); + m->mothurOut(" '" + toString(a) + "'"); } if(b == piSentinel) - cout << "'.\n"; + m->mothurOut( "'.\n"); else if(a != piSentinel) - cout << " and "; + m->mothurOut(" and "); if(b != piSentinel) { - cout << "<"; + m->mothurOut("<"); if(e != 0) - cout << "="; - cout << " '" << b << "'.\n"; + m->mothurOut("="); + m->mothurOut(" '" + toString(b) + "'.\n"); } } return false; @@ -192,11 +189,7 @@ bool ValidParameters::isValidParameter(string parameter, vector cParams, return true; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ValidParameters", "isValidParameters"); exit(1); } } @@ -212,10 +205,25 @@ string ValidParameters::validFile(map container, string paramete it = container.find(parameter); if(it != container.end()){ //no parameter given + if(isFile == true) { + + #ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + if (pid == 0) { + #endif + ableToOpen = openInputFile(it->second, in); + if (ableToOpen == 1) { return "not open"; } in.close(); + + #ifdef USE_MPI + } + #endif + } }else { return "not found"; } @@ -223,11 +231,7 @@ string ValidParameters::validFile(map container, string paramete } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function validFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ValidParameters class function validFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ValidParameters", "validFile"); exit(1); } } @@ -272,11 +276,7 @@ void ValidParameters::initParameterRanges() { parameterRanges["size"] = addParameters(sizeArray, rangeSize); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ValidParameters", "initParameterRanges"); exit(1); } } @@ -290,11 +290,7 @@ vector ValidParameters::addParameters(string parameters[], int size) { return pVector; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ValidParameters", "addParameters"); exit(1); } }