X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=71bfaf1d0f79b4866cebe71309e058a61bd2535e;hp=d527f8b87af8ab1b29537af212d7229d2e70a75b;hb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;hpb=37e0d78135e32b5aa58ca163f4d416716c78b67f diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp index d527f8b..71bfaf1 100644 --- a/rarefactsharedcommand.cpp +++ b/rarefactsharedcommand.cpp @@ -44,8 +44,8 @@ RareFactSharedCommand::RareFactSharedCommand(string option){ //make sure the user has already run the read.otu command if (globaldata->getSharedFile() == "") { - if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared command." << endl; abort = true; } - else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared command." << endl; abort = true; } + if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; } + else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; } } @@ -66,7 +66,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option){ } //make sure user did not use both the line and label parameters - if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; } + if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; } //if the user has not specified any line or labels use the ones from read.otu else if((line == "") && (label == "")) { allLines = globaldata->allLines; @@ -115,40 +115,31 @@ RareFactSharedCommand::RareFactSharedCommand(string option){ } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } //********************************************************************************************************************** void RareFactSharedCommand::help(){ try { - cout << "The rarefaction.shared command can only be executed after a successful read.otu command." << "\n"; - cout << "The rarefaction.shared command parameters are label, line, iters, groups and calc. No parameters are required, but you may not use " << "\n"; - cout << "both the line and label parameters at the same time. The rarefaction command should be in the following format: " << "\n"; - cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, calc=yourEstimators, groups=yourGroups)." << "\n"; - cout << "Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, groups=B-C, calc=sharedobserved)." << "\n"; - cout << "The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness." << "\n"; - cout << "The default value for groups is all the groups in your groupfile." << "\n"; + mothurOut("The rarefaction.shared command can only be executed after a successful read.otu command.\n"); + mothurOut("The rarefaction.shared command parameters are label, line, iters, groups and calc. No parameters are required, but you may not use \n"); + mothurOut("both the line and label parameters at the same time. The rarefaction command should be in the following format: \n"); + mothurOut("rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, calc=yourEstimators, groups=yourGroups).\n"); + mothurOut("Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, groups=B-C, calc=sharedobserved).\n"); + mothurOut("The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n"); + mothurOut("The default value for groups is all the groups in your groupfile.\n"); validCalculator->printCalc("sharedrarefaction", cout); - cout << "The label and line parameters are used to analyze specific lines in your input." << "\n"; - cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n"; + mothurOut("The label and line parameters are used to analyze specific lines in your input.\n"); + mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n"); + mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n"); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "RareFactSharedCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the RareFactSharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** @@ -181,7 +172,7 @@ int RareFactSharedCommand::execute(){ string lastLabel = lookup[0]->getLabel(); if (lookup.size() < 2) { - cout << "I cannot run the command without at least 2 valid groups."; + mothurOut("I cannot run the command without at least 2 valid groups."); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; } @@ -200,7 +191,7 @@ int RareFactSharedCommand::execute(){ rCurve->getSharedCurve(freq, nIters); delete rCurve; - cout << lookup[0]->getLabel() << '\t' << count << endl; + mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); userLines.erase(count); @@ -210,7 +201,7 @@ int RareFactSharedCommand::execute(){ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(lastLabel); - cout << lookup[0]->getLabel() << '\t' << count << endl; + mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); rCurve = new Rarefact(lookup, rDisplays); rCurve->getSharedCurve(freq, nIters); delete rCurve; @@ -232,12 +223,12 @@ int RareFactSharedCommand::execute(){ set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - cout << "Your file does not include the label "<< *it; + mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - cout << ". I will use " << lastLabel << "." << endl; + mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); needToRun = true; }else { - cout << ". Please refer to " << lastLabel << "." << endl; + mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); } } @@ -246,7 +237,7 @@ int RareFactSharedCommand::execute(){ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(lastLabel); - cout << lookup[0]->getLabel() << '\t' << count << endl; + mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); rCurve = new Rarefact(lookup, rDisplays); rCurve->getSharedCurve(freq, nIters); delete rCurve; @@ -261,13 +252,9 @@ int RareFactSharedCommand::execute(){ return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "RareFactSharedCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } }