X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=8cbb9d4a06ed2c3d578821520968f47630f6c0ce;hb=e911fa88572a16ef40e0b51fb132ab6e02370797;hp=b3aa54f77a883579a29c601c2d5e737e1c1cae09;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp index b3aa54f..8cbb9d4 100644 --- a/getsabundcommand.cpp +++ b/getsabundcommand.cpp @@ -27,29 +27,29 @@ GetSAbundCommand::GetSAbundCommand(string option){ string Array[] = {"line","label"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - parser = new OptionParser(); - parser->parse(option, parameters); delete parser; + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; - ValidParameters* validParameter = new ValidParameters(); - //check to make sure all parameters are valid for command - for (it = parameters.begin(); it != parameters.end(); it++) { - if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } //make sure the user has already run the read.otu command - if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { cout << "You must read a list or rabund before you can use the get.sabund command." << endl; abort = true; } + if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { mothurOut("You must read a list or rabund before you can use the get.sabund command."); mothurOutEndLine(); abort = true; } //check for optional parameter and set defaults // ...at some point should added some additional type checking... - line = validParameter->validFile(parameters, "line", false); + line = validParameter.validFile(parameters, "line", false); if (line == "not found") { line = ""; } else { if(line != "all") { splitAtDash(line, lines); allLines = 0; } else { allLines = 1; } } - label = validParameter->validFile(parameters, "label", false); + label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } else { if(label != "all") { splitAtDash(label, labels); allLines = 0; } @@ -57,7 +57,7 @@ GetSAbundCommand::GetSAbundCommand(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; @@ -65,8 +65,6 @@ GetSAbundCommand::GetSAbundCommand(string option){ lines = globaldata->lines; } - delete validParameter; - if (abort == false) { filename = getRootName(globaldata->inputFileName) + "sabund"; openOutputFile(filename, out); @@ -75,36 +73,27 @@ GetSAbundCommand::GetSAbundCommand(string option){ } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "GetSAbundCommand", "GetSAbundCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the GetSAbundCommand class function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } //********************************************************************************************************************** void GetSAbundCommand::help(){ try { - cout << "The get.sabund command can only be executed after a successful read.otu of a listfile." << "\n"; - cout << "The get.sabund command parameters are line and label. No parameters are required, and you may not use line and label at the same time." << "\n"; - cout << "The line and label allow you to select what distance levels you would like included in your .sabund file, and are separated by dashes." << "\n"; - cout << "The get.sabund command should be in the following format: get.sabund(line=yourLines, label=yourLabels)." << "\n"; - cout << "Example get.sabund(line=1-3-5)." << "\n"; - cout << "The default value for line and label are all lines in your inputfile." << "\n"; - cout << "The get.sabund command outputs a .sabund file containing the lines you selected." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n"; + mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n"); + mothurOut("The get.sabund command parameters are line and label. No parameters are required, and you may not use line and label at the same time.\n"); + mothurOut("The line and label allow you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n"); + mothurOut("The get.sabund command should be in the following format: get.sabund(line=yourLines, label=yourLabels).\n"); + mothurOut("Example get.sabund(line=1-3-5).\n"); + mothurOut("The default value for line and label are all lines in your inputfile.\n"); + mothurOut("The get.sabund command outputs a .sabund file containing the lines you selected.\n"); + mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n"); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "GetSAbundCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the GetSAbundCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** @@ -126,7 +115,7 @@ int GetSAbundCommand::execute(){ read->read(&*globaldata); order = globaldata->gorder; - lastOrder = order; + string lastLabel = order->getLabel(); input = globaldata->ginput; //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. @@ -138,7 +127,7 @@ int GetSAbundCommand::execute(){ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){ - cout << order->getLabel() << '\t' << count << endl; + mothurOut(order->getLabel()); mothurOutEndLine(); sabund = new SAbundVector(); *sabund = (order->getSAbundVector()); sabund->print(out); @@ -149,20 +138,24 @@ int GetSAbundCommand::execute(){ userLines.erase(count); } - if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) { - cout << lastOrder->getLabel() << '\t' << count << endl; + if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + delete order; + order = (input->getOrderVector(lastLabel)); + + mothurOut(order->getLabel()); mothurOutEndLine(); sabund = new SAbundVector(); - *sabund = (lastOrder->getSAbundVector()); + *sabund = (order->getSAbundVector()); sabund->print(out); delete sabund; - processedLabels.insert(lastOrder->getLabel()); - userLabels.erase(lastOrder->getLabel()); + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); } - if (count != 1) { delete lastOrder; } - lastOrder = order; - + + lastLabel = order->getLabel(); + + delete order; order = (input->getOrderVector()); count++; } @@ -171,37 +164,37 @@ int GetSAbundCommand::execute(){ set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - cout << "Your file does not include the label "<< *it; - if (processedLabels.count(lastOrder->getLabel()) != 1) { - cout << ". I will use " << lastOrder->getLabel() << "." << endl; + mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); needToRun = true; }else { - cout << ". Please refer to " << lastOrder->getLabel() << "." << endl; + mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); } } //run last line if you need to if (needToRun == true) { - cout << lastOrder->getLabel() << '\t' << count << endl; + if (order != NULL) { delete order; } + order = (input->getOrderVector(lastLabel)); + + mothurOut(order->getLabel()); mothurOutEndLine(); sabund = new SAbundVector(); - *sabund = (lastOrder->getSAbundVector()); + *sabund = (order->getSAbundVector()); sabund->print(out); delete sabund; + delete order; } - delete lastOrder; + globaldata->gorder = NULL; out.close(); return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "GetSAbundCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the GetSAbundCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //**********************************************************************************************************************