X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=58aa32cd785343419f0395acccf1dbe6b7bfa10b;hb=e911fa88572a16ef40e0b51fb132ab6e02370797;hp=c65080fd32022bcd9abb8d3cf10f73de8f181351;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc;p=mothur.git diff --git a/collectcommand.cpp b/collectcommand.cpp index c65080f..58aa32c 100644 --- a/collectcommand.cpp +++ b/collectcommand.cpp @@ -59,7 +59,7 @@ CollectCommand::CollectCommand(string option){ } //make sure the user has already run the read.otu command - if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the collect.single command." << endl; abort = true; } + if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the collect.single command."); mothurOutEndLine(); abort = true; } //check for optional parameter and set defaults // ...at some point should added some additional type checking... @@ -78,7 +78,7 @@ CollectCommand::CollectCommand(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; @@ -158,38 +158,29 @@ CollectCommand::CollectCommand(string option){ } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "CollectCommand", "CollectCommand"); exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - + } } //********************************************************************************************************************** void CollectCommand::help(){ try { - cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n"; - cout << "The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n"; - cout << "The collect.single command parameters are label, line, freq, calc and abund. No parameters are required, but you may not use " << "\n"; - cout << "both the line and label parameters at the same time. The collect.single command should be in the following format: " << "\n"; - cout << "collect.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n"; - cout << "Example collect(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-chao-ace-jack)." << "\n"; - cout << "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson." << "\n"; + mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n"); + mothurOut("The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n"); + mothurOut("The collect.single command parameters are label, line, freq, calc and abund. No parameters are required, but you may not use \n"); + mothurOut("both the line and label parameters at the same time. The collect.single command should be in the following format: \n"); + mothurOut("collect.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n"); + mothurOut("Example collect(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n"); + mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n"); validCalculator->printCalc("single", cout); - cout << "The label and line parameters are used to analyze specific lines in your input." << "\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("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 CollectCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "CollectCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the CollectCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** @@ -220,7 +211,7 @@ int CollectCommand::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. @@ -236,7 +227,7 @@ int CollectCommand::execute(){ cCurve->getCurve(freq); delete cCurve; - cout << order->getLabel() << '\t' << count << endl; + mothurOut(order->getLabel()); mothurOutEndLine(); processedLabels.insert(order->getLabel()); userLabels.erase(order->getLabel()); userLines.erase(count); @@ -244,18 +235,23 @@ int CollectCommand::execute(){ //you have a label the user want that is smaller than this line and the last line has not already been processed } - if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) { - cCurve = new Collect(lastOrder, cDisplays); + if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + + delete order; + order = (input->getOrderVector(lastLabel)); + + cCurve = new Collect(order, cDisplays); cCurve->getCurve(freq); delete cCurve; - cout << lastOrder->getLabel() << '\t' << count << endl; - processedLabels.insert(lastOrder->getLabel()); - userLabels.erase(lastOrder->getLabel()); + mothurOut(order->getLabel()); mothurOutEndLine(); + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); } - if (count != 1) { delete lastOrder; } - lastOrder = order; + lastLabel = order->getLabel(); + + delete order; order = (input->getOrderVector()); count++; } @@ -264,36 +260,36 @@ int CollectCommand::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) { - cCurve = new Collect(lastOrder, cDisplays); + if (order != NULL) { delete order; } + order = (input->getOrderVector(lastLabel)); + + mothurOut(order->getLabel()); mothurOutEndLine(); + + cCurve = new Collect(order, cDisplays); cCurve->getCurve(freq); delete cCurve; - - cout << lastOrder->getLabel() << '\t' << count << endl; + delete order; } - delete lastOrder; + for(int i=0;i