X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=ae2c52e7c03a9c713930bd77edc22bc402a1b51f;hb=5a9f3cce3e2e053c249e3e97507ce180f0854d76;hp=6127c2d6da7717112fb2c7fdb5c82910f03f8323;hpb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;p=mothur.git diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp index 6127c2d..ae2c52e 100644 --- a/collectsharedcommand.cpp +++ b/collectsharedcommand.cpp @@ -66,8 +66,8 @@ CollectSharedCommand::CollectSharedCommand(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; } } @@ -88,7 +88,7 @@ CollectSharedCommand::CollectSharedCommand(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; @@ -117,7 +117,7 @@ CollectSharedCommand::CollectSharedCommand(string option){ if (abort == false) { string fileNameRoot = getRootName(globaldata->inputFileName); -// format = globaldata->getFormat(); + format = globaldata->getFormat(); int i; validCalculator = new ValidCalculators(); @@ -175,51 +175,43 @@ CollectSharedCommand::CollectSharedCommand(string option){ } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "CollectSharedCommand", "CollectSharedCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the CollectSharedCommand class function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } //********************************************************************************************************************** void CollectSharedCommand::help(){ try { - cout << "The collect.shared command can only be executed after a successful read.otu command." << "\n"; - cout << "The collect.shared command parameters are label, line, freq, calc and groups. No parameters are required, but you may not use " << "\n"; - cout << "both the line and label parameters at the same time. The collect.shared command should be in the following format: " << "\n"; - cout << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, calc=yourEstimators, groups=yourGroups)." << "\n"; - cout << "Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n"; - cout << "The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan." << "\n"; - cout << "The default value for groups is all the groups in your groupfile." << "\n"; + mothurOut("The collect.shared command can only be executed after a successful read.otu command.\n"); + mothurOut("The collect.shared command parameters are label, line, freq, calc and groups. No parameters are required, but you may not use \n"); + mothurOut("both the line and label parameters at the same time. The collect.shared command should be in the following format: \n"); + mothurOut("collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, calc=yourEstimators, groups=yourGroups).\n"); + mothurOut("Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n"); + mothurOut("The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n"); + mothurOut("The default value for groups is all the groups in your groupfile.\n"); validCalculator->printCalc("shared", 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. list), '=' and parameters (i.e.yourListfile)." << "\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. list), '=' and parameters (i.e.yourListfile).\n\n"); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "CollectSharedCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the CollectSharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** CollectSharedCommand::~CollectSharedCommand(){ - delete order; - delete input; - delete cCurve; - delete read; - delete util; - delete validCalculator; + if (abort == false) { + delete input; globaldata->ginput = NULL; + delete read; + delete util; + delete validCalculator; + globaldata->gorder = NULL; + } } //********************************************************************************************************************** @@ -239,7 +231,7 @@ int CollectSharedCommand::execute(){ input = globaldata->ginput; order = input->getSharedOrderVector(); - SharedOrderVector* lastOrder = order; + string lastLabel = order->getLabel(); //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set processedLabels; @@ -259,29 +251,32 @@ int CollectSharedCommand::execute(){ cCurve->getSharedCurve(freq); delete cCurve; - cout << order->getLabel() << '\t' << count << endl; + mothurOut(order->getLabel()); mothurOutEndLine(); processedLabels.insert(order->getLabel()); userLabels.erase(order->getLabel()); userLines.erase(count); - - //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)) { + //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(lastLabel) != 1)) { + delete order; + order = input->getSharedOrderVector(lastLabel); + //create collectors curve - cCurve = new Collect(lastOrder, cDisplays); + cCurve = new Collect(order, cDisplays); cCurve->getSharedCurve(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(); //get next line to process + delete order; order = input->getSharedOrderVector(); count++; } @@ -290,25 +285,28 @@ int CollectSharedCommand::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); + delete order; + order = input->getSharedOrderVector(lastLabel); + + cCurve = new Collect(order, cDisplays); cCurve->getCurve(freq); delete cCurve; - cout << lastOrder->getLabel() << '\t' << count << endl; + mothurOut(order->getLabel()); mothurOutEndLine(); + delete order; } - delete lastOrder; for(int i=0;i