X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.cpp;h=fb74875159a0aabe98e8ea79a540802d25ca2f21;hb=315e38cf393c82be238da5b32574f225a020d25c;hp=6602bf93ae462ab54c9f97433222bd8fab17babc;hpb=0024441c1ff9a98467ba53cc7420a37c98f32e86;p=mothur.git diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp index 6602bf9..fb74875 100644 --- a/matrixoutputcommand.cpp +++ b/matrixoutputcommand.cpp @@ -22,66 +22,157 @@ //********************************************************************************************************************** -MatrixOutputCommand::MatrixOutputCommand(){ +MatrixOutputCommand::MatrixOutputCommand(string option){ try { globaldata = GlobalData::getInstance(); - validCalculator = new ValidCalculators(); + abort = false; + allLines = 1; + labels.clear(); + Groups.clear(); + Estimators.clear(); + + //allow user to run help + if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; } + + else { + //valid paramters for this command + string Array[] = {"label","calc","groups","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + + //check to make sure all parameters are valid for command + for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ + outputDir = ""; + outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + } + + //make sure the user has already run the read.otu command + if (globaldata->getSharedFile() == "") { + if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the dist.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 dist.shared command."); mothurOutEndLine(); abort = true; } + } - int i; - for (i=0; iEstimators.size(); i++) { - if (validCalculator->isValidCalculator("matrix", globaldata->Estimators[i]) == true) { - if (globaldata->Estimators[i] == "jabund") { - matrixCalculators.push_back(new JAbund()); - }else if (globaldata->Estimators[i] == "sorabund") { - matrixCalculators.push_back(new SorAbund()); - }else if (globaldata->Estimators[i] == "jclass") { - matrixCalculators.push_back(new Jclass()); - }else if (globaldata->Estimators[i] == "sorclass") { - matrixCalculators.push_back(new SorClass()); - }else if (globaldata->Estimators[i] == "jest") { - matrixCalculators.push_back(new Jest()); - }else if (globaldata->Estimators[i] == "sorest") { - matrixCalculators.push_back(new SorEst()); - }else if (globaldata->Estimators[i] == "thetayc") { - matrixCalculators.push_back(new ThetaYC()); - }else if (globaldata->Estimators[i] == "thetan") { - matrixCalculators.push_back(new ThetaN()); - }else if (globaldata->Estimators[i] == "morisitahorn") { - matrixCalculators.push_back(new MorHorn()); - }else if (globaldata->Estimators[i] == "braycurtis") { - matrixCalculators.push_back(new BrayCurtis()); + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + label = validParameter.validFile(parameters, "label", false); + if (label == "not found") { label = ""; } + else { + if(label != "all") { splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + } + + //if the user has not specified any labels use the ones from read.otu + if (label == "") { + allLines = globaldata->allLines; + labels = globaldata->labels; + } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + splitAtDash(groups, Groups); + globaldata->Groups = Groups; + } + + calc = validParameter.validFile(parameters, "calc", false); + if (calc == "not found") { calc = "jclass-thetayc"; } + else { + if (calc == "default") { calc = "jclass-thetayc"; } + } + splitAtDash(calc, Estimators); + + if (abort == false) { + + validCalculator = new ValidCalculators(); + + int i; + for (i=0; iisValidCalculator("matrix", Estimators[i]) == true) { + if (Estimators[i] == "jabund") { + matrixCalculators.push_back(new JAbund()); + }else if (Estimators[i] == "sorabund") { + matrixCalculators.push_back(new SorAbund()); + }else if (Estimators[i] == "jclass") { + matrixCalculators.push_back(new Jclass()); + }else if (Estimators[i] == "sorclass") { + matrixCalculators.push_back(new SorClass()); + }else if (Estimators[i] == "jest") { + matrixCalculators.push_back(new Jest()); + }else if (Estimators[i] == "sorest") { + matrixCalculators.push_back(new SorEst()); + }else if (Estimators[i] == "thetayc") { + matrixCalculators.push_back(new ThetaYC()); + }else if (Estimators[i] == "thetan") { + matrixCalculators.push_back(new ThetaN()); + }else if (Estimators[i] == "morisitahorn") { + matrixCalculators.push_back(new MorHorn()); + }else if (Estimators[i] == "braycurtis") { + matrixCalculators.push_back(new BrayCurtis()); + } + } } + } } - //reset calc for next command - globaldata->setCalc(""); - } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function MatrixOutputCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the MatrixOutputCommand class function MatrixOutputCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} + +//********************************************************************************************************************** + +void MatrixOutputCommand::help(){ + try { + mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n"); + mothurOut("The dist.shared command parameters are groups, calc and label. No parameters are required.\n"); + mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n"); + mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n"); + mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n"); + mothurOut("Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n"); + mothurOut("The default value for groups is all the groups in your groupfile.\n"); + mothurOut("The default value for calc is jclass and thetayc.\n"); + validCalculator->printCalc("matrix", cout); + mothurOut("The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n"); + mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); + } + catch(exception& e) { + errorOut(e, "MatrixOutputCommand", "help"); exit(1); - } + } } + + //********************************************************************************************************************** MatrixOutputCommand::~MatrixOutputCommand(){ - delete input; - delete read; + if (abort == false) { + delete input; globaldata->ginput = NULL; + delete read; + delete validCalculator; + } } //********************************************************************************************************************** int MatrixOutputCommand::execute(){ try { - int count = 1; - + + if (abort == true) { return 0; } + //if the users entered no valid calculators don't execute command - if (matrixCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; } + if (matrixCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; } //you have groups read = new ReadOTUFile(globaldata->inputFileName); @@ -89,81 +180,83 @@ int MatrixOutputCommand::execute(){ input = globaldata->ginput; lookup = input->getSharedRAbundVectors(); - vector lastLookup = lookup; + string lastLabel = lookup[0]->getLabel(); //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set processedLabels; - set userLabels = globaldata->labels; - set userLines = globaldata->lines; - - if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0;} + set userLabels = labels; + + if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups. I cannot run the command."); mothurOutEndLine(); return 0;} - numGroups = globaldata->Groups.size(); + numGroups = lookup.size(); //as long as you are not at the end of the file or done wih the lines you want - while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){ - cout << lookup[0]->getLabel() << '\t' << count << endl; + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); process(lookup); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); - userLines.erase(count); } - if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) { - cout << lastLookup[0]->getLabel() << '\t' << count << endl; - process(lastLookup); + if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); - processedLabels.insert(lastLookup[0]->getLabel()); - userLabels.erase(lastLookup[0]->getLabel()); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(lastLabel); + + mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); + process(lookup); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); } - //prevent memory leak - if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } } - lastLookup = lookup; + lastLabel = lookup[0]->getLabel(); //get next line to process + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(); - count++; } //output error messages about any remaining user labels 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(lastLookup[0]->getLabel()) != 1) { - cout << ". I will use " << lastLookup[0]->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 " << lastLookup[0]->getLabel() << "." << endl; + mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); } } - //run last line if you need to + //run last label if you need to if (needToRun == true) { - cout << lastLookup[0]->getLabel() << '\t' << count << endl; - process(lastLookup); - } - - for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input->getSharedRAbundVectors(lastLabel); + mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); + process(lookup); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + } + //reset groups parameter - globaldata->Groups.clear(); globaldata->setGroups(""); + globaldata->Groups.clear(); return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "MatrixOutputCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the MatrixOutputCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /***********************************************************/ void MatrixOutputCommand::printSims(ostream& out) { @@ -182,13 +275,9 @@ void MatrixOutputCommand::printSims(ostream& out) { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "MatrixOutputCommand", "printSims"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the MatrixOutputCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /***********************************************************/ void MatrixOutputCommand::process(vector thisLookup){ @@ -226,7 +315,7 @@ void MatrixOutputCommand::process(vector thisLookup){ } } - exportFileName = getRootName(globaldata->inputFileName) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist"; + exportFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist"; openOutputFile(exportFileName, out); printSims(out); out.close(); @@ -237,13 +326,9 @@ void MatrixOutputCommand::process(vector thisLookup){ } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "MatrixOutputCommand", "process"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the MatrixOutputCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /***********************************************************/