X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=b53e87dceb21cb87ec26e88828479808feddb69a;hb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;hp=66ef6ddf24d6132bd355663c3dbdd24d5662c18c;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp index 66ef6dd..b53e87d 100644 --- a/rarefactsharedcommand.cpp +++ b/rarefactsharedcommand.cpp @@ -13,99 +13,101 @@ //********************************************************************************************************************** -RareFactSharedCommand::RareFactSharedCommand(string option){ +RareFactSharedCommand::RareFactSharedCommand(string option) { try { globaldata = GlobalData::getInstance(); + abort = false; allLines = 1; - lines.clear(); labels.clear(); Estimators.clear(); - + Groups.clear(); + //allow user to run help if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; } else { //valid paramters for this command - string Array[] = {"iters","line","label","calc","groups"}; + string Array[] = {"iters","label","calc","groups", "jumble","outputdir","inputdir"}; 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->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() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); m->mothurOutEndLine(); abort = true; } + else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); m->mothurOutEndLine(); 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 } //check for optional parameter and set defaults // ...at some point should added some additional type checking... - 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; } else { allLines = 1; } } - //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 the user has not specified any line or labels use the ones from read.otu - else if((line == "") && (label == "")) { + //if the user has not specified any labels use the ones from read.otu + if(label == "") { allLines = globaldata->allLines; labels = globaldata->labels; - lines = globaldata->lines; } - calc = validParameter->validFile(parameters, "calc", false); + calc = validParameter.validFile(parameters, "calc", false); if (calc == "not found") { calc = "sharedobserved"; } else { if (calc == "default") { calc = "sharedobserved"; } } splitAtDash(calc, Estimators); - groups = validParameter->validFile(parameters, "groups", false); + groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { splitAtDash(groups, Groups); - globaldata->Groups = Groups; } + globaldata->Groups = Groups; string temp; - temp = validParameter->validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } + temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } convert(temp, nIters); - delete validParameter; + temp = validParameter.validFile(parameters, "jumble", false); if (temp == "not found") { temp = "T"; } + if (isTrue(temp)) { jumble = true; } + else { jumble = false; } + globaldata->jumble = jumble; if (abort == false) { - string fileNameRoot = getRootName(globaldata->inputFileName); - format = globaldata->getFormat(); - int i; + string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName)); +// format = globaldata->getFormat(); + validCalculator = new ValidCalculators(); - for (i=0; iisValidCalculator("sharedrarefaction", Estimators[i]) == true) { if (Estimators[i] == "sharedobserved") { rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", ""))); + outputNames.push_back(fileNameRoot+"shared.rarefaction"); }else if (Estimators[i] == "sharednseqs") { rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", ""))); + outputNames.push_back(fileNameRoot+"shared.r_nseqs"); } } } @@ -115,49 +117,41 @@ 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"; + m->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"; + m->mothurOut("The rarefaction.shared command can only be executed after a successful read.otu command.\n"); + m->mothurOut("The rarefaction.shared command parameters are label, iters, groups, jumble and calc. No parameters are required.\n"); + m->mothurOut("The rarefaction command should be in the following format: \n"); + m->mothurOut("rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n"); + m->mothurOut("Example rarefaction.shared(label=unique-0.01-0.03, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n"); + m->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"); + m->mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\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"; + m->mothurOut("The label parameter is used to analyze specific labels in your input.\n"); + m->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"); + m->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"; + m->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); - } } //********************************************************************************************************************** RareFactSharedCommand::~RareFactSharedCommand(){ - delete input; - delete rCurve; - delete read; - delete validCalculator; + if (abort == false) { + delete input; globaldata->ginput = NULL; + delete read; + delete validCalculator; + } } //********************************************************************************************************************** @@ -167,8 +161,6 @@ int RareFactSharedCommand::execute(){ if (abort == true) { return 0; } - int count = 1; - //if the users entered no valid calculators don't execute command if (rDisplays.size() == 0) { return 0; } @@ -177,10 +169,10 @@ int RareFactSharedCommand::execute(){ input = globaldata->ginput; lookup = input->getSharedRAbundVectors(); - vector lastLookup = lookup; - + string lastLabel = lookup[0]->getLabel(); + if (lookup.size() < 2) { - cout << "I cannot run the command without at least 2 valid groups."; + m->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; } @@ -188,80 +180,88 @@ int RareFactSharedCommand::execute(){ //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 = labels; - set userLines = lines; //as long as you are not at the end of the file or done wih the lines you want - while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){ + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ rCurve = new Rarefact(lookup, rDisplays); rCurve->getSharedCurve(freq, nIters); delete rCurve; - cout << lookup[0]->getLabel() << '\t' << count << endl; + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); 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; - rCurve = new Rarefact(lastLookup, rDisplays); + if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + rCurve = new Rarefact(lookup, rDisplays); rCurve->getSharedCurve(freq, nIters); delete rCurve; - processedLabels.insert(lastLookup[0]->getLabel()); - userLabels.erase(lastLookup[0]->getLabel()); + 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; + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl; + m->mothurOut(". Please refer to " + lastLabel + "."); m->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; - rCurve = new Rarefact(lastLookup, rDisplays); + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input->getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + rCurve = new Rarefact(lookup, rDisplays); rCurve->getSharedCurve(freq, nIters); delete rCurve; + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } } - for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } - for(int i=0;iGroups.clear(); + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); 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"; + m->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); - } }