X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=fb5527a03faa02c913e48a583e0a32705932ec45;hb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;hp=6461b3bc22922af68cba684893eb00f76e35a598;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc;p=mothur.git diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp index 6461b3b..fb5527a 100644 --- a/rarefactsharedcommand.cpp +++ b/rarefactsharedcommand.cpp @@ -12,176 +12,210 @@ #include "sharednseqs.h" //********************************************************************************************************************** - -RareFactSharedCommand::RareFactSharedCommand(string option){ +vector RareFactSharedCommand::setParameters(){ try { - globaldata = GlobalData::getInstance(); + CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq); + CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters); + CommandParameter pcalc("calc", "Multiple", "sharednseqs-sharedobserved", "sharedobserved", "", "", "",true,false); parameters.push_back(pcalc); + CommandParameter pjumble("jumble", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pjumble); + CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); - abort = false; + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "RareFactSharedCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string RareFactSharedCommand::getHelpString(){ + try { + string helpString = ""; + ValidCalculators validCalculator; + helpString += "The collect.shared command parameters are shared, label, freq, calc and groups. shared is required if there is no current sharedfile. \n"; + helpString += "The rarefaction.shared command parameters are shared, label, iters, groups, jumble and calc. shared is required if there is no current sharedfile. \n"; + helpString += "The rarefaction command should be in the following format: \n"; + helpString += "rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n"; + helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n"; + helpString += "Example rarefaction.shared(label=unique-0.01-0.03, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n"; + helpString += "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"; + helpString += "The default value for groups is all the groups in your groupfile, and jumble is true.\n"; + helpString += validCalculator.printCalc("sharedrarefaction"); + helpString += "The label parameter is used to analyze specific labels in your input.\n"; + helpString += "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"; + helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "RareFactSharedCommand", "getHelpString"); + exit(1); + } +} + +//********************************************************************************************************************** +RareFactSharedCommand::RareFactSharedCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["sharedrarefaction"] = tempOutNames; + outputTypes["sharedr_nseqs"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +RareFactSharedCommand::RareFactSharedCommand(string option) { + try { + abort = false; calledHelp = 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; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { - //valid paramters for this command - string Array[] = {"iters","line","label","calc","groups"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); + map::iterator it; ValidParameters validParameter; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (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; } + //initialize outputTypes + vector tempOutNames; + outputTypes["sharedrarefaction"] = tempOutNames; + outputTypes["sharedr_nseqs"] = tempOutNames; + + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("shared"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["shared"] = inputDir + it->second; } + } } - - //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; } + //get shared file + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { + //if there is a current shared file, use it + sharedfile = m->getSharedFile(); + if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); 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 = m->hasPath(sharedfile); } + + + //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; } + if(label != "all") { m->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 == "")) { - allLines = globaldata->allLines; - labels = globaldata->labels; - lines = globaldata->lines; - } calc = validParameter.validFile(parameters, "calc", false); if (calc == "not found") { calc = "sharedobserved"; } else { if (calc == "default") { calc = "sharedobserved"; } } - splitAtDash(calc, Estimators); + m->splitAtDash(calc, Estimators); groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); } - globaldata->Groups = Groups; + m->Groups = Groups; string temp; + temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; } + convert(temp, freq); + temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } convert(temp, nIters); - if (abort == false) { - - string fileNameRoot = getRootName(globaldata->inputFileName); -// format = globaldata->getFormat(); - - - validCalculator = new ValidCalculators(); - - for (int i=0; iisValidCalculator("sharedrarefaction", Estimators[i]) == true) { - if (Estimators[i] == "sharedobserved") { - rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", ""))); - }else if (Estimators[i] == "sharednseqs") { - rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", ""))); - } - } - } - } + temp = validParameter.validFile(parameters, "jumble", false); if (temp == "not found") { temp = "T"; } + if (m->isTrue(temp)) { jumble = true; } + else { jumble = false; } + m->jumble = jumble; } } 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"; - 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"; - } - 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"; - 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(){ - if (abort == false) { - delete input; globaldata->ginput = NULL; - delete read; - delete validCalculator; - } -} - //********************************************************************************************************************** int RareFactSharedCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile)); - int count = 1; + ValidCalculators validCalculator; + + for (int i=0; iinputFileName); - read->read(&*globaldata); - input = globaldata->ginput; + input = new InputData(sharedfile, "sharedfile"); lookup = input->getSharedRAbundVectors(); - vector lastLookup = lookup; + string lastLabel = lookup[0]->getLabel(); + + if (m->control_pressed) { + m->Groups.clear(); + delete input; + for(int i=0;imothurOut("I cannot run the command without at least 2 valid groups."); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; } @@ -189,80 +223,112 @@ 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 (m->control_pressed) { + m->Groups.clear(); + delete input; + for(int i=0;igetLabel()) == 1){ - + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); rCurve = new Rarefact(lookup, rDisplays); rCurve->getSharedCurve(freq, nIters); delete rCurve; - cout << lookup[0]->getLabel() << '\t' << count << endl; 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 ((m->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++; + } + + if (m->control_pressed) { + m->Groups.clear(); + delete input; + for(int i=0;i::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 + if (m->control_pressed) { + m->Groups.clear(); + delete input; + for(int i=0;igetLabel() << '\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(); + delete input; - //reset groups parameter - globaldata->Groups.clear(); + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + + 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); - } }