X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=ea460c026e4c4ea77684893920b328288d3f9f63;hb=c3396974063d6efc5e5850ddf4ed8ab65cc94bb9;hp=83fb35ed883fbb748d8cb5a6191aa136c692ae06;hpb=72ebb6fa35b45b149812d47c2b1cb8acaca64659;p=mothur.git diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp index 83fb35e..ea460c0 100644 --- a/rarefactsharedcommand.cpp +++ b/rarefactsharedcommand.cpp @@ -11,24 +11,72 @@ #include "sharedsobs.h" #include "sharednseqs.h" +//********************************************************************************************************************** +vector RareFactSharedCommand::getValidParameters(){ + try { + string Array[] = {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "RareFactSharedCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +RareFactSharedCommand::RareFactSharedCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["sharedrarefaction"] = tempOutNames; + outputTypes["sharedr_nseqs"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector RareFactSharedCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "RareFactSharedCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector RareFactSharedCommand::getRequiredFiles(){ + try { + string Array[] = {"shared"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "RareFactSharedCommand", "getRequiredFiles"); + exit(1); + } +} //********************************************************************************************************************** -RareFactSharedCommand::RareFactSharedCommand(string option){ +RareFactSharedCommand::RareFactSharedCommand(string option) { try { globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; labels.clear(); Estimators.clear(); Groups.clear(); //allow user to run help - if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; } + if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; } else { //valid paramters for this command - string Array[] = {"iters","label","calc","groups", "jumble"}; + string Array[] = {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -41,10 +89,21 @@ RareFactSharedCommand::RareFactSharedCommand(string option){ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["sharedrarefaction"] = tempOutNames; + outputTypes["sharedr_nseqs"] = tempOutNames; + //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 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; } + 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 += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it } @@ -53,7 +112,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option){ 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; } } @@ -68,27 +127,30 @@ RareFactSharedCommand::RareFactSharedCommand(string option){ 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; 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); temp = validParameter.validFile(parameters, "jumble", false); if (temp == "not found") { temp = "T"; } - if (isTrue(temp)) { jumble = true; } + if (m->isTrue(temp)) { jumble = true; } else { jumble = false; } globaldata->jumble = jumble; if (abort == false) { - string fileNameRoot = getRootName(globaldata->inputFileName); + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)); // format = globaldata->getFormat(); @@ -98,8 +160,10 @@ RareFactSharedCommand::RareFactSharedCommand(string option){ if (validCalculator->isValidCalculator("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"); outputTypes["sharedrarefaction"].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"); outputTypes["sharedr_nseqs"].push_back(fileNameRoot+"shared.r_nseqs"); } } } @@ -109,7 +173,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option){ } catch(exception& e) { - errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); + m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); exit(1); } } @@ -118,20 +182,21 @@ RareFactSharedCommand::RareFactSharedCommand(string option){ void RareFactSharedCommand::help(){ try { - mothurOut("The rarefaction.shared command can only be executed after a successful read.otu command.\n"); - mothurOut("The rarefaction.shared command parameters are label, iters, groups, jumble and calc. No parameters are required.\n"); - mothurOut("The rarefaction command should be in the following format: \n"); - mothurOut("rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n"); - mothurOut("Example rarefaction.shared(label=unique-0.01-0.03, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n"); - 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"); - mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\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("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"); + 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); - mothurOut("The label parameter is used to analyze specific labels 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. 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) { - errorOut(e, "RareFactSharedCommand", "help"); + m->errorOut(e, "RareFactSharedCommand", "help"); exit(1); } } @@ -151,7 +216,7 @@ RareFactSharedCommand::~RareFactSharedCommand(){ int RareFactSharedCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } //if the users entered no valid calculators don't execute command if (rDisplays.size() == 0) { return 0; } @@ -162,9 +227,18 @@ int RareFactSharedCommand::execute(){ input = globaldata->ginput; lookup = input->getSharedRAbundVectors(); string lastLabel = lookup[0]->getLabel(); + + if (m->control_pressed) { + globaldata->Groups.clear(); + 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; } @@ -175,25 +249,31 @@ int RareFactSharedCommand::execute(){ //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))) { + if (m->control_pressed) { + globaldata->Groups.clear(); + for(int i=0;igetLabel()) == 1){ - + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); rCurve = new Rarefact(lookup, rDisplays); rCurve->getSharedCurve(freq, nIters); delete rCurve; - mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); } - if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + 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); - mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); rCurve = new Rarefact(lookup, rDisplays); rCurve->getSharedCurve(freq, nIters); delete rCurve; @@ -213,25 +293,39 @@ int RareFactSharedCommand::execute(){ lookup = input->getSharedRAbundVectors(); } + if (m->control_pressed) { + globaldata->Groups.clear(); + for(int i=0;i::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - mothurOut("Your file does not include the label " + *it); + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } + if (m->control_pressed) { + globaldata->Groups.clear(); + for(int i=0;igetSharedRAbundVectors(lastLabel); - mothurOut(lookup[0]->getLabel()); mothurOutEndLine(); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); rCurve = new Rarefact(lookup, rDisplays); rCurve->getSharedCurve(freq, nIters); delete rCurve; @@ -242,11 +336,21 @@ int RareFactSharedCommand::execute(){ //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) { - errorOut(e, "RareFactSharedCommand", "execute"); + m->errorOut(e, "RareFactSharedCommand", "execute"); exit(1); } }