X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=fe92f97038eea51cd87a05608bad0e2525070c58;hb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;hp=71bfaf1d0f79b4866cebe71309e058a61bd2535e;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp index 71bfaf1..fe92f97 100644 --- a/rarefactsharedcommand.cpp +++ b/rarefactsharedcommand.cpp @@ -12,167 +12,216 @@ #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 if(option == "citation") { citation(); 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() == "") { 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; } + //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 != "")) { 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; - 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); + if (m->inUsersGroups("citation", Estimators)) { + ValidCalculators validCalc; validCalc.printCitations(Estimators); + //remove citation from list of calcs + for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } } + } 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) { - errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); + m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); exit(1); } } - -//********************************************************************************************************************** - -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, line, iters, groups and calc. No parameters are required, but you may not use \n"); - mothurOut("both the line and label parameters at the same time. The rarefaction command should be in the following format: \n"); - mothurOut("rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, calc=yourEstimators, groups=yourGroups).\n"); - mothurOut("Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, groups=B-C, 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.\n"); - validCalculator->printCalc("sharedrarefaction", cout); - 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. freq), '=' and parameters (i.e.yourFreq).\n\n"); - } - catch(exception& e) { - errorOut(e, "RareFactSharedCommand", "help"); - 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(); 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; } @@ -180,34 +229,44 @@ 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; - mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); - userLines.erase(count); } - 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() + "\t" + toString(count)); mothurOutEndLine(); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); rCurve = new Rarefact(lookup, rDisplays); rCurve->getSharedCurve(freq, nIters); delete rCurve; processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); } @@ -216,28 +275,43 @@ int RareFactSharedCommand::execute(){ //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++) { - 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(); } } - //run last line if you need to + if (m->control_pressed) { + m->Groups.clear(); + delete input; + for(int i=0;igetSharedRAbundVectors(lastLabel); - mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); rCurve = new Rarefact(lookup, rDisplays); rCurve->getSharedCurve(freq, nIters); delete rCurve; @@ -245,14 +319,20 @@ int RareFactSharedCommand::execute(){ } for(int i=0;iGroups.clear(); + delete input; + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } - //reset groups parameter - globaldata->Groups.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) { - errorOut(e, "RareFactSharedCommand", "execute"); + m->errorOut(e, "RareFactSharedCommand", "execute"); exit(1); } }