X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=fb5527a03faa02c913e48a583e0a32705932ec45;hb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;hp=0be8141636a1fffaacce16f2592e6bf8738ad400;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp index 0be8141..fb5527a 100644 --- a/rarefactsharedcommand.cpp +++ b/rarefactsharedcommand.cpp @@ -12,50 +12,63 @@ #include "sharednseqs.h" //********************************************************************************************************************** -vector RareFactSharedCommand::getValidParameters(){ +vector RareFactSharedCommand::setParameters(){ try { - string Array[] = {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + 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); + + 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", "getValidParameters"); - exit(1); - } -} -//********************************************************************************************************************** -RareFactSharedCommand::RareFactSharedCommand(){ - try { - //initialize outputTypes - vector tempOutNames; - outputTypes["sharedrarefaction"] = tempOutNames; - outputTypes["sharedr_nseqs"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); + m->errorOut(e, "RareFactSharedCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector RareFactSharedCommand::getRequiredParameters(){ +string RareFactSharedCommand::getHelpString(){ try { - vector myArray; - return myArray; + 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", "getRequiredParameters"); + m->errorOut(e, "RareFactSharedCommand", "getHelpString"); exit(1); } } + //********************************************************************************************************************** -vector RareFactSharedCommand::getRequiredFiles(){ +RareFactSharedCommand::RareFactSharedCommand(){ try { - string Array[] = {"shared"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["sharedrarefaction"] = tempOutNames; + outputTypes["sharedr_nseqs"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "RareFactSharedCommand", "getRequiredFiles"); + m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand"); exit(1); } } @@ -63,29 +76,23 @@ vector RareFactSharedCommand::getRequiredFiles(){ 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") { help(); abort = true; calledHelp = true; } else { - //valid paramters for this command - string Array[] = {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"}; - 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; } } @@ -94,18 +101,34 @@ RareFactSharedCommand::RareFactSharedCommand(string option) { outputTypes["sharedrarefaction"] = tempOutNames; outputTypes["sharedr_nseqs"] = tempOutNames; - //make sure the user has already run the read.otu command - if (globaldata->getSharedFile() == "") { - 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 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; } + } + } + + //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 = ""; - outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it - } - + 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... @@ -116,11 +139,6 @@ RareFactSharedCommand::RareFactSharedCommand(string option) { 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; - } calc = validParameter.validFile(parameters, "calc", false); if (calc == "not found") { calc = "sharedobserved"; } @@ -134,7 +152,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option) { else { m->splitAtDash(groups, Groups); } - globaldata->Groups = Groups; + m->Groups = Groups; string temp; temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; } @@ -146,28 +164,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option) { temp = validParameter.validFile(parameters, "jumble", false); if (temp == "not found") { temp = "T"; } if (m->isTrue(temp)) { jumble = true; } else { jumble = false; } - globaldata->jumble = jumble; - - if (abort == false) { - - string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(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", ""))); - 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"); - } - } - } - } + m->jumble = jumble; } @@ -177,59 +174,39 @@ RareFactSharedCommand::RareFactSharedCommand(string option) { exit(1); } } - -//********************************************************************************************************************** - -void RareFactSharedCommand::help(){ - try { - 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); - 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) { - m->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)); + + 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) { - globaldata->Groups.clear(); + m->Groups.clear(); + delete input; for(int i=0;icontrol_pressed) { - globaldata->Groups.clear(); + m->Groups.clear(); + delete input; for(int i=0;icontrol_pressed) { - globaldata->Groups.clear(); - for(int i=0;iGroups.clear(); + delete input; + for(int i=0;icontrol_pressed) { - globaldata->Groups.clear(); - for(int i=0;iGroups.clear(); + delete input; + 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; - } + 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();