X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=venncommand.cpp;h=98796b3466fcc344b5e4c990015316a5ae2a0582;hp=5cc0fea3affdfa6d021ff93bef964f478400f5bc;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18 diff --git a/venncommand.cpp b/venncommand.cpp index 5cc0fea..98796b3 100644 --- a/venncommand.cpp +++ b/venncommand.cpp @@ -17,51 +17,83 @@ #include "sharedace.h" #include "nseqs.h" - //********************************************************************************************************************** -vector VennCommand::getValidParameters(){ +vector VennCommand::setParameters(){ try { - string Array[] = {"groups","label","calc","permute", "abund","nseqs","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist); + CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pcalc("calc", "String", "", "", "", "", "","",false,false); parameters.push_back(pcalc); + CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund); + CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnseqs); + CommandParameter psharedotus("sharedotus", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(psharedotus); + CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize); + CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppermute); + 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, "VennCommand", "getValidParameters"); + m->errorOut(e, "VennCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -VennCommand::VennCommand(){ +string VennCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["svg"] = tempOutNames; + string helpString = ""; + helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, sharedotus, fontsize and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n"; + helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n"; + helpString += "The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n"; + helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n"; + helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n"; + helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n"; + helpString += "The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n"; + helpString += "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n"; + helpString += "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a shared file.\n"; + helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n"; + helpString += "If you have more than 4 groups, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\n"; + helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n"; + helpString += "The sharedotus parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=t.\n"; + helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n"; + helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "VennCommand", "VennCommand"); + m->errorOut(e, "VennCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector VennCommand::getRequiredParameters(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "VennCommand", "getRequiredParameters"); - exit(1); - } +string VennCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "svg") { pattern = "[filename],svg"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "VennCommand", "getOutputPattern"); + exit(1); + } } + //********************************************************************************************************************** -vector VennCommand::getRequiredFiles(){ +VennCommand::VennCommand(){ try { - string Array[] = {"list","shared","or"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["svg"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "VennCommand", "getRequiredFiles"); + m->errorOut(e, "VennCommand", "VennCommand"); exit(1); } } @@ -69,21 +101,19 @@ vector VennCommand::getRequiredFiles(){ VennCommand::VennCommand(string option) { try { - globaldata = GlobalData::getInstance(); abort = false; calledHelp = false; allLines = 1; - labels.clear(); //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string AlignArray[] = {"groups","label","calc","permute", "abund","nseqs","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); + map::iterator it; ValidParameters validParameter; @@ -92,16 +122,57 @@ VennCommand::VennCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - //make sure the user has already run the read.otu command - if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) { - m->mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn 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; } + } + + it = parameters.find("list"); + //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["list"] = inputDir + it->second; } + } } - //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 + //check for required parameters + listfile = validParameter.validFile(parameters, "list", true); + if (listfile == "not open") { listfile = ""; abort = true; } + else if (listfile == "not found") { listfile = ""; } + else { format = "list"; inputfile = listfile; m->setListFile(listfile); } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); } + + if ((sharedfile == "") && (listfile == "")) { + //is there are current file available for any of these? + //give priority to shared, then list, then rabund, then sabund + //if there is a current shared file, use it + sharedfile = m->getSharedFile(); + if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { + listfile = m->getListFile(); + if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a list or shared file."); 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(inputfile); } //check for optional parameter and set defaults // ...at some point should added some additional type checking... @@ -112,20 +183,13 @@ VennCommand::VennCommand(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; - } - groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { m->splitAtDash(groups, Groups); - globaldata->Groups = Groups; + m->setGroups(Groups); } - format = globaldata->getFormat(); calc = validParameter.validFile(parameters, "calc", false); if (calc == "not found") { if(format == "list") { calc = "sobs"; } @@ -138,58 +202,29 @@ VennCommand::VennCommand(string option) { } } 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; } } + } string temp; temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; } - convert(temp, abund); + m->mothurConvert(temp, abund); temp = validParameter.validFile(parameters, "nseqs", false); if (temp == "not found"){ temp = "f"; } nseqs = m->isTrue(temp); - temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; } + temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; } perm = m->isTrue(temp); - - if (abort == false) { - validCalculator = new ValidCalculators(); - - int i; - - if (format == "list") { - for (i=0; iisValidCalculator("vennsingle", Estimators[i]) == true) { - if (Estimators[i] == "sobs") { - vennCalculators.push_back(new Sobs()); - }else if (Estimators[i] == "chao") { - vennCalculators.push_back(new Chao1()); - }else if (Estimators[i] == "ace") { - if(abund < 5) - abund = 10; - vennCalculators.push_back(new Ace(abund)); - } - } - } - }else { - for (i=0; iisValidCalculator("vennshared", Estimators[i]) == true) { - if (Estimators[i] == "sharedsobs") { - vennCalculators.push_back(new SharedSobsCS()); - }else if (Estimators[i] == "sharedchao") { - vennCalculators.push_back(new SharedChao1()); - }else if (Estimators[i] == "sharedace") { - vennCalculators.push_back(new SharedAce()); - } - } - } - } - - //if the users entered no valid calculators don't execute command - if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); abort = true; } - else { venn = new Venn(outputDir, nseqs); } - } + + temp = validParameter.validFile(parameters, "sharedotus", false); if (temp == "not found"){ temp = "t"; } + sharedOtus = m->isTrue(temp); - } + temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; } + m->mothurConvert(temp, fontsize); - + } } catch(exception& e) { @@ -197,73 +232,58 @@ VennCommand::VennCommand(string option) { exit(1); } } - -//********************************************************************************************************************** - -void VennCommand::help(){ - try { - m->mothurOut("The venn command can only be executed after a successful read.otu command.\n"); - m->mothurOut("The venn command parameters are groups, calc, abund, nseqs, permute and label. No parameters are required.\n"); - m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n"); - m->mothurOut("The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n"); - m->mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n"); - m->mothurOut("Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n"); - m->mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n"); - m->mothurOut("The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n"); - m->mothurOut("The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file.\n"); - m->mothurOut("The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n"); - m->mothurOut("If you have more than 4 groups, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\n"); - m->mothurOut("The only estimators available four 4 groups are sharedsobs and sharedchao.\n"); - m->mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "VennCommand", "help"); - exit(1); - } -} - - -//********************************************************************************************************************** - -VennCommand::~VennCommand(){ - if (abort == false) { - delete input; globaldata->ginput = NULL; - delete read; - delete venn; - globaldata->sabund = NULL; - delete validCalculator; - } - -} - //********************************************************************************************************************** int VennCommand::execute(){ try { if (abort == true) { if (calledHelp) { return 0; } return 2; } + + ValidCalculators validCalculator; + + if (format == "list") { + for (int i=0; imothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0; } + + venn = new Venn(outputDir, nseqs, inputfile, fontsize, sharedOtus); + input = new InputData(inputfile, format); string lastLabel; if (format == "sharedfile") { - //you have groups - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; lookup = input->getSharedRAbundVectors(); lastLabel = lookup[0]->getLabel(); if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); } }else if (format == "list") { - //you are using just a list file and have only one group - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); - - sabund = globaldata->sabund; + sabund = input->getSAbundVector(); lastLabel = sabund->getLabel(); - input = globaldata->ginput; } //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. @@ -278,8 +298,8 @@ int VennCommand::execute(){ if (m->control_pressed) { for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } - globaldata->Groups.clear(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + m->clearGroups(); delete venn; delete input; + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } @@ -361,8 +381,8 @@ int VennCommand::execute(){ if (m->control_pressed) { for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } - globaldata->Groups.clear(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + m->clearGroups(); delete venn; delete input; + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } @@ -418,11 +438,12 @@ int VennCommand::execute(){ //reset groups parameter - globaldata->Groups.clear(); + m->clearGroups(); if (m->control_pressed) { + m->clearGroups(); delete venn; delete input; for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } @@ -433,8 +454,8 @@ int VennCommand::execute(){ if (m->control_pressed) { for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } - delete sabund; - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + delete sabund; delete venn; delete input; + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } @@ -475,7 +496,8 @@ int VennCommand::execute(){ if (m->control_pressed) { for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } + delete venn; delete input; return 0; } @@ -506,13 +528,15 @@ int VennCommand::execute(){ } if (m->control_pressed) { + delete venn; delete input; for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } } for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; } + delete venn; delete input; m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine();