X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlistcountcommand.cpp;fp=getlistcountcommand.cpp;h=404d35379730d3e3859a87654e795739f3f9b5cf;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=78f26047e0debdf3e620b2e0179bfab12fe93354;hpb=36a867cbd85d9c276d3c8d13f25a150bbbe2466b;p=mothur.git diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp index 78f2604..404d353 100644 --- a/getlistcountcommand.cpp +++ b/getlistcountcommand.cpp @@ -10,67 +10,68 @@ #include "getlistcountcommand.h" //********************************************************************************************************************** -vector GetListCountCommand::getValidParameters(){ +vector GetListCountCommand::setParameters(){ try { - string Array[] = {"list","label","sort","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "",false,false); parameters.push_back(parasort); + 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, "GetListCountCommand", "getValidParameters"); - exit(1); - } -} -//********************************************************************************************************************** -GetListCountCommand::GetListCountCommand(){ - try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["otu"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "GetListCountCommand", "GetListCountCommand"); + m->errorOut(e, "GetListCountCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector GetListCountCommand::getRequiredParameters(){ +string GetListCountCommand::getHelpString(){ try { - string Array[] = {"list"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + string helpString = ""; + helpString += "The get.otulist command parameters are list, sort and label. list is required, unless you have a valid current list file.\n"; + helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n"; + helpString += "The sort parameter allows you to select how you want the output displayed. Options are otu and name.\n"; + helpString += "If otu is selected the output will be otu number followed by the list of names in that otu.\n"; + helpString += "If name is selected the output will be a sequence name followed by its otu number.\n"; + helpString += "The get.otulist command should be in the following format: get.otulist(list=yourlistFile, label=yourLabels).\n"; + helpString += "Example get.otulist(list=amazon.fn.list, label=0.10).\n"; + helpString += "The default value for label is all lines in your inputfile.\n"; + helpString += "The get.otulist command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n"; + helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "GetListCountCommand", "getRequiredParameters"); + m->errorOut(e, "GetListCountCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector GetListCountCommand::getRequiredFiles(){ +GetListCountCommand::GetListCountCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["otu"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "GetListCountCommand", "getRequiredFiles"); + m->errorOut(e, "GetListCountCommand", "GetListCountCommand"); exit(1); } } //********************************************************************************************************************** GetListCountCommand::GetListCountCommand(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 { - //valid paramters for this command - string AlignArray[] = {"list","label","sort","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -86,8 +87,6 @@ GetListCountCommand::GetListCountCommand(string option) { //initialize outputTypes vector tempOutNames; outputTypes["otu"] = tempOutNames; - - string ranRead = globaldata->getListFile(); //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); @@ -108,10 +107,13 @@ GetListCountCommand::GetListCountCommand(string option) { //check for required parameters listfile = validParameter.validFile(parameters, "list", true); - if ((listfile == "not found") && (globaldata->getListFile() == "")) { m->mothurOut("You must read a listfile before running the get.listcount command."); m->mothurOutEndLine(); abort = true; } - else if ((listfile == "not found") && (globaldata->getListFile() != "")) { listfile = globaldata->getListFile(); } + if (listfile == "not found") { + listfile = m->getListFile(); + if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; } + } else if (listfile == "not open") { abort = true; } - else { globaldata->setListFile(listfile); } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... @@ -124,12 +126,6 @@ GetListCountCommand::GetListCountCommand(string option) { if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } - - //if the user has not specified any labels use the ones from read.otu - if ((label == "") && (ranRead != "")) { - allLines = globaldata->allLines; - labels = globaldata->labels; - } } } catch(exception& e) { @@ -139,58 +135,19 @@ GetListCountCommand::GetListCountCommand(string option) { } //********************************************************************************************************************** -void GetListCountCommand::help(){ - try { - m->mothurOut("The get.otulist command can only be executed after a successful read.otu command of a listfile or providing a list file using the list parameter.\n"); - m->mothurOut("The get.otulist command parameters are list, sort and label. No parameters are required.\n"); - m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n"); - m->mothurOut("The sort parameter allows you to select how you want the output displayed. Options are otu and name.\n"); - m->mothurOut("If otu is selected the output will be otu number followed by the list of names in that otu.\n"); - m->mothurOut("If name is selected the output will be a sequence name followed by its otu number.\n"); - m->mothurOut("The get.otulist command should be in the following format: get.otulist(list=yourlistFile, label=yourLabels).\n"); - m->mothurOut("Example get.otulist(list=amazon.fn.list, label=0.10).\n"); - m->mothurOut("The default value for label is all lines in your inputfile.\n"); - m->mothurOut("The get.otulist command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "GetListCountCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -GetListCountCommand::~GetListCountCommand(){} - -//********************************************************************************************************************** - int GetListCountCommand::execute(){ try { if (abort == true) { if (calledHelp) { return 0; } return 2; } - - globaldata->setFormat("list"); - - //read list file - read = new ReadOTUFile(listfile); - read->read(&*globaldata); - input = globaldata->ginput; - list = globaldata->gListVector; + input = new InputData(listfile, "list"); + list = input->getListVector(); string lastLabel = list->getLabel(); //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; - if (m->control_pressed) { - delete read; - delete input; - delete list; - globaldata->gListVector = NULL; - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } - return 0; - } + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { @@ -198,14 +155,7 @@ int GetListCountCommand::execute(){ process(list); - if (m->control_pressed) { - delete read; - delete input; - delete list; - globaldata->gListVector = NULL; - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); - return 0; - } + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); @@ -219,14 +169,8 @@ int GetListCountCommand::execute(){ process(list); - if (m->control_pressed) { - delete read; - delete input; - delete list; - globaldata->gListVector = NULL; - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); - return 0; - } + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); @@ -262,21 +206,12 @@ int GetListCountCommand::execute(){ process(list); - if (m->control_pressed) { - delete read; - delete input; - delete list; - globaldata->gListVector = NULL; - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); - return 0; - } + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } delete list; } - delete read; delete input; - globaldata->gListVector = NULL; m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine();