X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlistcountcommand.cpp;fp=getlistcountcommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=980c886cc0cb79f51f892ee13fe4dc2c3061b812;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp deleted file mode 100644 index 980c886..0000000 --- a/getlistcountcommand.cpp +++ /dev/null @@ -1,270 +0,0 @@ -/* - * getlistcountcommand.cpp - * Mothur - * - * Created by westcott on 10/12/09. - * Copyright 2009 Schloss Lab. All rights reserved. - * - */ - -#include "getlistcountcommand.h" - -//********************************************************************************************************************** -vector GetListCountCommand::setParameters(){ - try { - 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", "setParameters"); - exit(1); - } -} -//********************************************************************************************************************** -string GetListCountCommand::getHelpString(){ - try { - 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"; - return helpString; - } - catch(exception& e) { - m->errorOut(e, "GetListCountCommand", "getHelpString"); - exit(1); - } -} -//********************************************************************************************************************** -GetListCountCommand::GetListCountCommand(){ - try { - abort = true; calledHelp = true; - setParameters(); - vector tempOutNames; - outputTypes["otu"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "GetListCountCommand", "GetListCountCommand"); - exit(1); - } -} -//********************************************************************************************************************** -GetListCountCommand::GetListCountCommand(string option) { - try { - abort = false; calledHelp = false; - allLines = 1; - - //allow user to run help - if(option == "help") { help(); abort = true; calledHelp = true; } - else if(option == "citation") { citation(); abort = true; calledHelp = true;} - - else { - vector myArray = setParameters(); - - OptionParser parser(option); - map parameters = parser.getParameters(); - - ValidParameters validParameter; - map::iterator it; - - //check to make sure all parameters are valid for command - for (it = parameters.begin(); it != parameters.end(); it++) { - if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } - } - - //initialize outputTypes - vector tempOutNames; - outputTypes["otu"] = 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("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 = ""; } - - //check for required parameters - listfile = validParameter.validFile(parameters, "list", true); - 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 { m->setListFile(listfile); } - - - //check for optional parameter and set defaults - // ...at some point should added some additional type checking... - sort = validParameter.validFile(parameters, "sort", false); if (sort == "not found") { sort = "otu"; } - if ((sort != "otu") && (sort != "name")) { m->mothurOut( sort + " is not a valid sort option. Options are otu and name. I will use otu."); m->mothurOutEndLine(); sort = "otu"; } - - label = validParameter.validFile(parameters, "label", false); - if (label == "not found") { label = ""; } - else { - if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } - else { allLines = 1; } - } - } - } - catch(exception& e) { - m->errorOut(e, "GetListCountCommand", "GetListCountCommand"); - exit(1); - } -} -//********************************************************************************************************************** - -int GetListCountCommand::execute(){ - try { - if (abort == true) { if (calledHelp) { return 0; } return 2; } - - 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 input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - - if(allLines == 1 || labels.count(list->getLabel()) == 1){ - - process(list); - - if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - processedLabels.insert(list->getLabel()); - userLabels.erase(list->getLabel()); - } - - if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { - string saveLabel = list->getLabel(); - - delete list; - list = input->getListVector(lastLabel); - - process(list); - - if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - - processedLabels.insert(list->getLabel()); - userLabels.erase(list->getLabel()); - - //restore real lastlabel to save below - list->setLabel(saveLabel); - } - - lastLabel = list->getLabel(); - - delete list; - list = input->getListVector(); - } - - - //output error messages about any remaining user labels - set::iterator it; - bool needToRun = false; - for (it = userLabels.begin(); it != userLabels.end(); it++) { - m->mothurOut("Your file does not include the label " + *it); - if (processedLabels.count(lastLabel) != 1) { - m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); - needToRun = true; - }else { - m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); - } - } - - //run last label if you need to - if (needToRun == true) { - if (list != NULL) { delete list; } - list = input->getListVector(lastLabel); - - process(list); - - if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - delete list; - } - - delete input; - - 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) { - m->errorOut(e, "GetListCountCommand", "execute"); - exit(1); - } -} - -//********************************************************************************************************************** -//return 1 if error, 0 otherwise -void GetListCountCommand::process(ListVector* list) { - try { - string binnames; - if (outputDir == "") { outputDir += m->hasPath(listfile); } - string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu"; - m->openOutputFile(outputFileName, out); - outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName); - - m->mothurOut(list->getLabel()); m->mothurOutEndLine(); - - //for each bin in the list vector - for (int i = 0; i < list->getNumBins(); i++) { - if (m->control_pressed) { break; } - - binnames = list->get(i); - - if (sort == "otu") { - out << i+1 << '\t' << binnames << endl; - }else{ //sort = name - vector names; - m->splitAtComma(binnames, names); - - for (int j = 0; j < names.size(); j++) { - out << names[j] << '\t' << i+1 << endl; - } - } - } - - out.close(); - } - catch(exception& e) { - m->errorOut(e, "GetListCountCommand", "process"); - exit(1); - } -} -//********************************************************************************************************************** - -