X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.cpp;h=d5f5a8b8b8450deef538f564d59885b57647c430;hb=7439a3c94e96c9e0e78ca53f0356415a879f8b80;hp=c978bb19439db11e9fada887112ab708d7551fd2;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp index c978bb1..d5f5a8b 100644 --- a/getrabundcommand.cpp +++ b/getrabundcommand.cpp @@ -3,203 +3,295 @@ * Mothur * * Created by Sarah Westcott on 6/2/09. - * Copyright 2009 __MyCompanyName__. All rights reserved. + * Copyright 2009 Schloss Lab Umass Amherst. All rights reserved. * */ #include "getrabundcommand.h" //********************************************************************************************************************** +vector GetRAbundCommand::setParameters(){ + try { + CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(plist); + CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(psabund); + CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(psorted); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + 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, "GetRAbundCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string GetRAbundCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The get.rabund command parameters are list, sabund, label and sorted. list or sabund parameters are required, unless you have valid current files.\n"; + helpString += "The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n"; + helpString += "The sorted parameters allows you to print the rabund results sorted by abundance or not. The default is sorted.\n"; + helpString += "The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n"; + helpString += "Example get.rabund(sorted=F).\n"; + helpString += "The default value for label is all labels in your inputfile.\n"; + helpString += "The get.rabund command outputs a .rabund file containing the lines you selected.\n"; + helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "GetRAbundCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string GetRAbundCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "rabund") { pattern = "[filename],rabund"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "GetRAbundCommand", "getOutputPattern"); + exit(1); + } +} -GetRAbundCommand::GetRAbundCommand(string option){ +//********************************************************************************************************************** +GetRAbundCommand::GetRAbundCommand(){ try { - globaldata = GlobalData::getInstance(); - abort = false; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["rabund"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand"); + exit(1); + } +} +//********************************************************************************************************************** +GetRAbundCommand::GetRAbundCommand(string option) { + try { + abort = false; calledHelp = false; allLines = 1; - lines.clear(); - labels.clear(); //allow user to run help - if(option == "help") { 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[] = {"line","label"}; - 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->getListFile() == "") { cout << "You must read a listfile before you can use the get.rabund command." << endl; abort = true; } + //initialize outputTypes + vector tempOutNames; + outputTypes["rabund"] = 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; } + } + + it = parameters.find("sabund"); + //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["sabund"] = inputDir + it->second; } + } + } + + + //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); } + + sabundfile = validParameter.validFile(parameters, "sabund", true); + if (sabundfile == "not open") { sabundfile = ""; abort = true; } + else if (sabundfile == "not found") { sabundfile = ""; } + else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); } + //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; } - } + string temp; + temp = validParameter.validFile(parameters, "sorted", false); if (temp == "not found") { temp = "T"; } + sorted = m->isTrue(temp); 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 != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; 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; - } - - if (abort == false) { - filename = getRootName(globaldata->inputFileName) + "rabund"; - openOutputFile(filename, out); + if ((listfile == "") && (sabundfile == "")) { + //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 + listfile = m->getListFile(); + if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + sabundfile = m->getSabundFile(); + if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a list or sabund 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); } + } - - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GetRAbundCommand class Function GetRAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the GetRAbundCommand class function GetRAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} -//********************************************************************************************************************** -void GetRAbundCommand::help(){ - try { - cout << "The get.rabund command can only be executed after a successful read.otu of a listfile." << "\n"; - cout << "The get.rabund command parameters are line and label. No parameters are required, and you may not use line and label at the same time." << "\n"; - cout << "The line and label allow you to select what distance levels you would like included in your .rabund file, and are separated by dashes." << "\n"; - cout << "The get.rabund command should be in the following format: get.rabund(line=yourLines, label=yourLabels)." << "\n"; - cout << "Example get.rabund(line=1-3-5)." << "\n"; - cout << "The default value for line and label are all lines in your inputfile." << "\n"; - cout << "The get.rabund command outputs a .rabund file containing the lines you selected." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n"; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GetRAbundCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand"); exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the GetRAbundCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } + } } - -//********************************************************************************************************************** - -GetRAbundCommand::~GetRAbundCommand(){ -} - //********************************************************************************************************************** int GetRAbundCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } - int count = 1; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile)); + filename = getOutputFileName("rabund", variables); + m->openOutputFile(filename, out); - //read first line - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; - list = globaldata->gListVector; - ListVector* lastList = list; + input = new InputData(inputfile, format); + rabund = input->getRAbundVector(); + string lastLabel = rabund->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; - set userLines = lines; - - while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; delete input; return 0; } + + while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){ - cout << list->getLabel() << '\t' << count << endl; - rabund = new RAbundVector(); - *rabund = (list->getRAbundVector()); - rabund->print(out); - delete rabund; + if(allLines == 1 || labels.count(rabund->getLabel()) == 1){ + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); + + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; delete rabund; return 0; } + + if(sorted) { rabund->print(out); } + else { rabund->nonSortedPrint(out); } - processedLabels.insert(list->getLabel()); - userLabels.erase(list->getLabel()); - userLines.erase(count); + processedLabels.insert(rabund->getLabel()); + userLabels.erase(rabund->getLabel()); } - if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) { - cout << lastList->getLabel() << '\t' << count << endl; - rabund = new RAbundVector(); - *rabund = (lastList->getRAbundVector()); - rabund->print(out); + if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = rabund->getLabel(); + delete rabund; + rabund = input->getRAbundVector(lastLabel); + + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); + + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; delete rabund; return 0; } + + if(sorted) { rabund->print(out); } + else { rabund->nonSortedPrint(out); } - processedLabels.insert(lastList->getLabel()); - userLabels.erase(lastList->getLabel()); + processedLabels.insert(rabund->getLabel()); + userLabels.erase(rabund->getLabel()); + + //restore real lastlabel to save below + rabund->setLabel(saveLabel); } - if (count != 1) { delete lastList; } - lastList = list; + lastLabel = rabund->getLabel(); - list = input->getListVector(); - count++; + delete rabund; + rabund = input->getRAbundVector(); } //output error messages about any remaining user labels set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - cout << "Your file does not include the label "<< *it; - if (processedLabels.count(lastList->getLabel()) != 1) { - cout << ". I will use " << lastList->getLabel() << "." << endl; + 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 { - cout << ". Please refer to " << lastList->getLabel() << "." << endl; + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } - //run last line if you need to + //run last label if you need to if (needToRun == true) { - cout << lastList->getLabel() << '\t' << count << endl; - rabund = new RAbundVector(); - *rabund = (lastList->getRAbundVector()); - rabund->print(out); + if (rabund != NULL) { delete rabund; } + rabund = input->getRAbundVector(lastLabel); + + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); + + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; delete rabund; return 0; } + + if(sorted) { rabund->print(out); } + else { rabund->nonSortedPrint(out); } + delete rabund; } - delete lastList; - + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["rabund"].push_back(filename); + m->mothurOutEndLine(); + out.close(); + + //set rabund file as new current rabundfile + string current = ""; + itTypes = outputTypes.find("rabund"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); } + } + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GetRAbundCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "GetRAbundCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the GetRAbundCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //**********************************************************************************************************************