X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.cpp;h=0b2d4ee3ed0de4daf04da29b9ad5a3595143c4b1;hb=5334a314651228c55fd0f206dec0209bc3148b24;hp=b0f7a92638663095cf860ed6b8ff34a9ada9402c;hpb=0024441c1ff9a98467ba53cc7420a37c98f32e86;p=mothur.git diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp index b0f7a92..0b2d4ee 100644 --- a/getrabundcommand.cpp +++ b/getrabundcommand.cpp @@ -3,42 +3,161 @@ * 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" //********************************************************************************************************************** - -GetRAbundCommand::GetRAbundCommand(){ +vector GetRAbundCommand::getValidParameters(){ + try { + string Array[] = {"label","sorted","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetRAbundCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +GetRAbundCommand::GetRAbundCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["rabund"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetRAbundCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetRAbundCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetRAbundCommand::getRequiredFiles(){ + try { + string Array[] = {"list"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetRAbundCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +GetRAbundCommand::GetRAbundCommand(string option) { try { globaldata = GlobalData::getInstance(); - filename = getRootName(globaldata->inputFileName) + "rabund"; + abort = false; calledHelp = false; + allLines = 1; + labels.clear(); + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } - openOutputFile(filename, out); + else { + //valid paramters for this command + string Array[] = {"label","sorted","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + + //check to make sure all parameters are valid for command + for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //if the user changes the output directory command factory will send this info to us in the output parameter + string 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 + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["rabund"] = tempOutNames; + + //make sure the user has already run the read.otu command + if (globaldata->getListFile() == "") { m->mothurOut("You must read a listfile before you can use the get.rabund command."); m->mothurOutEndLine(); abort = true; } + + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + + 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") { 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 == "") { + allLines = globaldata->allLines; + labels = globaldata->labels; + } + + if (abort == false) { + filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "rabund"; + m->openOutputFile(filename, out); + } + } + } 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"; + m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand"); exit(1); + } +} +//********************************************************************************************************************** + +void GetRAbundCommand::help(){ + try { + m->mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n"); + m->mothurOut("The get.rabund command parameters are label and sorted. No parameters are required.\n"); + m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n"); + m->mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not. The default is sorted.\n"); + m->mothurOut("The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n"); + m->mothurOut("Example get.rabund(sorted=F).\n"); + m->mothurOut("The default value for label is all labels in your inputfile.\n"); + m->mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n"); } - catch(...) { - cout << "An unknown error has occurred in the GetRAbundCommand class function GetRAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + catch(exception& e) { + m->errorOut(e, "GetRAbundCommand", "help"); exit(1); - } - + } } //********************************************************************************************************************** -GetRAbundCommand::~GetRAbundCommand(){ -} +GetRAbundCommand::~GetRAbundCommand(){} //********************************************************************************************************************** int GetRAbundCommand::execute(){ try { - int count = 1; + + if (abort == true) { if (calledHelp) { return 0; } return 2; } //read first line read = new ReadOTUFile(globaldata->inputFileName); @@ -46,81 +165,110 @@ int GetRAbundCommand::execute(){ input = globaldata->ginput; list = globaldata->gListVector; - ListVector* lastList = list; + 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 = globaldata->labels; - set userLines = globaldata->lines; - + set userLabels = labels; + + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; globaldata->gListVector = NULL; return 0; } - while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){ - cout << list->getLabel() << '\t' << count << endl; - rabund = new RAbundVector(); + if(allLines == 1 || labels.count(list->getLabel()) == 1){ + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); + rabund = new RAbundVector(); *rabund = (list->getRAbundVector()); - rabund->print(out); + + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; } + + + if(sorted) { rabund->print(out); } + else { rabund->nonSortedPrint(out); } + delete rabund; processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); - userLines.erase(count); } - if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) { - cout << lastList->getLabel() << '\t' << count << endl; + if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = list->getLabel(); + + delete list; + list = input->getListVector(lastLabel); + + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); rabund = new RAbundVector(); - *rabund = (lastList->getRAbundVector()); - rabund->print(out); + *rabund = (list->getRAbundVector()); + + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; } + + if(sorted) { rabund->print(out); } + else { rabund->nonSortedPrint(out); } + delete rabund; - processedLabels.insert(lastList->getLabel()); - userLabels.erase(lastList->getLabel()); + processedLabels.insert(list->getLabel()); + userLabels.erase(list->getLabel()); + + //restore real lastlabel to save below + list->setLabel(saveLabel); } - if (count != 1) { delete lastList; } - lastList = list; + lastLabel = list->getLabel(); + delete list; list = input->getListVector(); - count++; } //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; + if (list != NULL) { delete list; } + list = input->getListVector(lastLabel); + + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); rabund = new RAbundVector(); - *rabund = (lastList->getRAbundVector()); - rabund->print(out); + *rabund = (list->getRAbundVector()); + + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; } + + if(sorted) { rabund->print(out); } + else { rabund->nonSortedPrint(out); } + delete rabund; + delete list; } - delete lastList; - + + m->mothurOutEndLine(); + m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["rabund"].push_back(filename); + m->mothurOutEndLine(); + out.close(); + + globaldata->gListVector = NULL; + 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); - } } //**********************************************************************************************************************