X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=getrabundcommand.cpp;h=0b2d4ee3ed0de4daf04da29b9ad5a3595143c4b1;hb=fca3f55d5ded10c3dc77856f3cc4a1c53b02bb6f;hp=b0bf81980a54d7bb6f8992b49f0af83d3169f4f8;hpb=348a7bac1d3c5d17ae0e4a93b78f69f4e200a190;p=mothur.git diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp index b0bf819..0b2d4ee 100644 --- a/getrabundcommand.cpp +++ b/getrabundcommand.cpp @@ -10,21 +10,67 @@ #include "getrabundcommand.h" //********************************************************************************************************************** - -GetRAbundCommand::GetRAbundCommand(string option){ +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(); - abort = false; + 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 { //valid paramters for this command - string Array[] = {"line","label","sorted"}; + string Array[] = {"label","sorted","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -37,48 +83,48 @@ GetRAbundCommand::GetRAbundCommand(string option){ 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() == "") { mothurOut("You must read a listfile before you can use the get.rabund command."); mothurOutEndLine(); abort = true; } + 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 = isTrue(temp); - - line = validParameter.validFile(parameters, "line", false); - if (line == "not found") { line = ""; } - else { - if(line != "all") { splitAtDash(line, lines); allLines = 0; } - else { allLines = 1; } - } + 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 != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; } - //if the user has not specified any line or labels use the ones from read.otu - else if((line == "") && (label == "")) { + //if the user has not specified any labels use the ones from read.otu + if(label == "") { allLines = globaldata->allLines; labels = globaldata->labels; - lines = globaldata->lines; } if (abort == false) { - filename = getRootName(globaldata->inputFileName) + "rabund"; - openOutputFile(filename, out); + filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "rabund"; + m->openOutputFile(filename, out); } } } catch(exception& e) { - errorOut(e, "GetRAbundCommand", "GetRAbundCommand"); + m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand"); exit(1); } } @@ -86,36 +132,32 @@ GetRAbundCommand::GetRAbundCommand(string option){ void GetRAbundCommand::help(){ try { - mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n"); - mothurOut("The get.rabund command parameters are line, label and sorted. No parameters are required, and you may not use line and label at the same time.\n"); - mothurOut("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"); - mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not. The default is sorted.\n"); - mothurOut("The get.rabund command should be in the following format: get.rabund(line=yourLines, label=yourLabels, sorted=yourSorted).\n"); - mothurOut("Example get.rabund(line=1-3-5, sorted=F).\n"); - mothurOut("The default value for line and label are all lines in your inputfile.\n"); - mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n"); + 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(exception& e) { - errorOut(e, "GetRAbundCommand", "help"); + m->errorOut(e, "GetRAbundCommand", "help"); exit(1); } } //********************************************************************************************************************** -GetRAbundCommand::~GetRAbundCommand(){ - if (abort == false) { globaldata->gListVector = NULL; } -} +GetRAbundCommand::~GetRAbundCommand(){} //********************************************************************************************************************** int GetRAbundCommand::execute(){ try { - if (abort == true) { return 0; } - - int count = 1; + if (abort == true) { if (calledHelp) { return 0; } return 2; } //read first line read = new ReadOTUFile(globaldata->inputFileName); @@ -128,16 +170,19 @@ int GetRAbundCommand::execute(){ //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(); remove(filename.c_str()); delete list; globaldata->gListVector = NULL; return 0; } + + while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){ - mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine(); + if(allLines == 1 || labels.count(list->getLabel()) == 1){ + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); rabund = new RAbundVector(); *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); } @@ -145,17 +190,20 @@ int GetRAbundCommand::execute(){ processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); - userLines.erase(count); } - if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = list->getLabel(); + delete list; list = input->getListVector(lastLabel); - mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine(); + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); rabund = new RAbundVector(); *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); } @@ -163,50 +211,62 @@ int GetRAbundCommand::execute(){ 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(); - count++; } //output error messages about any remaining user labels set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - mothurOut("Your file does not include the label " + *it); + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + 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) { - delete list; + if (list != NULL) { delete list; } list = input->getListVector(lastLabel); - mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine(); + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); rabund = new RAbundVector(); *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; } - + + 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) { - errorOut(e, "GetRAbundCommand", "execute"); + m->errorOut(e, "GetRAbundCommand", "execute"); exit(1); } }