X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=ca8c8a66a9445c21a7472301dce1bce71abe34b3;hb=8ef6687c1f586285d01c000cc5e359bf9c07c717;hp=f5beb32b6a8296411dcd66afa18efc6b3be24577;hpb=016a30dacbe75869aef5fdb58d2d1bf9eb8f9b33;p=mothur.git diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp index f5beb32..ca8c8a6 100644 --- a/getsabundcommand.cpp +++ b/getsabundcommand.cpp @@ -11,12 +11,11 @@ //********************************************************************************************************************** -GetSAbundCommand::GetSAbundCommand(string option){ +GetSAbundCommand::GetSAbundCommand(string option) { try { globaldata = GlobalData::getInstance(); abort = false; allLines = 1; - lines.clear(); labels.clear(); //allow user to run help @@ -24,7 +23,7 @@ GetSAbundCommand::GetSAbundCommand(string option){ else { //valid paramters for this command - string Array[] = {"line","label"}; + string Array[] = {"label","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -37,18 +36,17 @@ GetSAbundCommand::GetSAbundCommand(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 += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + } + //make sure the user has already run the read.otu command - if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { cout << "You must read a list or rabund before you can use the get.sabund command." << endl; abort = true; } + if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { m->mothurOut("You must read a list or rabund before you can use the get.sabund command."); m->mothurOutEndLine(); abort = true; } //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; } - } - label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } else { @@ -56,53 +54,41 @@ GetSAbundCommand::GetSAbundCommand(string option){ 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 == "")) { + //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) + "sabund"; + filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "sabund"; openOutputFile(filename, out); } } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the GetSAbundCommand class function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } //********************************************************************************************************************** void GetSAbundCommand::help(){ try { - cout << "The get.sabund command can only be executed after a successful read.otu of a listfile." << "\n"; - cout << "The get.sabund 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 .sabund file, and are separated by dashes." << "\n"; - cout << "The get.sabund command should be in the following format: get.sabund(line=yourLines, label=yourLabels)." << "\n"; - cout << "Example get.sabund(line=1-3-5)." << "\n"; - cout << "The default value for line and label are all lines in your inputfile." << "\n"; - cout << "The get.sabund command outputs a .sabund file containing the lines you selected." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n"; + m->mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n"); + m->mothurOut("The get.sabund command parameters is label. No parameters are required.\n"); + m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n"); + m->mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n"); + m->mothurOut("Example get.sabund().\n"); + m->mothurOut("The default value for label is all labels in your inputfile.\n"); + m->mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n"); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "GetSAbundCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the GetSAbundCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** @@ -117,8 +103,6 @@ int GetSAbundCommand::execute(){ if (abort == true) { return 0; } - int count = 1; - //using order vector so you don't have to distinguish between the list and rabund files read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); @@ -130,35 +114,44 @@ int GetSAbundCommand::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; + + if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } - while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){ - cout << order->getLabel() << '\t' << count << endl; + if(allLines == 1 || labels.count(order->getLabel()) == 1){ + m->mothurOut(order->getLabel()); m->mothurOutEndLine(); sabund = new SAbundVector(); *sabund = (order->getSAbundVector()); sabund->print(out); delete sabund; + + if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } processedLabels.insert(order->getLabel()); userLabels.erase(order->getLabel()); - userLines.erase(count); } if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = order->getLabel(); + delete order; order = (input->getOrderVector(lastLabel)); - cout << order->getLabel() << '\t' << count << endl; + m->mothurOut(order->getLabel()); m->mothurOutEndLine(); sabund = new SAbundVector(); *sabund = (order->getSAbundVector()); sabund->print(out); delete sabund; + + if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } processedLabels.insert(order->getLabel()); userLabels.erase(order->getLabel()); + + //restore real lastlabel to save below + order->setLabel(saveLabel); } @@ -166,48 +159,52 @@ int GetSAbundCommand::execute(){ delete order; order = (input->getOrderVector()); - 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; + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - cout << ". I will use " << lastLabel << "." << endl; + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - cout << ". Please refer to " << lastLabel << "." << 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) { - delete order; + if (order != NULL) { delete order; } order = (input->getOrderVector(lastLabel)); - cout << order->getLabel() << '\t' << count << endl; + m->mothurOut(order->getLabel()); m->mothurOutEndLine(); sabund = new SAbundVector(); *sabund = (order->getSAbundVector()); sabund->print(out); delete sabund; + + if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } + delete order; } globaldata->gorder = NULL; out.close(); + + m->mothurOutEndLine(); + m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + m->mothurOut(filename); m->mothurOutEndLine(); + m->mothurOutEndLine(); + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "GetSAbundCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the GetSAbundCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //**********************************************************************************************************************