X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=ca8c8a66a9445c21a7472301dce1bce71abe34b3;hb=4dbf93479b205ec5d72663e5b01611000266bc13;hp=80a44297b48bfde50c633edfe7354e2f3e0cb115;hpb=f37a59b81c339f574d97042ff6e364146feb457a;p=mothur.git diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp index 80a4429..ca8c8a6 100644 --- a/getsabundcommand.cpp +++ b/getsabundcommand.cpp @@ -11,7 +11,7 @@ //********************************************************************************************************************** -GetSAbundCommand::GetSAbundCommand(string option){ +GetSAbundCommand::GetSAbundCommand(string option) { try { globaldata = GlobalData::getInstance(); abort = false; @@ -23,7 +23,7 @@ GetSAbundCommand::GetSAbundCommand(string option){ else { //valid paramters for this command - string Array[] = {"label"}; + string Array[] = {"label","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -36,8 +36,14 @@ 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() == "")) { mothurOut("You must read a list or rabund before you can use the get.sabund command."); mothurOutEndLine(); 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... @@ -55,14 +61,14 @@ GetSAbundCommand::GetSAbundCommand(string option){ } if (abort == false) { - filename = getRootName(globaldata->inputFileName) + "sabund"; + filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "sabund"; openOutputFile(filename, out); } } } catch(exception& e) { - errorOut(e, "GetSAbundCommand", "GetSAbundCommand"); + m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand"); exit(1); } } @@ -70,17 +76,17 @@ GetSAbundCommand::GetSAbundCommand(string option){ void GetSAbundCommand::help(){ try { - mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n"); - mothurOut("The get.sabund command parameters is label. No parameters are required.\n"); - 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"); - mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n"); - mothurOut("Example get.sabund().\n"); - mothurOut("The default value for label is all labels in your inputfile.\n"); - mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\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) { - errorOut(e, "GetSAbundCommand", "help"); + m->errorOut(e, "GetSAbundCommand", "help"); exit(1); } } @@ -109,31 +115,43 @@ int GetSAbundCommand::execute(){ set processedLabels; set userLabels = labels; + 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))) { if(allLines == 1 || labels.count(order->getLabel()) == 1){ - mothurOut(order->getLabel()); mothurOutEndLine(); + 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()); } if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = order->getLabel(); + delete order; order = (input->getOrderVector(lastLabel)); - mothurOut(order->getLabel()); mothurOutEndLine(); + 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); } @@ -147,12 +165,12 @@ int GetSAbundCommand::execute(){ 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(); } } @@ -161,21 +179,30 @@ int GetSAbundCommand::execute(){ if (order != NULL) { delete order; } order = (input->getOrderVector(lastLabel)); - mothurOut(order->getLabel()); mothurOutEndLine(); + 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) { - errorOut(e, "GetSAbundCommand", "execute"); + m->errorOut(e, "GetSAbundCommand", "execute"); exit(1); } }