X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlistcountcommand.cpp;h=7757122776136ce25edf778709db6c4102a37b9a;hb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;hp=fcc42ced634b80790d6aa3f5977ea6ef3121f77a;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp index fcc42ce..7757122 100644 --- a/getlistcountcommand.cpp +++ b/getlistcountcommand.cpp @@ -10,13 +10,13 @@ #include "getlistcountcommand.h" //********************************************************************************************************************** -GetListCountCommand::GetListCountCommand(string option){ +GetListCountCommand::GetListCountCommand(string option) { try { globaldata = GlobalData::getInstance(); abort = false; allLines = 1; labels.clear(); - + //allow user to run help if(option == "help") { help(); abort = true; } @@ -57,7 +57,7 @@ GetListCountCommand::GetListCountCommand(string option){ //check for required parameters listfile = validParameter.validFile(parameters, "list", true); - if ((listfile == "not found") && (globaldata->getListFile() == "")) { mothurOut("You must read a listfile before running the get.listcount command."); mothurOutEndLine(); abort = true; } + if ((listfile == "not found") && (globaldata->getListFile() == "")) { m->mothurOut("You must read a listfile before running the get.listcount command."); m->mothurOutEndLine(); abort = true; } else if ((listfile == "not found") && (globaldata->getListFile() != "")) { listfile = globaldata->getListFile(); } else if (listfile == "not open") { abort = true; } else { globaldata->setListFile(listfile); } @@ -80,7 +80,7 @@ GetListCountCommand::GetListCountCommand(string option){ } } catch(exception& e) { - errorOut(e, "GetListCountCommand", "GetListCountCommand"); + m->errorOut(e, "GetListCountCommand", "GetListCountCommand"); exit(1); } } @@ -88,17 +88,17 @@ GetListCountCommand::GetListCountCommand(string option){ void GetListCountCommand::help(){ try { - mothurOut("The get.listcount command can only be executed after a successful read.otu command of a listfile or providing a list file using the list parameter.\n"); - mothurOut("The get.listcount command parameters are list and label. No parameters are required.\n"); - mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n"); - mothurOut("The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels).\n"); - mothurOut("Example get.listcount(list=amazon.fn.list, label=0.10).\n"); - mothurOut("The default value for label is all lines in your inputfile.\n"); - mothurOut("The get.listcount command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n"); + m->mothurOut("The get.listcount command can only be executed after a successful read.otu command of a listfile or providing a list file using the list parameter.\n"); + m->mothurOut("The get.listcount command parameters are list and label. No parameters are required.\n"); + m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n"); + m->mothurOut("The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels).\n"); + m->mothurOut("Example get.listcount(list=amazon.fn.list, label=0.10).\n"); + m->mothurOut("The default value for label is all lines in your inputfile.\n"); + m->mothurOut("The get.listcount command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n"); } catch(exception& e) { - errorOut(e, "GetListCountCommand", "help"); + m->errorOut(e, "GetListCountCommand", "help"); exit(1); } } @@ -126,12 +126,30 @@ int GetListCountCommand::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; - + + if (m->control_pressed) { + delete read; + delete input; + delete list; + globaldata->gListVector = NULL; + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { if(allLines == 1 || labels.count(list->getLabel()) == 1){ process(list); + + if (m->control_pressed) { + delete read; + delete input; + delete list; + globaldata->gListVector = NULL; + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); @@ -144,6 +162,15 @@ int GetListCountCommand::execute(){ list = input->getListVector(lastLabel); process(list); + + if (m->control_pressed) { + delete read; + delete input; + delete list; + globaldata->gListVector = NULL; + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); @@ -163,12 +190,12 @@ int GetListCountCommand::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(); } } @@ -177,17 +204,33 @@ int GetListCountCommand::execute(){ if (list != NULL) { delete list; } list = input->getListVector(lastLabel); - process(list); + process(list); + + if (m->control_pressed) { + delete read; + delete input; + delete list; + globaldata->gListVector = NULL; + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + delete list; } delete read; + delete input; globaldata->gListVector = NULL; + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + return 0; } catch(exception& e) { - errorOut(e, "GetListCountCommand", "execute"); + m->errorOut(e, "GetListCountCommand", "execute"); exit(1); } } @@ -200,11 +243,14 @@ void GetListCountCommand::process(ListVector* list) { if (outputDir == "") { outputDir += hasPath(listfile); } string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + list->getLabel() + ".otu"; openOutputFile(outputFileName, out); + outputNames.push_back(outputFileName); - mothurOut(list->getLabel()); mothurOutEndLine(); + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); //for each bin in the list vector for (int i = 0; i < list->getNumBins(); i++) { + if (m->control_pressed) { break; } + binnames = list->get(i); out << i+1 << '\t' << binnames << endl; } @@ -212,7 +258,7 @@ void GetListCountCommand::process(ListVector* list) { out.close(); } catch(exception& e) { - errorOut(e, "GetListCountCommand", "process"); + m->errorOut(e, "GetListCountCommand", "process"); exit(1); } }