X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.cpp;h=c79eb63c31b576359f8b6bf270bea83ba25028d2;hb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;hp=9955a19f677dd96cccf7b9f4171e0f7d28b9deac;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git diff --git a/parselistscommand.cpp b/parselistscommand.cpp index 9955a19..c79eb63 100644 --- a/parselistscommand.cpp +++ b/parselistscommand.cpp @@ -9,19 +9,66 @@ #include "parselistscommand.h" +//********************************************************************************************************************** +vector ParseListCommand::setParameters(){ + try { + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string ParseListCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The parse.list command reads a list and group file and generates a list file for each group in the groupfile. \n"; + helpString += "The parse.list command parameters are list, group and label.\n"; + helpString += "The list and group parameters are required.\n"; + helpString += "The label parameter is used to read specific labels in your input you want to use.\n"; + helpString += "The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n"; + helpString += "Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n"; + helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +ParseListCommand::ParseListCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["list"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "ParseListCommand"); + exit(1); + } +} //********************************************************************************************************************** ParseListCommand::ParseListCommand(string option) { try { - abort = false; + abort = false; calledHelp = false; allLines = 1; //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[] = {"list","group", "label", "outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -33,7 +80,11 @@ ParseListCommand::ParseListCommand(string option) { for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - + + //initialize outputTypes + vector tempOutNames; + outputTypes["list"] = tempOutNames; + //if the user changes the input directory command factory will send this info to us in the output parameter string inputDir = validParameter.validFile(parameters, "inputdir", false); if (inputDir == "not found"){ inputDir = ""; } @@ -42,7 +93,7 @@ ParseListCommand::ParseListCommand(string option) { it = parameters.find("list"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["list"] = inputDir + it->second; } } @@ -50,7 +101,7 @@ ParseListCommand::ParseListCommand(string option) { it = parameters.find("group"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["group"] = inputDir + it->second; } } @@ -63,12 +114,28 @@ ParseListCommand::ParseListCommand(string option) { //check for required parameters listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not open") { abort = true; } - else if (listfile == "not found") { listfile = ""; } + else if (listfile == "not found") { + listfile = m->getListFile(); + if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); + abort = true; + + } + } groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } - else if (groupfile == "not found") { groupfile = ""; } - else { + else if (groupfile == "not found") { + groupfile = m->getListFile(); + if (groupfile != "") { + m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); + groupMap = new GroupMap(groupfile); + + int error = groupMap->readMap(); + if (error == 1) { abort = true; } + }else { m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine(); abort = true; } + }else { groupMap = new GroupMap(groupfile); int error = groupMap->readMap(); @@ -83,7 +150,7 @@ ParseListCommand::ParseListCommand(string option) { label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; allLines = 1; } else { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } } @@ -95,33 +162,13 @@ ParseListCommand::ParseListCommand(string option) { } } //********************************************************************************************************************** -void ParseListCommand::help(){ - try { - m->mothurOut("The parse.list command reads a list and group file and generates a list file for each group in the groupfile \n"); - m->mothurOut("The parse.list command parameters are list, group and label.\n"); - m->mothurOut("The list and group parameters are required.\n"); - m->mothurOut("The label parameter is used to read specific labels in your input you want to use.\n"); - m->mothurOut("The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n"); - m->mothurOut("Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n"); - - } - catch(exception& e) { - m->errorOut(e, "ParseListCommand", "help"); - exit(1); - } -} -//********************************************************************************************************************** -ParseListCommand::~ParseListCommand(){} -//********************************************************************************************************************** int ParseListCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } //set fileroot - string fileroot = outputDir + getRootName(getSimpleName(listfile)); - vector outputNames; + string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile)); //fill filehandles with neccessary ofstreams int i; @@ -131,8 +178,8 @@ int ParseListCommand::execute(){ filehandles[groupMap->namesOfGroups[i]] = temp; string filename = fileroot + groupMap->namesOfGroups[i] + ".list"; - outputNames.push_back(filename); - openOutputFile(filename, *temp); + outputNames.push_back(filename); outputTypes["list"].push_back(filename); + m->openOutputFile(filename, *temp); } //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. @@ -146,7 +193,7 @@ int ParseListCommand::execute(){ if (m->control_pressed) { delete input; delete list; delete groupMap; for (i=0; inamesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; } @@ -155,7 +202,7 @@ int ParseListCommand::execute(){ if (m->control_pressed) { delete input; delete list; delete groupMap; for (i=0; inamesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; } @@ -168,7 +215,7 @@ int ParseListCommand::execute(){ userLabels.erase(list->getLabel()); } - 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; @@ -194,7 +241,7 @@ int ParseListCommand::execute(){ if (m->control_pressed) { delete input; delete groupMap; for (i=0; inamesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; } @@ -215,7 +262,7 @@ int ParseListCommand::execute(){ if (m->control_pressed) { delete input; delete groupMap; for (i=0; inamesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; } @@ -240,10 +287,17 @@ int ParseListCommand::execute(){ delete input; if (m->control_pressed) { - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; } + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("list"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); } + } + m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } @@ -278,7 +332,7 @@ int ParseListCommand::parse(ListVector* thisList) { string bin = list->get(i); vector names; - splitAtComma(bin, names); //parses bin into individual sequence names + m->splitAtComma(bin, names); //parses bin into individual sequence names //parse bin into list of sequences in each group for (int j = 0; j < names.size(); j++) {