X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.cpp;h=4e61a58d9e5cb4bc640c544797c87a363580575e;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=ce014fcaf439d2d838cd630cbb5b012f2c8b8efe;hpb=a218321731df14d231bbc08e79906f757cf1540d;p=mothur.git diff --git a/parselistscommand.cpp b/parselistscommand.cpp index ce014fc..4e61a58 100644 --- a/parselistscommand.cpp +++ b/parselistscommand.cpp @@ -9,19 +9,88 @@ #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); + } +} +//********************************************************************************************************************** +string ParseListCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "list") { outputFileName = "list"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "getOutputFileNameTag"); + 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 if(option == "citation") { citation(); 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 +102,11 @@ 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 +115,7 @@ 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 +123,7 @@ 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 +136,29 @@ 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; + + } + }else { m->setListFile(listfile); } 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 { + m->setGroupFile(groupfile); groupMap = new GroupMap(groupfile); int error = groupMap->readMap(); @@ -76,61 +166,44 @@ ParseListCommand::ParseListCommand(string option) { } //do you have all files needed - if ((listfile == "") || (groupfile == "")) { mothurOut("You must enter both a listfile and groupfile for the parse.list command. "); mothurOutEndLine(); abort = true; } + if ((listfile == "") || (groupfile == "")) { m->mothurOut("You must enter both a listfile and groupfile for the parse.list command. "); m->mothurOutEndLine(); abort = true; } //check for optional parameter and set defaults // ...at some point should added some additional type checking... 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; } } } } catch(exception& e) { - errorOut(e, "ParseListCommand", "ParseListCommand"); - exit(1); - } -} -//********************************************************************************************************************** -void ParseListCommand::help(){ - try { - mothurOut("The parse.list command reads a list and group file and generates a list file for each group in the groupfile \n"); - mothurOut("The parse.list command parameters are list, group and label.\n"); - mothurOut("The list and group parameters are required.\n"); - mothurOut("The label parameter is used to read specific labels in your input you want to use.\n"); - mothurOut("The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n"); - mothurOut("Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n"); - mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n"); - - } - catch(exception& e) { - errorOut(e, "ParseListCommand", "help"); + m->errorOut(e, "ParseListCommand", "ParseListCommand"); 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)); + string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile)); //fill filehandles with neccessary ofstreams int i; ofstream* temp; - for (i=0; inamesOfGroups.size(); i++) { + vector gGroups = groupMap->getNamesOfGroups(); + for (i=0; inamesOfGroups[i]] = temp; + filehandles[gGroups[i]] = temp; - string filename = fileroot + groupMap->namesOfGroups[i] + ".list"; - openOutputFile(filename, *temp); + string filename = fileroot + gGroups[i] + "." + getOutputFileNameTag("list"); + 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. @@ -141,25 +214,40 @@ int ParseListCommand::execute(){ list = input->getListVector(); string lastLabel = list->getLabel(); + if (m->control_pressed) { + delete input; delete list; delete groupMap; + vector gGroups = groupMap->getNamesOfGroups(); + for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); + return 0; + } + while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + + if (m->control_pressed) { + delete input; delete list; delete groupMap; + for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); + return 0; + } if(allLines == 1 || labels.count(list->getLabel()) == 1){ + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); parse(list); - mothurOut(list->getLabel()); mothurOutEndLine(); - + processedLabels.insert(list->getLabel()); 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; list = input->getListVector(lastLabel); //get new list vector to process + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); parse(list); - mothurOut(list->getLabel()); mothurOutEndLine(); processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); @@ -175,27 +263,41 @@ int ParseListCommand::execute(){ list = input->getListVector(); //get new list vector to process } + if (m->control_pressed) { + delete input; delete groupMap; + for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); + return 0; + } + //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(); } } + if (m->control_pressed) { + delete input; delete groupMap; + for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); + return 0; + } + //run last label if you need to if (needToRun == true) { if (list != NULL) { delete list; } list = input->getListVector(lastLabel); //get new list vector to process + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); parse(list); - mothurOut(list->getLabel()); mothurOutEndLine(); delete list; } @@ -205,17 +307,36 @@ int ParseListCommand::execute(){ delete it3->second; } + delete groupMap; + delete input; + + if (m->control_pressed) { + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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(); } + m->mothurOutEndLine(); return 0; } catch(exception& e) { - errorOut(e, "ParseListCommand", "execute"); + m->errorOut(e, "ParseListCommand", "execute"); exit(1); } } /**********************************************************************************************************************/ -void ParseListCommand::parse(ListVector* thisList) { +int ParseListCommand::parse(ListVector* thisList) { try { map groupVector; @@ -230,18 +351,19 @@ void ParseListCommand::parse(ListVector* thisList) { for (int i = 0; i < thisList->getNumBins(); i++) { + if (m->control_pressed) { return 0; } map groupBins; 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++) { string group = groupMap->getGroup(names[j]); - if (group == "not found") { mothurOut(names[j] + " is not in your groupfile. please correct."); mothurOutEndLine(); exit(1); } + if (group == "not found") { m->mothurOut(names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); exit(1); } itGroup = groupBins.find(group); if(itGroup == groupBins.end()) { @@ -263,11 +385,12 @@ void ParseListCommand::parse(ListVector* thisList) { for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { (*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl; // label numBins listvector for that group } - + + return 0; } catch(exception& e) { - errorOut(e, "ParseListCommand", "parse"); + m->errorOut(e, "ParseListCommand", "parse"); exit(1); } }