X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.cpp;h=9cf5a73a56802b65bae10d1c28187f214ebcfb56;hb=2e77272b6f5987bd2bde592bb15262a8c69ea9e0;hp=9955a19f677dd96cccf7b9f4171e0f7d28b9deac;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git diff --git a/parselistscommand.cpp b/parselistscommand.cpp index 9955a19..9cf5a73 100644 --- a/parselistscommand.cpp +++ b/parselistscommand.cpp @@ -9,6 +9,55 @@ #include "parselistscommand.h" +//********************************************************************************************************************** +vector ParseListCommand::getValidParameters(){ + try { + string Array[] = {"list","group", "label", "outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "getValidParameters"); + exit(1); + } +} + +//********************************************************************************************************************** +ParseListCommand::ParseListCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["list"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "ParseListCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector ParseListCommand::getRequiredParameters(){ + try { + string Array[] = {"list","group"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ParseListCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParseListCommand", "getRequiredFiles"); + exit(1); + } +} //********************************************************************************************************************** ParseListCommand::ParseListCommand(string option) { try { @@ -33,7 +82,11 @@ 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 +95,7 @@ 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 +103,7 @@ 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; } } @@ -83,7 +136,7 @@ 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; } } } @@ -97,7 +150,7 @@ 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 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"); @@ -120,8 +173,7 @@ int ParseListCommand::execute(){ if (abort == true) { return 0; } //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 +183,8 @@ 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 +198,7 @@ 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 +207,7 @@ 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 +220,7 @@ 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 +246,7 @@ 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 +267,7 @@ 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; } @@ -240,7 +292,7 @@ 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; } @@ -278,7 +330,7 @@ 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++) {