X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.cpp;h=4e61a58d9e5cb4bc640c544797c87a363580575e;hb=529ec122f7cac4af987e121d150b878d7c7a0d5d;hp=2d26ef3672a364cd694e01d48922d9d53e56b0db;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677;p=mothur.git diff --git a/parselistscommand.cpp b/parselistscommand.cpp index 2d26ef3..4e61a58 100644 --- a/parselistscommand.cpp +++ b/parselistscommand.cpp @@ -10,50 +10,72 @@ #include "parselistscommand.h" //********************************************************************************************************************** -vector ParseListCommand::getValidParameters(){ +vector ParseListCommand::setParameters(){ try { - string Array[] = {"list","group", "label", "outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + 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", "getValidParameters"); + m->errorOut(e, "ParseListCommand", "setParameters"); exit(1); } } - //********************************************************************************************************************** -ParseListCommand::ParseListCommand(){ +string ParseListCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["list"] = tempOutNames; + 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", "ParseListCommand"); + m->errorOut(e, "ParseListCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector ParseListCommand::getRequiredParameters(){ +string ParseListCommand::getOutputFileNameTag(string type, string inputName=""){ try { - string Array[] = {"list","group"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + 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", "getRequiredParameters"); + m->errorOut(e, "ParseListCommand", "getOutputFileNameTag"); exit(1); } } + //********************************************************************************************************************** -vector ParseListCommand::getRequiredFiles(){ +ParseListCommand::ParseListCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["list"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "ParseListCommand", "getRequiredFiles"); + m->errorOut(e, "ParseListCommand", "ParseListCommand"); exit(1); } } @@ -65,11 +87,10 @@ ParseListCommand::ParseListCommand(string option) { //allow user to run help 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(); @@ -115,12 +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(); @@ -147,25 +185,6 @@ 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 { @@ -177,11 +196,12 @@ int ParseListCommand::execute(){ //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"; + string filename = fileroot + gGroups[i] + "." + getOutputFileNameTag("list"); outputNames.push_back(filename); outputTypes["list"].push_back(filename); m->openOutputFile(filename, *temp); } @@ -196,8 +216,9 @@ 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()); } outputTypes.clear(); + vector gGroups = groupMap->getNamesOfGroups(); + for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -205,8 +226,8 @@ 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()); } outputTypes.clear(); + for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -243,10 +264,10 @@ 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()); } outputTypes.clear(); - return 0; + delete input; delete groupMap; + for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); + return 0; } //output error messages about any remaining user labels @@ -264,10 +285,10 @@ 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()); } outputTypes.clear(); - return 0; + delete input; delete groupMap; + for (i=0; imothurRemove(outputNames[i]); } outputTypes.clear(); + return 0; } //run last label if you need to @@ -291,7 +312,7 @@ int ParseListCommand::execute(){ delete input; if (m->control_pressed) { - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }