X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.cpp;h=9459294fa49945a00b270c1d98529de0a93c008d;hb=19fcbbdba99658f5eca244803280f9ee7f9f6607;hp=fdacc3a58fb799ba9b1fcff2497d9ba5ab562ccd;hpb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;p=mothur.git diff --git a/parselistscommand.cpp b/parselistscommand.cpp index fdacc3a..9459294 100644 --- a/parselistscommand.cpp +++ b/parselistscommand.cpp @@ -10,50 +10,51 @@ #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"); - exit(1); - } -} - -//********************************************************************************************************************** -ParseListCommand::ParseListCommand(){ - try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["list"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "ParseListCommand", "ParseListCommand"); + m->errorOut(e, "ParseListCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector ParseListCommand::getRequiredParameters(){ +string ParseListCommand::getHelpString(){ try { - string Array[] = {"list","group"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + 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", "getRequiredParameters"); + m->errorOut(e, "ParseListCommand", "getHelpString"); 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 +66,10 @@ 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 +115,29 @@ 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 +164,6 @@ 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 { @@ -197,7 +195,7 @@ 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()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -206,7 +204,7 @@ 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()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -245,7 +243,7 @@ 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()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -266,7 +264,7 @@ 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()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -291,10 +289,17 @@ 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; } + //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(); }