#include "parselistscommand.h"
//**********************************************************************************************************************
-vector<string> ParseListCommand::getValidParameters(){
+vector<string> ParseListCommand::setParameters(){
try {
- string Array[] = {"list","group", "label", "outputdir","inputdir"};
- vector<string> 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<string> 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<string> tempOutNames;
- outputTypes["list"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ParseListCommand", "ParseListCommand");
+ m->errorOut(e, "ParseListCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ParseListCommand::getRequiredParameters(){
+string ParseListCommand::getHelpString(){
try {
- string Array[] = {"list","group"};
- vector<string> 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<string> ParseListCommand::getRequiredFiles(){
+ParseListCommand::ParseListCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "ParseListCommand", "getRequiredFiles");
+ m->errorOut(e, "ParseListCommand", "ParseListCommand");
exit(1);
}
}
//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<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
//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();
}
}
//**********************************************************************************************************************
-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 {
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(); }
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