#include "getlabelcommand.h"
-//**********************************************************************************************************************
-GetlabelCommand::GetlabelCommand(string option) {
+//**********************************************************************************************************************
+vector<string> GetlabelCommand::setParameters(){
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(psabund);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
- //allow user to run help
- if(option == "help") { help(); abort = true; }
-
- else {
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund or rabund before you can use the get.label command."); m->mothurOutEndLine(); abort = true; }
- }
-
+ 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, "GetlabelCommand", "GetlabelCommand");
+ m->errorOut(e, "GetlabelCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-
-void GetlabelCommand::help(){
+GetlabelCommand::GetlabelCommand(){
try {
- m->mothurOut("The get.label command can only be executed after a successful read.otu command.\n");
- m->mothurOut("You may not use any parameters with the get.label command.\n");
- m->mothurOut("The get.label command should be in the following format: \n");
- m->mothurOut("get.label()\n");
- m->mothurOut("Example get.label().\n");
+ abort = true; calledHelp = true;
+ setParameters();
}
catch(exception& e) {
- m->errorOut(e, "GetlabelCommand", "help");
+ m->errorOut(e, "GetlabelCommand", "CollectCommand");
exit(1);
}
}
-
//**********************************************************************************************************************
-
-GetlabelCommand::~GetlabelCommand(){
+string GetlabelCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.label command parameters are list, sabund and rabund file. \n";
+ helpString += "The get.label command should be in the following format: \n";
+ helpString += "get.label()\n";
+ helpString += "Example get.label().\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetlabelCommand", "getHelpString");
+ exit(1);
+ }
}
+//**********************************************************************************************************************
+GetlabelCommand::GetlabelCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //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 = ""; }
+ else {
+ string path;
+
+ it = parameters.find("rabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["rabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("sabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["sabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ 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; }
+ }
+ }
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { listfile = ""; abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
+
+ sabundfile = validParameter.validFile(parameters, "sabund", true);
+ if (sabundfile == "not open") { sabundfile = ""; abort = true; }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+ else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
+
+ rabundfile = validParameter.validFile(parameters, "rabund", true);
+ if (rabundfile == "not open") { rabundfile = ""; abort = true; }
+ else if (rabundfile == "not found") { rabundfile = ""; }
+ else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
+
+ if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
+ //is there are current file available for any of these?
+ //give priority to list, then rabund, then sabund
+ //if there is a current shared file, use it
+
+ listfile = m->getListFile();
+ if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else {
+ rabundfile = m->getRabundFile();
+ if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
+ else {
+ sabundfile = m->getSabundFile();
+ if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a list, sabund or rabund file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
int GetlabelCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- filename = globaldata->inputFileName;
- ifstream in;
- openInputFile(filename, in);
- string label;
- int numBins = 0;
- int count = -1;
- while(in.good()) {
- if(count > numBins)
- count = 0;
- if(count == 0) {
- m->mothurOut(label); m->mothurOutEndLine();
- in >> numBins;
- }
- in >> label;
- count++;
- }
+ InputData* input = new InputData(inputfile, format);
+ OrderVector* order = input->getOrderVector();
+ string label = order->getLabel();
+
+ while (order != NULL) {
+
+ if (m->control_pressed) { delete input; delete order; return 0; }
+
+ label = order->getLabel();
+
+ m->mothurOut(label); m->mothurOutEndLine();
+
+ delete order;
+ order = input->getOrderVector();
+ }
+
+ delete input;
- in.close();
return 0;
}
exit(1);
}
}
+//**********************************************************************************************************************
+
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