#include "getsabundcommand.h"
//**********************************************************************************************************************
-
+vector<string> GetSAbundCommand::getValidParameters(){
+ try {
+ string Array[] = {"label","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetSAbundCommand::GetSAbundCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSAbundCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSAbundCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"list","rabund"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
GetSAbundCommand::GetSAbundCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+
//if the user changes the output directory command factory will send this info to us in the output parameter
string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
}
//make sure the user has already run the read.otu command
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
}
if (abort == false) {
- filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "sabund";
- openOutputFile(filename, out);
+ filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "sabund";
+ m->openOutputFile(filename, out);
}
}
int GetSAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//using order vector so you don't have to distinguish between the list and rabund files
read = new ReadOTUFile(globaldata->inputFileName);
set<string> processedLabels;
set<string> userLabels = labels;
- if (m->control_pressed) { out.close(); remove(filename.c_str()); delete read; delete input; delete order; globaldata->gorder = NULL; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
sabund->print(out);
delete sabund;
- if (m->control_pressed) { out.close(); remove(filename.c_str()); delete read; delete input; delete order; globaldata->gorder = NULL; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = order->getLabel();
delete order;
sabund->print(out);
delete sabund;
- if (m->control_pressed) { out.close(); remove(filename.c_str()); delete read; delete input; delete order; globaldata->gorder = NULL; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
sabund->print(out);
delete sabund;
- if (m->control_pressed) { out.close(); remove(filename.c_str()); delete read; delete input; delete order; globaldata->gorder = NULL; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
delete order;
}
globaldata->gorder = NULL;
- delete read; delete input;
out.close();
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(filename); m->mothurOutEndLine();
+ m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);
m->mothurOutEndLine();
return 0;