#include "rabundvector.hpp"
#include "sabundvector.hpp"
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getValidParameters(){
+ try {
+ string Array[] = {"taxonomy","cutoff","label","name","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PhylotypeCommand::PhylotypeCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"taxonomy"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
/**********************************************************************************************************************/
PhylotypeCommand::PhylotypeCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+
//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 = ""; }
int PhylotypeCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- vector<string> outputNames;
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//reads in taxonomy file and makes all the taxonomies the same length
//by appending the last taxon to a given taxonomy as many times as needed to
string outputRabundFile = fileroot + "tx.rabund";
m->openOutputFile(outputRabundFile, outRabund);
- outputNames.push_back(outputListFile);
- outputNames.push_back(outputSabundFile);
- outputNames.push_back(outputRabundFile);
+ outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
+ outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
+ outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
int count = 1;
//start at leaves of tree and work towards root, processing the labels the user wants
return 0;
}
+ //set list file as new current listfile
+ string current = "";
+ itTypes = outputTypes.find("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+ }
+
+ //set rabund file as new current rabundfile
+ itTypes = outputTypes.find("rabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+ }
+
+ //set sabund file as new current sabundfile
+ itTypes = outputTypes.find("sabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
+ }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }