#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 {
+ //initialize outputTypes
+ 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 {
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 = ""; }
if (abort == true) { return 0; }
- vector<string> outputNames;
-
//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
//make it as long as the longest taxonomy in the file
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