X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sensspeccommand.cpp;fp=sensspeccommand.cpp;h=78dce1794003457a077fe993958c75909c1020a7;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=8489bfefc841f6dd34fea17ef15b416e08c4c6c8;hpb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2;p=mothur.git

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 8489bfe..78dce17 100644
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -9,6 +9,53 @@
 
 #include "sensspeccommand.h"
 
+//**********************************************************************************************************************
+vector<string> SensSpecCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"list", "phylip", "column", "name", "hard", "label", "cutoff", "precision", "outputdir", "inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SensSpecCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+SensSpecCommand::SensSpecCommand(){	
+	try {
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["sensspec"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SensSpecCommand", "SensSpecCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> SensSpecCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"list","phylip","column","or"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SensSpecCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> SensSpecCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SensSpecCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //***************************************************************************************************************
 
 SensSpecCommand::SensSpecCommand(string option)  {
@@ -38,6 +85,10 @@ SensSpecCommand::SensSpecCommand(string option)  {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["sensspec"] = 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 = "";		}
@@ -159,6 +210,7 @@ int SensSpecCommand::execute(){
 		if (abort == true) { return 0; }
 
 		setUpOutput();
+		outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
 		if(format == "phylip")		{	processPhylip();	}
 		else if(format == "column")	{	processColumn();	}