X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.cpp;h=8683fc3fa80154729ea5228fcaa38fb03726603a;hb=1d5962b46d9e72a2b855b4176d1c47df9a163fac;hp=efd7073fae39fd493ef28f22d81d6bfdcf795859;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/readotucommand.cpp b/readotucommand.cpp
index efd7073..8683fc3 100644
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -9,6 +9,55 @@
 
 #include "readotucommand.h"
 
+//**********************************************************************************************************************
+vector<string> ReadOtuCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ReadOtuCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+ReadOtuCommand::ReadOtuCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["rabund"] = tempOutNames;
+		outputTypes["shared"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ReadOtuCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"list","shared","relabund","sabund","rabund","or"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ReadOtuCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ReadOtuCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 ReadOtuCommand::ReadOtuCommand(string option)  {
 	try {
@@ -34,7 +83,12 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 			for (it = parameters.begin(); it != parameters.end(); it++) { 
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
-	
+			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["rabund"] = tempOutNames;
+			outputTypes["shared"] = tempOutNames;
+			
 			globaldata->newRead();
 			
 			//if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -255,6 +309,8 @@ int ReadOtuCommand::execute(){
 				//m->mothurOutEndLine();
 			}
 			
+			outputTypes = shared->getOutputFiles();
+			
 			delete shared;
 		}
 		return 0;