X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;fp=rarefactsharedcommand.cpp;h=0be8141636a1fffaacce16f2592e6bf8738ad400;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=c0f5ec0c4daba141c9267817836522e0d22c1a3a;hpb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index c0f5ec0..0be8141 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -11,6 +11,54 @@
 #include "sharedsobs.h"
 #include "sharednseqs.h"
 
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+RareFactSharedCommand::RareFactSharedCommand(){	
+	try {
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["sharedrarefaction"] = tempOutNames;
+		outputTypes["sharedr_nseqs"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getRequiredFiles(){	
+	try {
+		string Array[] =  {"shared"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactSharedCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 RareFactSharedCommand::RareFactSharedCommand(string option)  {
@@ -41,6 +89,11 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["sharedrarefaction"] = tempOutNames;
+			outputTypes["sharedr_nseqs"] = tempOutNames;
+			
 			//make sure the user has already run the read.otu command
 			if (globaldata->getSharedFile() == "") {
 				if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); m->mothurOutEndLine(); abort = true; }
@@ -107,10 +160,10 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
 					if (validCalculator->isValidCalculator("sharedrarefaction", Estimators[i]) == true) { 
 						if (Estimators[i] == "sharedobserved") { 
 							rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
-							outputNames.push_back(fileNameRoot+"shared.rarefaction");
+							outputNames.push_back(fileNameRoot+"shared.rarefaction"); outputTypes["sharedrarefaction"].push_back(fileNameRoot+"shared.rarefaction");
 						}else if (Estimators[i] == "sharednseqs") { 
 							rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
-							outputNames.push_back(fileNameRoot+"shared.r_nseqs");
+							outputNames.push_back(fileNameRoot+"shared.r_nseqs"); outputTypes["sharedr_nseqs"].push_back(fileNameRoot+"shared.r_nseqs");
 						}
 					}
 				}