X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.cpp;h=5eed4566a74565c5641720dd519ae4df77e90b31;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=6e2cce79736a9f01edbaa44bd31e145921850a30;hpb=f0a594f6676ef5a52d1f122b6de70de2fda08c81;p=mothur.git

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 6e2cce7..5eed456 100644
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -70,6 +70,7 @@ PCACommand::PCACommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -116,12 +117,12 @@ PCACommand::PCACommand(string option)  {
 			sharedfile = validParameter.validFile(parameters, "shared", true);
 			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
 			else if (sharedfile == "not found") { sharedfile = ""; }
-			else {  mode = "sharedfile"; inputFile = sharedfile; }
+			else {  mode = "sharedfile"; inputFile = sharedfile; m->setSharedFile(sharedfile); }
 			
 			relabundfile = validParameter.validFile(parameters, "relabund", true);
 			if (relabundfile == "not open") { relabundfile = ""; abort = true; }	
 			else if (relabundfile == "not found") { relabundfile = ""; }
-			else {  mode = "relabund"; inputFile = relabundfile; }
+			else {  mode = "relabund"; inputFile = relabundfile; m->setRelAbundFile(relabundfile); }
 			
 			
 			if ((sharedfile == "") && (relabundfile == "")) {