X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.cpp;fp=pcacommand.cpp;h=5eed4566a74565c5641720dd519ae4df77e90b31;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=e273e5fe7079ffab790ccf5498e69675a0fafeef;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/pcacommand.cpp b/pcacommand.cpp
index e273e5f..5eed456 100644
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -117,12 +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 == "")) {