X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removegroupscommand.cpp;h=9db35cb4bcb1fb78daa9545ecf4464b29c09d2e2;hp=4f4b1580582b953c3b8318acc68345cc8d45ae48;hb=499f4ac6e321f9f03d4c3aa25c3b6880892c8b83;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 4f4b158..9db35cb 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -355,11 +355,19 @@ int RemoveGroupsCommand::execute(){
 			
 			//make sure groups are valid
 			//takes care of user setting groupNames that are invalid or setting groups=all
-			SharedUtil* util = new SharedUtil();
 			vector<string> namesGroups = groupMap->getNamesOfGroups();
-			util->setGroups(Groups, namesGroups);
-			delete util;
-			
+			vector<string> checkedGroups;
+            for (int i = 0; i < Groups.size(); i++) {
+                if (m->inUsersGroups(Groups[i], namesGroups)) { checkedGroups.push_back(Groups[i]); }
+                else {  m->mothurOut("[WARNING]: " + Groups[i] + " is not a valid group in your groupfile, ignoring.\n"); }
+            }
+            
+            if (checkedGroups.size() == 0) { m->mothurOut("[ERROR]: no valid groups, aborting.\n"); delete groupMap; return 0; }
+			else {
+                Groups = checkedGroups;
+                m->setGroups(Groups);
+            }
+            
 			//fill names with names of sequences that are from the groups we want to remove 
 			fillNames();
 			
@@ -369,7 +377,7 @@ int RemoveGroupsCommand::execute(){
                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
             }
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, true, false);
             if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
             
             vector<string> gNamesOfGroups = ct.getNamesOfGroups();
@@ -552,9 +560,9 @@ int RemoveGroupsCommand::readShared(){
 		m->setGroups(groupsToKeep);
 		m->clearAllGroups();
 		m->saveNextLabel = "";
-		m->printedHeaders = false;
-		m->currentBinLabels.clear();
-		m->binLabelsInFile.clear();
+		m->printedSharedHeaders = false;
+		m->currentSharedBinLabels.clear();
+		m->sharedBinLabelsInFile.clear();
 		
 		InputData input(sharedfile, "sharedfile");
 		lookup = input.getSharedRAbundVectors();