X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.cpp;h=481fd1decfc4516eb5e1cf618c6b4d40cffbc8a9;hb=133dddf9ffde5059e3ea8290a2e7742843e3f2b7;hp=9e9955671e41a6cfff3dc882e29ccbc4de9414ca;hpb=0746c58a680458c0bc874b3a5fc1334b12ed2f18;p=mothur.git

diff --git a/groupmap.cpp b/groupmap.cpp
index 9e99556..481fd1d 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -44,6 +44,7 @@ int GroupMap::readMap() {
 			m->gobble(fileHandle);
 		}
 		fileHandle.close();
+		m->setAllGroups(namesOfGroups);
 		return error;
 }
 /************************************************************/
@@ -69,6 +70,7 @@ int GroupMap::readDesignMap() {
 			m->gobble(fileHandle);
 		}
 		fileHandle.close();
+		m->setAllGroups(namesOfGroups);
 		return error;
 }
 
@@ -89,7 +91,15 @@ string GroupMap::getGroup(string sequenceName) {
 /************************************************************/
 
 void GroupMap::setGroup(string sequenceName, string groupN) {
-	groupmap[sequenceName] = groupN;
+	setNamesOfGroups(groupN);
+	
+	it = groupmap.find(sequenceName);
+	
+	if (it != groupmap.end()) {  m->mothurOut("Your groupfile contains more than 1 sequence named " + sequenceName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
+	else {
+		groupmap[sequenceName] = groupN;	//store data in map
+		seqsPerGroup[groupN]++;  //increment number of seqs in that group
+	}
 }
 
 /************************************************************/