X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.cpp;h=0e0be0e8cf2799527e2664bb79b1cdded09e215c;hb=a98eb683e17d8e49583bf2d215ab7562a4cdca75;hp=939cdb9040e67c62416f76cda30b86dbead73654;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/groupmap.cpp b/groupmap.cpp
index 939cdb9..0e0be0e 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -14,7 +14,7 @@
  GroupMap::GroupMap(string filename) {
 	m = MothurOut::getInstance();
 	groupFileName = filename;
-	openInputFile(filename, fileHandle);
+	m->openInputFile(filename, fileHandle);
 	index = 0;
 }
 
@@ -25,13 +25,13 @@
 int GroupMap::readMap() {
 		string seqName, seqGroup;
 		int error = 0;
-	
+
 		while(fileHandle){
-			fileHandle >> seqName;			//read from first column
+			fileHandle >> seqName;	m->gobble(fileHandle);		//read from first column
 			fileHandle >> seqGroup;			//read from second column
 			
 			if (m->control_pressed) {  fileHandle.close();  return 1; }
-			
+	
 			setNamesOfGroups(seqGroup);
 			
 			it = groupmap.find(seqName);
@@ -41,7 +41,7 @@ int GroupMap::readMap() {
 				groupmap[seqName] = seqGroup;	//store data in map
 				seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
 			}
-			gobble(fileHandle);
+			m->gobble(fileHandle);
 		}
 		fileHandle.close();
 		return error;
@@ -61,26 +61,28 @@ string GroupMap::getGroup(string sequenceName) {
 }
 
 /************************************************************/
+
 void GroupMap::setGroup(string sequenceName, string groupN) {
 	groupmap[sequenceName] = groupN;
 }
+
 /************************************************************/
 void GroupMap::setNamesOfGroups(string seqGroup) {
-			int i, count;
-			count = 0;
-			for (i=0; i<namesOfGroups.size(); i++) {
-				if (namesOfGroups[i] != seqGroup) {
-					count++; //you have not found this group
-				}else {
-					break; //you already have it
-				}
-			}
-			if (count == namesOfGroups.size()) {
-				namesOfGroups.push_back(seqGroup); //new group
-				seqsPerGroup[seqGroup] = 0;
-				groupIndex[seqGroup] = index;
-				index++;
-			}
+	int i, count;
+	count = 0;
+	for (i=0; i<namesOfGroups.size(); i++) {
+		if (namesOfGroups[i] != seqGroup) {
+			count++; //you have not found this group
+		}else {
+			break; //you already have it
+		}
+	}
+	if (count == namesOfGroups.size()) {
+		namesOfGroups.push_back(seqGroup); //new group
+		seqsPerGroup[seqGroup] = 0;
+		groupIndex[seqGroup] = index;
+		index++;
+	}
 }
 /************************************************************/
 bool GroupMap::isValidGroup(string groupname) {