X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.cpp;h=1fc5c01b796a67bd948a70147fa4dead9320ea08;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=52a90031d380fedddd275bd5ebbb6a3f8600964c;hpb=e03de8796670a0c747aed63483daa09c8b86aea0;p=mothur.git

diff --git a/treemap.cpp b/treemap.cpp
index 52a9003..1fc5c01 100644
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -12,6 +12,7 @@
 /************************************************************/
 
  TreeMap::TreeMap(string filename) {
+	m = MothurOut::getInstance();
 	groupFileName = filename;
 	m->openInputFile(filename, fileHandle);
 }
@@ -20,28 +21,38 @@
  TreeMap::~TreeMap(){}
 
 /************************************************************/
-void TreeMap::readMap() {
+int TreeMap::readMap() {
 		string seqName, seqGroup;
-	
+		int error = 0;
+		
 		while(fileHandle){
-			fileHandle >> seqName;			//read from first column
+			fileHandle >> seqName;      	//read from first column
 			fileHandle >> seqGroup;			//read from second column
-
-			namesOfSeqs.push_back(seqName);
+			
+			if (m->control_pressed) {  fileHandle.close();  return 1; }
+			
 			setNamesOfGroups(seqGroup);
 					
-			treemap[seqName].groupname = seqGroup;	//store data in map
-			
-			it2 = seqsPerGroup.find(seqGroup);
-			if (it2 == seqsPerGroup.end()) { //if it's a new group
-				seqsPerGroup[seqGroup] = 1;
-			}else {//it's a group we already have
-				seqsPerGroup[seqGroup]++;
+			map<string, GroupIndex>::iterator itCheck = treemap.find(seqName);
+			if (itCheck != treemap.end()) { error = 1; m->mothurOut("[WARNING]: Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
+			else {
+				namesOfSeqs.push_back(seqName);
+				treemap[seqName].groupname = seqGroup;	//store data in map
+				
+				it2 = seqsPerGroup.find(seqGroup);
+				if (it2 == seqsPerGroup.end()) { //if it's a new group
+					seqsPerGroup[seqGroup] = 1;
+				}else {//it's a group we already have
+					seqsPerGroup[seqGroup]++;
+				}				
 			}
-
+			
 			m->gobble(fileHandle);
 		}
 		fileHandle.close();
+	
+
+		return error;
 }
 /************************************************************/
 void TreeMap::addSeq(string seqName, string seqGroup) {
@@ -170,13 +181,13 @@ void TreeMap::print(ostream& output){
 }
 
 /************************************************************/
-void TreeMap::makeSim(GroupMap* groupmap) {
+void TreeMap::makeSim(vector<string> ThisnamesOfGroups) {
 	try {
 		//set names of groups
-		namesOfGroups = groupmap->namesOfGroups;
+		namesOfGroups = ThisnamesOfGroups;
 		
 		//set names of seqs to names of groups
-		namesOfSeqs = groupmap->namesOfGroups;
+		namesOfSeqs = ThisnamesOfGroups;
 		
 		// make map where key and value are both the group name since that what the tree.shared command wants
 		for (int i = 0; i < namesOfGroups.size(); i++) {