X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.cpp;h=52a90031d380fedddd275bd5ebbb6a3f8600964c;hb=a4f05f09c250323132a4b9427f41a3ededaec634;hp=bb624480e79640d8a23fc6fe4c47c8ba8c6b82a4;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/treemap.cpp b/treemap.cpp
index bb62448..52a9003 100644
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -13,7 +13,7 @@
 
  TreeMap::TreeMap(string filename) {
 	groupFileName = filename;
-	openInputFile(filename, fileHandle);
+	m->openInputFile(filename, fileHandle);
 }
 
 /************************************************************/
@@ -26,10 +26,10 @@ void TreeMap::readMap() {
 		while(fileHandle){
 			fileHandle >> seqName;			//read from first column
 			fileHandle >> seqGroup;			//read from second column
-			
+
 			namesOfSeqs.push_back(seqName);
 			setNamesOfGroups(seqGroup);
-						
+					
 			treemap[seqName].groupname = seqGroup;	//store data in map
 			
 			it2 = seqsPerGroup.find(seqGroup);
@@ -39,11 +39,26 @@ void TreeMap::readMap() {
 				seqsPerGroup[seqGroup]++;
 			}
 
-			gobble(fileHandle);
+			m->gobble(fileHandle);
 		}
 		fileHandle.close();
 }
 /************************************************************/
+void TreeMap::addSeq(string seqName, string seqGroup) {
+	
+		namesOfSeqs.push_back(seqName);
+		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]++;
+		}
+}
+/************************************************************/
 void TreeMap::removeSeq(string seqName) {
 	
 	//erase name from namesOfSeqs