made read.tree not require a groupfile, if one is not given all seqs are assumed...

[mothur.git] / treemap.cpp

diff --git a/treemap.cpp b/treemap.cpp
index dcef7f7c19174f1aaf6a1435931c9005f986f638..52a90031d380fedddd275bd5ebbb6a3f8600964c 100644 (file)
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -13,7 +13,7 @@
 
  TreeMap::TreeMap(string filename) {
        groupFileName = filename;
-       openInputFile(filename, fileHandle);
+       m->openInputFile(filename, fileHandle);
 }
 
 /************************************************************/
@@ -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