added else if (matrix == "sim2") { }

[mothur.git] / groupmap.h

diff --git a/groupmap.h b/groupmap.h
index 54085a19bab041d0caf17981c8c6c81f05a0c8b9..29c174134eee5689e5210775dbde2f220010d551 100644 (file)
--- a/groupmap.h
+++ b/groupmap.h
@@ -2,7 +2,7 @@
 #define GROUPMAP_H
 /*
  *  groupmap.h
- *  Dotur
+ *  Mothur
  *
  *  Created by Sarah Westcott on 12/1/08.
  *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
@@ -26,7 +26,13 @@ public:
        bool isValidGroup(string);  //return true if string is a valid group
        string getGroup(string);
        void setGroup(string, string);
-       vector<string> namesOfGroups;
+       vector<string> getNamesOfGroups() {
+               sort(namesOfGroups.begin(), namesOfGroups.end());
+               groupIndex.clear();
+               for (int i = 0; i < namesOfGroups.size(); i++) { groupIndex[namesOfGroups[i]] = i; }
+               return namesOfGroups;
+       }
+       void setNamesOfGroups(vector<string> sn) { namesOfGroups = sn; }
        map<string, int> groupIndex;  //groupname, vectorIndex in namesOfGroups. - used by collectdisplays and libshuff commands.
        int getNumSeqs()  {  return groupmap.size();  }
        vector<string> getNamesSeqs();
@@ -34,6 +40,7 @@ public:
        int getNumSeqs(string); //return the number of seqs in a given group
                        
 private:
+       vector<string> namesOfGroups;
        MothurOut* m;
        ifstream fileHandle;
        string groupFileName;