sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / groupmap.h

diff --git a/groupmap.h b/groupmap.h
index 54085a19bab041d0caf17981c8c6c81f05a0c8b9..d6984952188de368c765bf2997198f1fefb8bce5 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.
@@ -17,16 +17,24 @@
 
 class GroupMap {
 public:
-       GroupMap() {};
+       GroupMap() { m = MothurOut::getInstance(); }
        GroupMap(string);
        ~GroupMap();
        int readMap();
+    int readMap(string);
        int readDesignMap();
+    int readDesignMap(string);
        int getNumGroups();
        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 +42,7 @@ public:
        int getNumSeqs(string); //return the number of seqs in a given group
                        
 private:
+       vector<string> namesOfGroups;
        MothurOut* m;
        ifstream fileHandle;
        string groupFileName;