moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / groupmap.h

diff --git a/groupmap.h b/groupmap.h
deleted file mode 100644 (file)
index 29c1741..0000000
--- a/groupmap.h
+++ /dev/null
@@ -1,54 +0,0 @@
-#ifndef GROUPMAP_H
-#define GROUPMAP_H
-/*
- *  groupmap.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 12/1/08.
- *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "mothurout.h"
-
-/* This class is a representation of the groupfile.  It is used by all the shared commands to determine what group a 
-       certain sequence belongs to. */
-
-class GroupMap {
-public:
-       GroupMap() {};
-       GroupMap(string);
-       ~GroupMap();
-       int readMap();
-       int readDesignMap();
-       int getNumGroups();
-       bool isValidGroup(string);  //return true if string is a valid group
-       string getGroup(string);
-       void setGroup(string, string);
-       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();
-       vector<string> getNamesSeqs(vector<string>); //get names of seqs belonging to a group or set of groups
-       int getNumSeqs(string); //return the number of seqs in a given group
-                       
-private:
-       vector<string> namesOfGroups;
-       MothurOut* m;
-       ifstream fileHandle;
-       string groupFileName;
-       int index;
-       map<string, string>::iterator it;
-       void setNamesOfGroups(string); 
-       map<string, string> groupmap; //sequence name and groupname
-       map<string, int> seqsPerGroup;  //maps groupname to number of seqs in that group
-};
-
-#endif