added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / groupmap.h

diff --git a/groupmap.h b/groupmap.h
index 75e0fdcf8a7f9f69df01245f6e09e1e9038bde93..8a1cfff6f660e0042f8a44784e8abff7864c5c2e 100644 (file)
--- a/groupmap.h
+++ b/groupmap.h
@@ -5,35 +5,41 @@
  *  Dotur
  *
  *  Created by Sarah Westcott on 12/1/08.
- *  Copyright 2008 __MyCompanyName__. All rights reserved.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
-#include "utilities.hpp"
+#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();
-       void readMap();
+       int readMap();
        int getNumGroups();
+       bool isValidGroup(string);  //return true if string is a valid group
        string getGroup(string);
+       void setGroup(string, string);
        vector<string> namesOfGroups;
-       
-       
+       map<string, int> groupIndex;  //groupname, vectorIndex in namesOfGroups. - used by collectdisplays and libshuff commands.
+       int getNumSeqs()  {  return groupmap.size();  }
+       vector<string> getNamesSeqs();
+       int getNumSeqs(string); //return the number of seqs in a given group
+                       
 private:
+       MothurOut* m;
        ifstream fileHandle;
        string groupFileName;
-       int numGroups;
+       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
\ No newline at end of file
+#endif