X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=groupmap.h;h=54085a19bab041d0caf17981c8c6c81f05a0c8b9;hb=bdb5d82e2a73829b4e1fa42656ad9bcb57e3e948;hp=75e0fdcf8a7f9f69df01245f6e09e1e9038bde93;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/groupmap.h b/groupmap.h
index 75e0fdc..54085a1 100644
--- a/groupmap.h
+++ b/groupmap.h
@@ -5,35 +5,43 @@
  *  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 readDesignMap();
 	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();
+	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:
+	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