X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=groupmap.h;h=d6984952188de368c765bf2997198f1fefb8bce5;hp=75e0fdcf8a7f9f69df01245f6e09e1e9038bde93;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/groupmap.h b/groupmap.h
index 75e0fdc..d698495 100644
--- a/groupmap.h
+++ b/groupmap.h
@@ -2,38 +2,55 @@
 #define GROUPMAP_H
 /*
  *  groupmap.h
- *  Dotur
+ *  Mothur
  *
  *  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() { m = MothurOut::getInstance(); }
 	GroupMap(string);
 	~GroupMap();
-	void readMap();
+	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);
-	vector<string> namesOfGroups;
-	
-	
+	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 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