X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.h;h=29c174134eee5689e5210775dbde2f220010d551;hb=8e3e7b1e124f45cb1f2ca9d764ff67fa9b2e532b;hp=fd6c14605065ea3fd1f12613d89b6bca9a1e0861;hpb=9354b70bb84f6dd52ff4a1955754bcbf7edeedbf;p=mothur.git

diff --git a/groupmap.h b/groupmap.h
index fd6c146..29c1741 100644
--- 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.
@@ -10,6 +10,7 @@
  */
 
 #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. */
@@ -19,18 +20,28 @@ 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;
+	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;