X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.h;h=5397e02e7c158e5074a7f8e626d813561cc6d9b6;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=8a1cfff6f660e0042f8a44784e8abff7864c5c2e;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/groupmap.h b/groupmap.h
index 8a1cfff..5397e02 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.
@@ -17,25 +17,42 @@
 
 class GroupMap {
 public:
-	GroupMap() {};
+	GroupMap() { m = MothurOut::getInstance(); }
 	GroupMap(string);
 	~GroupMap();
 	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);
 	void setGroup(string, string);
-	vector<string> namesOfGroups;
-	map<string, int> groupIndex;  //groupname, vectorIndex in namesOfGroups. - used by collectdisplays and libshuff commands.
+	vector<string> getNamesOfGroups() {
+		sort(namesOfGroups.begin(), namesOfGroups.end());
+		groupIndex.clear();
+		for (int i = 0; i < namesOfGroups.size(); i++) { groupIndex[namesOfGroups[i]] = i; }
+		return namesOfGroups;
+	}
+    vector<string> getNamesSeqs();
+	void setNamesOfGroups(vector<string> sn) { namesOfGroups = sn; }
 	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
-			
+    int getCopy(GroupMap*);
+    int renameSeq(string, string);
+    int print(ofstream&);
+    int print(ofstream&, vector<string>); //print certain groups
+    
+    
+    map<string, int> groupIndex;  //groupname, vectorIndex in namesOfGroups. - used by collectdisplays and libshuff commands.
+    
 private:
+	vector<string> namesOfGroups;
 	MothurOut* m;
 	ifstream fileHandle;
 	string groupFileName;
-	int index;
+    int index;
 	map<string, string>::iterator it;
 	void setNamesOfGroups(string); 
 	map<string, string> groupmap; //sequence name and groupname