X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=3019386a64d8947bccfcee23a9705e3b7e5d3898;hb=8c8acb6218f58f662466e4111ab8aa4da0caf93c;hp=6cdf4933266362c0cbaa3333d05045385668ab6b;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 6cdf493..3019386 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -36,21 +36,33 @@ class MothurOut {
 		void setReleaseDate(string r) { releaseDate = r; }
 		string getVersion() { return version; }
 		void setVersion(string r) { version = r; }
-		vector<string> Groups;
+	
+		void addGroup(string g) { Groups.push_back(g); }
+		void setGroups(vector<string>& g) { sort(g.begin(), g.end()); Groups = g; }
+		void clearGroups() { Groups.clear(); }
+	    int getNumGroups() { return Groups.size(); }
+		vector<string> getGroups() { sort(Groups.begin(), Groups.end()); return Groups; }
+		void addAllGroup(string g) { namesOfGroups.push_back(g); }
+		void setAllGroups(vector<string>& g) { sort(g.begin(), g.end()); namesOfGroups = g; }
+		void clearAllGroups() { namesOfGroups.clear(); }
+		int getNumAllGroups() { return namesOfGroups.size(); }
+	
+		vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
 		vector<string> Treenames;
 		map<string, string> names;
-		vector<string> namesOfGroups;
+		vector<string> binLabelsInFile;
+		vector<string> currentBinLabels;
 		string saveNextLabel, argv, sharedHeaderMode;
 		bool printedHeaders;
 		
 		//functions from mothur.h
 		//file operations
-		vector<unsigned long int> divideFile(string, int&);
+		vector<unsigned long long> divideFile(string, int&);
 		int divideFile(string, int&, vector<string>&);
-		vector<unsigned long int> setFilePosEachLine(string, int&);
-		vector<unsigned long int> setFilePosFasta(string, int&);
+		vector<unsigned long long> setFilePosEachLine(string, int&);
+		vector<unsigned long long> setFilePosFasta(string, int&);
 		string sortFile(string, string);
-		void appendFiles(string, string);
+		int appendFiles(string, string);
 		int renameFile(string, string); //oldname, newname
 		string getFullPathName(string);
 		string hasPath(string);
@@ -193,7 +205,8 @@ class MothurOut {
 		string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
 		string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
-	
+		vector<string> Groups;
+		vector<string> namesOfGroups;
 		ofstream out;
 		
 		int mem_usage(double&, double&);