X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=785263b4a11474ba939df4c97ae5f94ce6206d5a;hb=74dc92cf53df65fd8b14d8eaf35489bbecbccac6;hp=f68e45324d0939182be7eb1b4b373b2c502d5c80;hpb=65b6a38d00b3a72021611211e7c25392022c69ed;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index f68e453..785263b 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);
@@ -69,7 +81,10 @@ class MothurOut {
 		void gobble(istringstream&);
 		map<string, int> readNames(string);
 		int readNames(string, map<string, string>&);
+		int readNames(string, map<string, vector<string> >&);
 		int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
+		void mothurRemove(string);
+	
 		
 		//searchs and checks
 		bool checkReleaseVersion(ifstream&, string);
@@ -91,6 +106,7 @@ class MothurOut {
 		void splitAtDash(string&, set<string>&);
 		void splitAtDash(string&, vector<string>&);
 		void splitAtChar(string&, vector<string>&, char);
+		int removeConfidences(string&);
 		
 		//math operation
 		int factorial(int num);
@@ -192,7 +208,8 @@ 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&);