X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=6f04f892dbb588700c884d27071fb613457fb35b;hb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;hp=f6f505dce6409db716561b061a2e66eda3efae5a;hpb=86c838c428a9e7d26f902f5492738241fa72c4e7;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index f6f505d..6f04f89 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -12,7 +12,6 @@
 
 #include "mothur.h"
 
-
 /***********************************************/
 
 class MothurOut {
@@ -21,8 +20,10 @@ class MothurOut {
 		static MothurOut* getInstance();
 		void setFileName(string);
 		
-		void mothurOut(string);
-		void mothurOutEndLine();
+		void mothurOut(string); //writes to cout and the logfile
+		void mothurOutEndLine(); //writes to cout and the logfile
+		void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
+		void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
 		void mothurOutJustToLog(string);
 		void errorOut(exception&, string, string);
 		void closeLog();
@@ -35,15 +36,29 @@ 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;
-		string saveNextLabel, argv;
+		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&);
+		int divideFile(string, int&, vector<string>&);
 		vector<unsigned long int> setFilePosEachLine(string, int&);
 		vector<unsigned long int> setFilePosFasta(string, int&);
 		string sortFile(string, string);
@@ -65,7 +80,9 @@ class MothurOut {
 		void gobble(istream&);
 		void gobble(istringstream&);
 		map<string, int> readNames(string);
+		int readNames(string, map<string, string>&);
 		int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
+		void mothurRemove(string);
 		
 		//searchs and checks
 		bool checkReleaseVersion(ifstream&, string);
@@ -94,6 +111,7 @@ class MothurOut {
 		float ceilDist(float, int);
 		float roundDist(float, int);
 		unsigned int fromBase36(string);
+		int getRandomIndex(int); //highest
 
 		int control_pressed;
 		bool executing, runParse, jumble, gui;
@@ -175,7 +193,9 @@ class MothurOut {
 			processors = "1";
 			flowfile = "";
 			gui = false;
-		};
+			printedHeaders = false;
+			sharedHeaderMode = "";
+		}
 		~MothurOut();
 
 		string logFileName;
@@ -185,7 +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&);