X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=47e5ca45cf52c61f8c14ce55c2e3c77dc83003c1;hb=1bf53bca7e26bf091588bc8ca6e68cbfae1df6fe;hp=f6f505dce6409db716561b061a2e66eda3efae5a;hpb=86c838c428a9e7d26f902f5492738241fa72c4e7;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index f6f505d..47e5ca4 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();
@@ -39,11 +40,15 @@ class MothurOut {
 		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 +70,9 @@ 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 +101,7 @@ 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 +183,9 @@ class MothurOut {
 			processors = "1";
 			flowfile = "";
 			gui = false;
-		};
+			printedHeaders = false;
+			sharedHeaderMode = "";
+		}
 		~MothurOut();
 
 		string logFileName;