X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.h;h=363a7a88041ac97bfd207558fc4fa445af7d442b;hp=f99eac1917cbe2ce5a1ce278c66d27d1df71737e;hb=499f4ac6e321f9f03d4c3aa25c3b6880892c8b83;hpb=ac663461b19ad1436a06aa63f97221d1ff105482

diff --git a/mothurout.h b/mothurout.h
index f99eac1..363a7a8 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -67,10 +67,12 @@ class MothurOut {
 		vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
 		vector<string> Treenames;
 		//map<string, string> names;
-		vector<string> binLabelsInFile;
-		vector<string> currentBinLabels;
+		vector<string> sharedBinLabelsInFile;
+		vector<string> currentSharedBinLabels;
+        vector<string> listBinLabelsInFile;
+        //vector<string> currentListBinLabels;
 		string saveNextLabel, argv, sharedHeaderMode, groupMode;
-		bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
+		bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
 		
 		//functions from mothur.h
 		//file operations
@@ -93,7 +95,9 @@ class MothurOut {
 		string getRootName(string);
 		bool isBlank(string);
 		int openOutputFile(string, ofstream&);
+        int openOutputFileBinary(string, ofstream&);
 		int openOutputFileAppend(string, ofstream&);
+        int openOutputFileBinaryAppend(string, ofstream&);
 		int openInputFile(string, ifstream&);
 		int openInputFile(string, ifstream&, string); //no error given 
 		string getline(ifstream&);
@@ -107,6 +111,8 @@ class MothurOut {
         map<string, int> readNames(string);
         map<string, int> readNames(string, unsigned long int&);
         int readTax(string, map<string, string>&);
+        vector<consTax> readConsTax(string);
+        int readConsTax(string, map<string, consTax2>&);
         int readNames(string, map<string, string>&, map<string, int>&);
 		int readNames(string, map<string, string>&);
         int readNames(string, map<string, string>&, bool);
@@ -134,6 +140,9 @@ class MothurOut {
 		bool isTrue(string);
 		bool isContainingOnlyDigits(string);
 		bool isNumeric1(string);
+        bool isLabelEquivalent(string, string);
+        string getSimpleLabel(string);
+        string findEdianness();
 	
 		
 		//string manipulation
@@ -151,13 +160,17 @@ class MothurOut {
         string makeList(vector<string>&);
         bool isSubset(vector<string>, vector<string>); //bigSet, subset
         int checkName(string&);
+        map<string, vector<string> > parseClasses(string);
 		
 		//math operation
+        double max(vector<double>&); //returns largest value in vector
+        double min(vector<double>&); //returns smallest value in vector
 		int factorial(int num);
 		vector<vector<double> > binomial(int);
 		float ceilDist(float, int);
 		float roundDist(float, int);
 		unsigned int fromBase36(string);
+        double median(vector<double>);
 		int getRandomIndex(int); //highest
         double getStandardDeviation(vector<int>&);
         vector<double> getStandardDeviation(vector< vector<double> >&);
@@ -259,7 +272,8 @@ class MothurOut {
             counttablefile = "";
             summaryfile = "";
 			gui = false;
-			printedHeaders = false;
+			printedSharedHeaders = false;
+            printedListHeaders = false;
 			commandInputsConvertError = false;
             mothurCalling = false;
             debug = false;