X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.h;h=1747b1480c732ae42f361940ff57dcbe151bbc7b;hp=77b1b6d4ec1efb758973d332aa8e4df00619f58b;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=372fb21ea66ced432b109225851a1b80ef0491a3

diff --git a/mothurout.h b/mothurout.h
index 77b1b6d..1747b14 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -66,11 +66,11 @@ 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;
 		string saveNextLabel, argv, sharedHeaderMode, groupMode;
-		bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
+		bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
 		
 		//functions from mothur.h
 		//file operations
@@ -82,6 +82,7 @@ class MothurOut {
 		vector<unsigned long long> setFilePosFasta(string, int&);
 		string sortFile(string, string);
 		int appendFiles(string, string);
+        int appendBinaryFiles(string, string);
         int appendFilesWithoutHeaders(string, string);
 		int renameFile(string, string); //oldname, newname
 		string getFullPathName(string);
@@ -93,9 +94,15 @@ 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 
+        int openInputFileBinary(string, ifstream&);
+        int openInputFileBinary(string, ifstream&, string);
+		int openInputFile(string, ifstream&, string); //no error given
+    
+        bool checkLocations(string&, string);  //filename, inputDir. checks for file in ./, inputdir, default and mothur's exe location.  Returns false if cant be found. If found completes name with location
 		string getline(ifstream&);
 		string getline(istringstream&);
 		void gobble(istream&);
@@ -136,6 +143,9 @@ class MothurOut {
 		bool isTrue(string);
 		bool isContainingOnlyDigits(string);
 		bool isNumeric1(string);
+        bool isLabelEquivalent(string, string);
+        string getSimpleLabel(string);
+        string findEdianness();
 	
 		
 		//string manipulation
@@ -156,11 +166,14 @@ class MothurOut {
         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> >&);
@@ -262,7 +275,8 @@ class MothurOut {
             counttablefile = "";
             summaryfile = "";
 			gui = false;
-			printedHeaders = false;
+			printedSharedHeaders = false;
+            printedListHeaders = false;
 			commandInputsConvertError = false;
             mothurCalling = false;
             debug = false;