X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=3cf6fa4963672b5d69acb7de389eb266b957ba24;hb=875ab4b2eec77b920e9fa0042f9a2aae2faff2b0;hp=4a46e051b67bb08caee8c4d97f3947c366d01926;hpb=a54ba6143022dc7294f4fdc468fc10b627c64b0e;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 4a46e05..3cf6fa4 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -40,6 +40,7 @@ class MothurOut {
 		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 mothurOutJustToScreen(string); //writes to cout
 		void mothurOutJustToLog(string);
 		void errorOut(exception&, string, string);
 		void closeLog();
@@ -69,7 +70,7 @@ class MothurOut {
 		vector<string> binLabelsInFile;
 		vector<string> currentBinLabels;
 		string saveNextLabel, argv, sharedHeaderMode, groupMode;
-		bool printedHeaders, commandInputsConvertError, changedSeqNames;
+		bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
 		
 		//functions from mothur.h
 		//file operations
@@ -92,7 +93,9 @@ 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&);
@@ -106,6 +109,8 @@ 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);
@@ -150,6 +155,7 @@ 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
 		int factorial(int num);
@@ -162,6 +168,7 @@ class MothurOut {
         vector<double> getStandardDeviation(vector< vector<double> >&);
         vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
         vector<double> getAverages(vector< vector<double> >&);
+        double getAverage(vector<double>);
         vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&);
         vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&, vector< vector<seqDist> >&);
         vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&, string);
@@ -264,6 +271,7 @@ class MothurOut {
 			sharedHeaderMode = "";
             groupMode = "group";
             changedSeqNames = false;
+            modifyNames = true;
 		}
 		~MothurOut();