X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=3cf6fa4963672b5d69acb7de389eb266b957ba24;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=643ecd58a149aebc1ac88f500d4658de98d5e145;hpb=c48d91112209b841444923670dca5454da0e2a4d;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 643ecd5..3cf6fa4 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -70,7 +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
@@ -93,7 +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&);
@@ -107,6 +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);
@@ -151,6 +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);
@@ -163,6 +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);
@@ -265,6 +271,7 @@ class MothurOut {
 			sharedHeaderMode = "";
             groupMode = "group";
             changedSeqNames = false;
+            modifyNames = true;
 		}
 		~MothurOut();