changes while testing

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 4a46e051b67bb08caee8c4d97f3947c366d01926..f99eac1917cbe2ce5a1ce278c66d27d1df71737e 100644 (file)
--- 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
@@ -162,6 +163,7 @@ 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 +266,7 @@ class MothurOut {
                        sharedHeaderMode = "";
             groupMode = "group";
             changedSeqNames = false;
+            modifyNames = true;
                }
                ~MothurOut();