added make.lefse command. fixed bug in make.contigs with trimming reverse barcodes...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 4a46e051b67bb08caee8c4d97f3947c366d01926..efb3823aa74fb162bc1e1d0090d3af958f89f777 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
@@ -106,6 +107,8 @@ 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);
@@ -162,6 +165,7 @@ 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 +268,7 @@ class MothurOut {
                        sharedHeaderMode = "";
             groupMode = "group";
             changedSeqNames = false;
+            modifyNames = true;
                }
                ~MothurOut();