added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index e61490267270680e6800cfa31a68b47cb1bbbbc3..d2a36b351902f3bc25d7c2132fb2c20f15421b23 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -53,7 +53,7 @@ class MothurOut {
                vector<string> binLabelsInFile;
                vector<string> currentBinLabels;
                string saveNextLabel, argv, sharedHeaderMode;
-               bool printedHeaders;
+               bool printedHeaders, commandInputsConvertError;
                
                //functions from mothur.h
                //file operations
@@ -84,6 +84,9 @@ class MothurOut {
                int readNames(string, map<string, vector<string> >&);
                int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
                int mothurRemove(string);
+               bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+               bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+               bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
        
                
                //searchs and checks
@@ -94,8 +97,10 @@ class MothurOut {
                void getNumSeqs(ifstream&, int&);
                int getNumSeqs(ifstream&);
                int getNumNames(string);
+               int getNumChar(string, char);
                bool isTrue(string);
                bool isContainingOnlyDigits(string);
+               bool isNumeric1(string);
        
                
                //string manipulation
@@ -197,6 +202,7 @@ class MothurOut {
                        flowfile = "";
                        gui = false;
                        printedHeaders = false;
+                       commandInputsConvertError = false;
                        sharedHeaderMode = "";
                }
                ~MothurOut();