1.23.0

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 6f04f892dbb588700c884d27071fb613457fb35b..d2a36b351902f3bc25d7c2132fb2c20f15421b23 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -53,16 +53,16 @@ class MothurOut {
                vector<string> binLabelsInFile;
                vector<string> currentBinLabels;
                string saveNextLabel, argv, sharedHeaderMode;
-               bool printedHeaders;
+               bool printedHeaders, commandInputsConvertError;
                
                //functions from mothur.h
                //file operations
-               vector<unsigned long int> divideFile(string, int&);
+               vector<unsigned long long> divideFile(string, int&);
                int divideFile(string, int&, vector<string>&);
-               vector<unsigned long int> setFilePosEachLine(string, int&);
-               vector<unsigned long int> setFilePosFasta(string, int&);
+               vector<unsigned long long> setFilePosEachLine(string, int&);
+               vector<unsigned long long> setFilePosFasta(string, int&);
                string sortFile(string, string);
-               void appendFiles(string, string);
+               int appendFiles(string, string);
                int renameFile(string, string); //oldname, newname
                string getFullPathName(string);
                string hasPath(string);
@@ -81,8 +81,13 @@ class MothurOut {
                void gobble(istringstream&);
                map<string, int> readNames(string);
                int readNames(string, map<string, string>&);
+               int readNames(string, map<string, vector<string> >&);
                int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
-               void mothurRemove(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
                bool checkReleaseVersion(ifstream&, string);
@@ -92,8 +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
@@ -104,6 +111,7 @@ class MothurOut {
                void splitAtDash(string&, set<string>&);
                void splitAtDash(string&, vector<string>&);
                void splitAtChar(string&, vector<string>&, char);
+               int removeConfidences(string&);
                
                //math operation
                int factorial(int num);
@@ -194,6 +202,7 @@ class MothurOut {
                        flowfile = "";
                        gui = false;
                        printedHeaders = false;
+                       commandInputsConvertError = false;
                        sharedHeaderMode = "";
                }
                ~MothurOut();