working on chimera.perseus. made removeConfidences function smarter. Fixed bug in...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 013aa541444227deab43ec80eda7948dfd402bb6..785263b4a11474ba939df4c97ae5f94ce6206d5a 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -62,7 +62,7 @@ class MothurOut {
                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 +81,10 @@ 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);
+       
                
                //searchs and checks
                bool checkReleaseVersion(ifstream&, string);
@@ -104,6 +106,7 @@ 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);