changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 9ce698be4e1963e6af9abee67673ded3e1743fde..b19c05a68381c3ca96e19264e0eca931e22a0895 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -82,6 +82,7 @@ class MothurOut {
                int appendFiles(string, string);
                int renameFile(string, string); //oldname, newname
                string getFullPathName(string);
+        string findProgramPath(string programName);
                string hasPath(string);
                string getExtension(string);
                string getPathName(string);
@@ -96,6 +97,7 @@ class MothurOut {
                string getline(istringstream&);
                void gobble(istream&);
                void gobble(istringstream&);
+        vector<string> splitWhiteSpace(string& rest, char[], int);
                map<string, int> readNames(string);
                int readNames(string, map<string, string>&);
                int readNames(string, map<string, vector<string> >&);
@@ -130,6 +132,7 @@ class MothurOut {
                void splitAtChar(string&, vector<string>&, char);
         void splitAtChar(string&, string&, char);
                int removeConfidences(string&);
+        string makeList(vector<string>&);
                
                //math operation
                int factorial(int num);
@@ -140,7 +143,7 @@ class MothurOut {
                int getRandomIndex(int); //highest
 
                int control_pressed;
-               bool executing, runParse, jumble, gui, mothurCalling;
+               bool executing, runParse, jumble, gui, mothurCalling, debug;
                
                //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
                string getPhylipFile()          { return phylipfile;            }
@@ -225,6 +228,7 @@ class MothurOut {
                        printedHeaders = false;
                        commandInputsConvertError = false;
             mothurCalling = false;
+            debug = false;
                        sharedHeaderMode = "";
                }
                ~MothurOut();