added cluster.classic command

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 92363f5b6f26996b2e83badf681befa1ae9e3e0a..efe1294245d915a66dc76e0baea439b8cf9caa1a 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -12,6 +12,7 @@
 
 #include "mothur.h"
 
+
 /***********************************************/
 
 class MothurOut {
@@ -27,17 +28,67 @@ class MothurOut {
                void closeLog();
                string getDefaultPath() { return defaultPath; }
                void setDefaultPath(string);
+               string getOutputDir() { return outputDir; }
+               void setOutputDir(string);
                
                string getReleaseDate() { return releaseDate; }
                void setReleaseDate(string r) { releaseDate = r; }
                string getVersion() { return version; }
                void setVersion(string r) { version = r; }
-
+               
+               //functions from mothur.h
+               //file operations
+               vector<unsigned long int> divideFile(string, int&);
+               vector<unsigned long int> setFilePosEachLine(string, int&);
+               vector<unsigned long int> setFilePosFasta(string, int&);
+               string sortFile(string, string);
+               void appendFiles(string, string);
+               int renameFile(string, string); //oldname, newname
+               string getFullPathName(string);
+               string hasPath(string);
+               string getExtension(string);
+               string getPathName(string);
+               string getSimpleName(string);
+               string getRootName(string);
+               bool isBlank(string);
+               int openOutputFile(string, ofstream&);
+               int openOutputFileAppend(string, ofstream&);
+               int openInputFile(string, ifstream&);
+               int openInputFile(string, ifstream&, string); //no error given 
+               string getline(ifstream&);
+               string getline(istringstream&);
+               void gobble(istream&);
+               void gobble(istringstream&);
+               
+               //searchs and checks
+               bool checkReleaseVersion(ifstream&, string);
+               bool anyLabelsToProcess(string, set<string>&, string);
+               bool inUsersGroups(vector<string>, vector<string>);
+               bool inUsersGroups(string, vector<string>);
+               void getNumSeqs(ifstream&, int&);
+               int getNumSeqs(ifstream&);
+               int getNumNames(string);
+               bool isTrue(string);
+       
+               
+               //string manipulation
+               void splitAtEquals(string&, string&);
+               void splitAtComma(string&, string&);    
+               void splitAtComma(string&, vector<string>&);
+               void splitAtDash(string&, set<int>&);
+               void splitAtDash(string&, set<string>&);
+               void splitAtDash(string&, vector<string>&);
+               void splitAtChar(string&, vector<string>&, char);
+               
+               //math operation
+               int factorial(int num);
+               vector<vector<double> > binomial(int);
+               float ceilDist(float, int);
+               float roundDist(float, int);
 
                int control_pressed;
                bool executing;
                
-
        private:
                static MothurOut* _uniqueInstance;
                MothurOut( const MothurOut& ); // Disable copy constructor
@@ -46,7 +97,7 @@ class MothurOut {
                ~MothurOut();
 
                string logFileName;
-               string defaultPath;
+               string defaultPath, outputDir;
                string releaseDate, version;
                
                ofstream out;