#include "mothur.h"
+
/***********************************************/
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
~MothurOut();
string logFileName;
- string defaultPath;
+ string defaultPath, outputDir;
+ string releaseDate, version;
+
ofstream out;
int mem_usage(double&, double&);