#include "mothur.h"
-
/***********************************************/
class MothurOut {
static MothurOut* getInstance();
void setFileName(string);
- void mothurOut(string);
- void mothurOutEndLine();
+ void mothurOut(string); //writes to cout and the logfile
+ void mothurOutEndLine(); //writes to cout and the logfile
+ void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
+ void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
void mothurOutJustToLog(string);
void errorOut(exception&, string, string);
void closeLog();
vector<string> Treenames;
map<string, string> names;
vector<string> namesOfGroups;
- string saveNextLabel, argv;
+ vector<string> binLabelsInFile;
+ vector<string> currentBinLabels;
+ string saveNextLabel, argv, sharedHeaderMode;
+ bool printedHeaders;
//functions from mothur.h
//file operations
vector<unsigned long int> divideFile(string, int&);
+ int divideFile(string, int&, vector<string>&);
vector<unsigned long int> setFilePosEachLine(string, int&);
vector<unsigned long int> setFilePosFasta(string, int&);
string sortFile(string, string);
void gobble(istream&);
void gobble(istringstream&);
map<string, int> readNames(string);
+ int readNames(string, map<string, string>&);
int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
+ void mothurRemove(string);
//searchs and checks
bool checkReleaseVersion(ifstream&, string);
float ceilDist(float, int);
float roundDist(float, int);
unsigned int fromBase36(string);
+ int getRandomIndex(int); //highest
int control_pressed;
bool executing, runParse, jumble, gui;
processors = "1";
flowfile = "";
gui = false;
- };
+ printedHeaders = false;
+ sharedHeaderMode = "";
+ }
~MothurOut();
string logFileName;