X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=47e5ca45cf52c61f8c14ce55c2e3c77dc83003c1;hb=1bf53bca7e26bf091588bc8ca6e68cbfae1df6fe;hp=92363f5b6f26996b2e83badf681befa1ae9e3e0a;hpb=050220fe7822cc660615972a0054cf4a83eefbe4;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 92363f5..47e5ca4 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -20,35 +20,182 @@ 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();
 		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; }
-
+		vector<string> Groups;
+		vector<string> Treenames;
+		map<string, string> names;
+		vector<string> namesOfGroups;
+		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 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&);
+		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);
+		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);
+		bool isContainingOnlyDigits(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);
+		unsigned int fromBase36(string);
+		int getRandomIndex(int); //highest
 
 		int control_pressed;
-		bool executing;
+		bool executing, runParse, jumble, gui;
+		
+		//current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
+		string getPhylipFile()		{ return phylipfile;		}
+		string getColumnFile()		{ return columnfile;		}
+		string getListFile()		{ return listfile;			}
+		string getRabundFile()		{ return rabundfile;		}
+		string getSabundFile()		{ return sabundfile;		}
+		string getNameFile()		{ return namefile;			}	
+		string getGroupFile()		{ return groupfile;			}	
+		string getOrderFile()		{ return orderfile;			}
+		string getOrderGroupFile()	{ return ordergroupfile;	}
+		string getTreeFile()		{ return treefile;			}
+		string getSharedFile()		{ return sharedfile;		}
+		string getRelAbundFile()	{ return relabundfile;		}
+		string getDesignFile()		{ return designfile;		}
+		string getFastaFile()		{ return fastafile;			}
+		string getSFFFile()			{ return sfffile;			}
+		string getQualFile()		{ return qualfile;			}
+		string getOligosFile()		{ return oligosfile;		}
+		string getAccnosFile()		{ return accnosfile;		}
+		string getTaxonomyFile()	{ return taxonomyfile;		}
+		string getFlowFile()		{ return flowfile;			}
+		string getProcessors()		{ return processors;		}
+		
+		void setListFile(string f)			{ listfile = getFullPathName(f);			}
+		void setTreeFile(string f)			{ treefile = getFullPathName(f);			}
+		void setGroupFile(string f)			{ groupfile = getFullPathName(f);			}		
+		void setPhylipFile(string f)		{ phylipfile = getFullPathName(f);			}
+		void setColumnFile(string f)		{ columnfile = getFullPathName(f);			}
+		void setNameFile(string f)			{ namefile = getFullPathName(f);			}	
+		void setRabundFile(string f)		{ rabundfile = getFullPathName(f);			}
+		void setSabundFile(string f)		{ sabundfile = getFullPathName(f);			}
+		void setSharedFile(string f)		{ sharedfile = getFullPathName(f);			}
+		void setRelAbundFile(string f)		{ relabundfile = getFullPathName(f);		}
+		void setOrderFile(string f)			{ orderfile = getFullPathName(f);			}
+		void setOrderGroupFile(string f)	{ ordergroupfile = getFullPathName(f);		}
+		void setDesignFile(string f)		{ designfile = getFullPathName(f);			}
+		void setFastaFile(string f)			{ fastafile = getFullPathName(f);			}
+		void setSFFFile(string f)			{ sfffile = getFullPathName(f);				}
+		void setQualFile(string f)			{ qualfile = getFullPathName(f);			}
+		void setOligosFile(string f)		{ oligosfile = getFullPathName(f);			}
+		void setAccnosFile(string f)		{ accnosfile = getFullPathName(f);			}
+		void setTaxonomyFile(string f)		{ taxonomyfile = getFullPathName(f);		}
+		void setFlowFile(string f)			{ flowfile = getFullPathName(f);			}
+		void setProcessors(string p)		{ processors = p;							}
+		
+		void printCurrentFiles();
+		bool hasCurrentFiles();
+		void clearCurrentFiles();
 		
-
 	private:
 		static MothurOut* _uniqueInstance;
 		MothurOut( const MothurOut& ); // Disable copy constructor
 		void operator=( const MothurOut& ); // Disable assignment operator
-		MothurOut() { control_pressed = false; defaultPath=""; };
+		MothurOut() { 
+			control_pressed = false; defaultPath=""; 
+			phylipfile = "";
+			columnfile = "";
+			listfile = "";
+			rabundfile = "";
+			sabundfile = "";
+			namefile = "";
+			groupfile = "";
+			designfile = "";
+			orderfile = "";
+			treefile = "";
+			sharedfile = "";
+			ordergroupfile = "";
+			relabundfile = "";
+			fastafile = "";
+			qualfile = "";
+			sfffile = "";
+			oligosfile = "";
+			accnosfile = "";
+			taxonomyfile = "";
+			processors = "1";
+			flowfile = "";
+			gui = false;
+			printedHeaders = false;
+			sharedHeaderMode = "";
+		}
 		~MothurOut();
 
 		string logFileName;
-		string defaultPath;
+		string defaultPath, outputDir;
 		string releaseDate, version;
-		
+	
+		string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
+		string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
+
+	
 		ofstream out;
 		
 		int mem_usage(double&, double&);