X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.h;h=3cf6fa4963672b5d69acb7de389eb266b957ba24;hp=bf356ae285fba010f41f2bbc51b9ce093ead1b1b;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=a86aff4f80701bf0d436f02c0095920114e1cba2

diff --git a/mothurout.h b/mothurout.h
index bf356ae..3cf6fa4 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -12,6 +12,22 @@
 
 #include "mothur.h"
 
+/***********************************************/
+struct logger {
+    
+    logger() {}
+    ~logger() {}
+    
+    template< class T >
+    logger& operator <<( const T& o ) {
+        cout << o; return *this;
+    }
+    
+    logger& operator<<(ostream& (*m)(ostream&) ) {
+        cout << m; return *this;
+    }
+    
+}; 
 /***********************************************/
 
 class MothurOut {
@@ -20,23 +36,254 @@ 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 mothurOutJustToScreen(string); //writes to cout
 		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; }
+	
+		void addGroup(string g) { Groups.push_back(g); }
+		void setGroups(vector<string>& g) { sort(g.begin(), g.end()); Groups = g; }
+		void clearGroups() { Groups.clear(); }
+	    int getNumGroups() { return Groups.size(); }
+		vector<string> getGroups() { sort(Groups.begin(), Groups.end()); return Groups; }
+		void addAllGroup(string g) { namesOfGroups.push_back(g); }
+		void setAllGroups(vector<string>& g) { sort(g.begin(), g.end()); namesOfGroups = g; }
+		void clearAllGroups() { namesOfGroups.clear(); }
+		int getNumAllGroups() { return namesOfGroups.size(); }
+	
+		vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
+		vector<string> Treenames;
+		//map<string, string> names;
+		vector<string> binLabelsInFile;
+		vector<string> currentBinLabels;
+		string saveNextLabel, argv, sharedHeaderMode, groupMode;
+		bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
+		
+		//functions from mothur.h
+		//file operations
+        bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable.
+		vector<unsigned long long> divideFile(string, int&); //divides splitting unevenness by sequence
+        vector<unsigned long long> divideFilePerLine(string, int&); //divides splitting unevenness at line breaks
+		int divideFile(string, int&, vector<string>&);
+		vector<unsigned long long> setFilePosEachLine(string, int&);
+		vector<unsigned long long> setFilePosFasta(string, int&);
+		string sortFile(string, string);
+		int appendFiles(string, string);
+        int appendFilesWithoutHeaders(string, string);
+		int renameFile(string, string); //oldname, newname
+		string getFullPathName(string);
+        string findProgramPath(string programName);
+		string hasPath(string);
+		string getExtension(string);
+		string getPathName(string);
+		string getSimpleName(string);
+		string getRootName(string);
+		bool isBlank(string);
+		int openOutputFile(string, ofstream&);
+        int openOutputFileBinary(string, ofstream&);
+		int openOutputFileAppend(string, ofstream&);
+        int openOutputFileBinaryAppend(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&);
+        vector<string> splitWhiteSpace(string& rest, char[], int);
+        vector<string> splitWhiteSpace(string);
+        set<string> readAccnos(string);
+        int readAccnos(string, vector<string>&);
+        map<string, int> readNames(string);
+        map<string, int> readNames(string, unsigned long int&);
+        int readTax(string, map<string, string>&);
+        vector<consTax> readConsTax(string);
+        int readConsTax(string, map<string, consTax2>&);
+        int readNames(string, map<string, string>&, map<string, int>&);
+		int readNames(string, map<string, string>&);
+        int readNames(string, map<string, string>&, bool);
+        int readNames(string, map<string, string>&, int);
+		int readNames(string, map<string, vector<string> >&);
+		int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
+		int mothurRemove(string);
+		bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+        bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+		bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+		bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+	
+		
+		//searchs and checks
+		bool checkReleaseVersion(ifstream&, string);
+		bool anyLabelsToProcess(string, set<string>&, string);
+		bool inUsersGroups(vector<string>, vector<string>);
+        bool inUsersGroups(vector<int>, vector< vector<int> >);
+		bool inUsersGroups(string, vector<string>);
+        bool inUsersGroups(int, vector<int>);
+		void getNumSeqs(ifstream&, int&);
+		int getNumSeqs(ifstream&);
+		int getNumNames(string);
+		int getNumChar(string, char);
+		bool isTrue(string);
+		bool isContainingOnlyDigits(string);
+		bool isNumeric1(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);
+        void splitAtChar(string&, string&, char);
+        vector<string> splitWhiteSpaceWithQuotes(string);
+		int removeConfidences(string&);
+        string removeQuotes(string);
+        string makeList(vector<string>&);
+        bool isSubset(vector<string>, vector<string>); //bigSet, subset
+        int checkName(string&);
+        map<string, vector<string> > parseClasses(string);
+		
+		//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
+        double getStandardDeviation(vector<int>&);
+        vector<double> getStandardDeviation(vector< vector<double> >&);
+        vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
+        vector<double> getAverages(vector< vector<double> >&);
+        double getAverage(vector<double>);
+        vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&);
+        vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&, vector< vector<seqDist> >&);
+        vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&, string);
+        vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&);
 
 		int control_pressed;
-		bool executing;
-
+		bool executing, runParse, jumble, gui, mothurCalling, debug;
+		
+		//current files - if you add a new type you must edit optionParser->getParameters, get.current and set.current commands and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes. add a get and set function.
+		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 getBiomFile()		{ return biomfile;			}
+        string getCountTableFile()	{ return counttablefile;	}
+        string getSummaryFile()     { return summaryfile;       }
+		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);	groupMode = "group";		}		
+		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 setBiomFile(string f)			{ biomfile = getFullPathName(f);			}
+        void setSummaryFile(string f)		{ summaryfile = getFullPathName(f);			}
+        void setCountTableFile(string f)	{ counttablefile = getFullPathName(f);	groupMode = "count";	}
+        void setProcessors(string p)		{ processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");	}
+		
+		void printCurrentFiles();
+		bool hasCurrentFiles();
+		void clearCurrentFiles();
+        set<string> getCurrentTypes(); 
+		
 	private:
 		static MothurOut* _uniqueInstance;
 		MothurOut( const MothurOut& ); // Disable copy constructor
 		void operator=( const MothurOut& ); // Disable assignment operator
-		MothurOut() { control_pressed = false; };
+		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 = "";
+            biomfile = "";
+            counttablefile = "";
+            summaryfile = "";
+			gui = false;
+			printedHeaders = false;
+			commandInputsConvertError = false;
+            mothurCalling = false;
+            debug = false;
+			sharedHeaderMode = "";
+            groupMode = "group";
+            changedSeqNames = false;
+            modifyNames = true;
+		}
 		~MothurOut();
 
 		string logFileName;
+		string defaultPath, outputDir;
+		string releaseDate, version;
+	
+		string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
+		string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile;
+
+		vector<string> Groups;
+		vector<string> namesOfGroups;
 		ofstream out;
 		
 		int mem_usage(double&, double&);