X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=a1d950661d8d0f3f8084859a85110db97846cd4d;hb=5d6d303e481489e226fdf8d6c5385b99b50718bc;hp=d2ba6b94f0b12a6bd31df7763e0d4b32d705d3ea;hpb=e189982e0a9b7352ad57cc38ccee675f128be22e;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index d2ba6b9..a1d9506 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -1,46 +1,112 @@
-#ifndef MOTHUROUT_H
-#define MOTHUROUT_H
-
-/*
- *  mothurOut.h
- *  Mothur
- *
- *  Created by westcott on 2/25/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothur.h"
-
-/***********************************************/
-
-class MothurOut {
-	
-	public:
-		static MothurOut* getInstance();
-		void setFileName(string);
-		
-		void mothurOut(string);
-		void mothurOutEndLine();
-		void mothurOutJustToLog(string);
-		void errorOut(exception&, string, string);
-		void closeLog();
-
-		int control_pressed;
-		bool executing;
-
-	private:
-		static MothurOut* _uniqueInstance;
-		MothurOut( const MothurOut& ); // Disable copy constructor
-		void operator=( const MothurOut& ); // Disable assignment operator
-		MothurOut() { control_pressed = false; };
-		~MothurOut();
-
-		string logFileName;
-		ofstream out;
-
-};
-/***********************************************/
-
-#endif
-
+#ifndef MOTHUROUT_H
+#define MOTHUROUT_H
+
+/*
+ *  mothurOut.h
+ *  Mothur
+ *
+ *  Created by westcott on 2/25/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+
+
+/***********************************************/
+
+class MothurOut {
+	
+	public:
+		static MothurOut* getInstance();
+		void setFileName(string);
+		
+		void mothurOut(string);
+		void mothurOutEndLine();
+		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; }
+		
+		//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);
+		unsigned int fromBase36(string);
+
+		int control_pressed;
+		bool executing;
+		
+	private:
+		static MothurOut* _uniqueInstance;
+		MothurOut( const MothurOut& ); // Disable copy constructor
+		void operator=( const MothurOut& ); // Disable assignment operator
+		MothurOut() { control_pressed = false; defaultPath=""; };
+		~MothurOut();
+
+		string logFileName;
+		string defaultPath, outputDir;
+		string releaseDate, version;
+		
+		ofstream out;
+		
+		int mem_usage(double&, double&);
+
+};
+/***********************************************/
+
+#endif
+