From: westcott <westcott>
Date: Wed, 28 Apr 2010 11:09:48 +0000 (+0000)
Subject: added set.logfile command
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=84f93a9e670eb7f7e69e0468b9be4c53890c07f2

added set.logfile command
---

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index cc3b4b6..3ee1d81 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -14,6 +14,8 @@
 		A7639F8D1175DF35008F5578 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
 		A76AAD02117F322B003D8DA1 /* phylosummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylosummary.h; sourceTree = "<group>"; };
 		A76AAD03117F322B003D8DA1 /* phylosummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylosummary.cpp; sourceTree = "<group>"; };
+		A76C4A1011876BAF0009460B /* setlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setlogfilecommand.h; sourceTree = SOURCE_ROOT; };
+		A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setlogfilecommand.cpp; sourceTree = SOURCE_ROOT; };
 		A78254461164D7790002E2DD /* chimerapintailcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerapintailcommand.h; sourceTree = "<group>"; };
 		A78254471164D7790002E2DD /* chimerapintailcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerapintailcommand.cpp; sourceTree = "<group>"; };
 		A7825502116519F70002E2DD /* chimerabellerophoncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerabellerophoncommand.h; sourceTree = "<group>"; };
@@ -734,6 +736,8 @@
 				A7DA20FD113FECD400BF472F /* seqsummarycommand.h */,
 				A7DA2102113FECD400BF472F /* setdircommand.cpp */,
 				A7DA2103113FECD400BF472F /* setdircommand.h */,
+				A76C4A1011876BAF0009460B /* setlogfilecommand.h */,
+				A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */,
 				A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
 				A7DA2110113FECD400BF472F /* sharedcommand.h */,
 				A7DA2154113FECD400BF472F /* summarycommand.cpp */,
diff --git a/commandfactory.cpp b/commandfactory.cpp
index aaeec67..cad0442 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -71,6 +71,7 @@
 #include "chimeraslayercommand.h"
 #include "chimerapintailcommand.h"
 #include "chimerabellerophoncommand.h"
+#include "setlogfilecommand.h"
 
 /*******************************************************/
 
@@ -97,6 +98,8 @@ CommandFactory::CommandFactory(){
 	command = new NoCommand(s);
 	
 	outputDir = ""; inputDir = "";
+	logFileName = "";
+	append = false;
 	
 	//initialize list of valid commands
 	commands["read.dist"]			= "read.dist"; 
@@ -149,6 +152,7 @@ CommandFactory::CommandFactory(){
 	commands["merge.files"]			= "merge.files";
 	commands["parse.list"]			= "parse.list";
 	commands["parse.sff"]			= "parse.sff";
+	commands["set.logfile"]			= "set.logfile";
 	commands["classify.seqs"]		= "MPIEnabled"; 
 	commands["dist.seqs"]			= "MPIEnabled";
 	commands["filter.seqs"]			= "MPIEnabled";
@@ -260,6 +264,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "pcoa")					{	command = new PCACommand(optionString);						}
 		else if(commandName == "otu.hierarchy")			{	command = new OtuHierarchyCommand(optionString);			}
 		else if(commandName == "set.dir")				{	command = new SetDirectoryCommand(optionString);			}
+		else if(commandName == "set.logfile")			{	command = new SetLogFileCommand(optionString);				}
 		else if(commandName == "parse.list")			{	command = new ParseListCommand(optionString);				}
 		else if(commandName == "parse.sff")				{	command = new ParseSFFCommand(optionString);				}
 		else											{	command = new NoCommand(optionString);						}
diff --git a/commandfactory.hpp b/commandfactory.hpp
index 3b6a17e..44e78fd 100644
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -22,9 +22,12 @@ public:
 	Command* getCommand();
 	bool isValidCommand(string);
 	void printCommands(ostream&);
-	void setOutputDirectory(string o)	{	outputDir = o;		}
-	void setInputDirectory(string i)	{	inputDir = i;		}
-	string getOutputDir()			{	return outputDir;		}
+	void setOutputDirectory(string o)		{	outputDir = o;		}
+	void setInputDirectory(string i)		{	inputDir = i;		}
+	void setLogfileName(string n, bool a)	{	logFileName = n;  append = a;		}
+	string getLogfileName()					{	return logFileName; 	}
+	bool getAppend()						{	return append;			}
+	string getOutputDir()					{	return outputDir;		}
 	bool MPIEnabled(string);
 
 private:
@@ -32,7 +35,8 @@ private:
 	MothurOut* m;
 	map<string, string> commands;
 	map<string, string>::iterator it;
-	string outputDir, inputDir;
+	string outputDir, inputDir, logFileName;
+	bool append;
 	
 	static CommandFactory* _uniqueInstance;
 	CommandFactory( const CommandFactory& ); // Disable copy constructor
diff --git a/engine.hpp b/engine.hpp
index 74687d2..0020a7f 100644
--- a/engine.hpp
+++ b/engine.hpp
@@ -27,7 +27,10 @@ public:
 	virtual ~Engine(){}
 	virtual bool getInput() = 0;
 	virtual string getCommand();
-	virtual string getOutputDir()	{	return cFactory->getOutputDir();  }
+	virtual string getOutputDir()			{	return cFactory->getOutputDir();	}
+	virtual string getLogFileName()			{	return cFactory->getLogfileName(); 	}
+	virtual bool getAppend()				{	return cFactory->getAppend();		}
+
 	vector<string> getOptions()		{	return options;		}
 protected:
 	vector<string> options;
diff --git a/makefile b/makefile
index d4aac7f..181b897 100644
--- a/makefile
+++ b/makefile
@@ -239,7 +239,8 @@ mothur : \
 		./qstat.o\
 		./shen.o\
 		./logsd.o\
-		./geom.o
+		./geom.o\
+		./setlogfilecommand.o
 	$(CC) $(LNK_OPTIONS) \
 		./sharedutilities.o\
 		./treegroupscommand.o\
@@ -437,7 +438,8 @@ mothur : \
 		./qstat.o\
 		./shen.o\
 		./logsd.o\
-		./geom.o\
+		./geom.o\
+		./setlogfilecommand.o\
 		-o ../Release/mothur
 
 clean : 
@@ -638,7 +640,8 @@ clean :
 		./qstat.o\
 		./shen.o\
 		./logsd.o\
-		./geom.o\
+		./geom.o\
+		./setlogfilecommand.o\
 		mothur
 
 install : mothur
@@ -1623,9 +1626,13 @@ install : mothur
 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
 	$(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
 
-# Item # 171 -- phylosummary --
+# Item # 197 -- phylosummary --
 ./phylosummary.o : phylosummary.cpp
 	$(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
+
+# Item # 198 -- setlogfilecommand --
+./setlogfilecommand.o : setlogfilecommand.cpp
+	$(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
 
 
 
diff --git a/mothur.cpp b/mothur.cpp
index 2d35c69..4f91c2e 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -1,171 +1,193 @@
-/*
- *  interface.cpp
- *  
- *
- *  Created by Pat Schloss on 8/14/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- */
- 
-#include "mothur.h"
-#include "engine.hpp"
-#include "globaldata.hpp"
-#include "mothurout.h"
-
-
-/**************************************************************************************************/
-
-GlobalData* GlobalData::_uniqueInstance = 0;
-CommandFactory* CommandFactory::_uniqueInstance = 0;
-MothurOut* MothurOut::_uniqueInstance = 0;
-
-/***********************************************************************/
-volatile int ctrlc_pressed = 0;
-void ctrlc_handler ( int sig ) {
-	MothurOut* m = MothurOut::getInstance();
-    ctrlc_pressed = 1;
-	m->control_pressed = ctrlc_pressed;
-	
-	if (m->executing) { //if mid command quit execution, else quit mothur
-		m->mothurOutEndLine(); m->mothurOut("quitting command...");  m->mothurOutEndLine();
-	}else{
-		m->mothurOut("quitting mothur");  m->mothurOutEndLine();
-		exit(1);
-	}
-}
-/***********************************************************************/
-int main(int argc, char *argv[]){
-	MothurOut* m = MothurOut::getInstance();
-	try {
-		
-		signal(SIGINT, ctrlc_handler );
-				
-		time_t ltime = time(NULL); /* calendar time */  
-		string logFileName = "mothur." + toString(ltime) + ".logfile";
-		
-		#ifdef USE_MPI
-			MPI_Init(&argc, &argv); 
-		#endif
-
-		m->setFileName(logFileName);
-		
-				
-		//version
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-			system("clear");
-			#if defined (__APPLE__) || (__MACH__)
-				m->mothurOutJustToLog("Mac version");
-				m->mothurOutEndLine(); m->mothurOutEndLine();
-			#else
-				m->mothurOutJustToLog("Linux version");
-				>m->mothurOutEndLine(); m->mothurOutEndLine();
-			#endif
-
-		#else
-			system("CLS");
-			m->mothurOutJustToLog("Windows version");
-			m->mothurOutEndLine(); m->mothurOutEndLine();
-		#endif		
-		
-		#ifdef USE_READLINE
-			m->mothurOutJustToLog("Using ReadLine");
-			m->mothurOutEndLine(); m->mothurOutEndLine();
-		#endif
-		
-		//header
-		m->mothurOut("mothur v.1.9");
-		m->mothurOutEndLine();		
-		m->mothurOut("Last updated: 4/16/2010");
-		m->mothurOutEndLine();	
-		m->mothurOutEndLine();		
-		m->mothurOut("by");
-		m->mothurOutEndLine();		
-		m->mothurOut("Patrick D. Schloss");
-		m->mothurOutEndLine();
-		m->mothurOutEndLine();			
-		m->mothurOut("Department of Microbiology & Immunology");
-		m->mothurOutEndLine();	
-		m->mothurOut("University of Michigan");
-		m->mothurOutEndLine();			
-		m->mothurOut("pschloss@umich.edu");
-		m->mothurOutEndLine();		
-		m->mothurOut("http://www.mothur.org");
-		m->mothurOutEndLine();
-		m->mothurOutEndLine();
-		m->mothurOut("When using, please cite:");
-		m->mothurOutEndLine();
-		m->mothurOut("Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.");
-		m->mothurOutEndLine();	
-		m->mothurOutEndLine();		
-		m->mothurOut("Distributed under the GNU General Public License");
-		m->mothurOutEndLine();
-		m->mothurOutEndLine();			
-		m->mothurOut("Type 'help()' for information on the commands that are available");
-		m->mothurOutEndLine();
-		m->mothurOutEndLine();			
-		m->mothurOut("Type 'quit()' to exit program");
-		m->mothurOutEndLine();	
-		
-		#ifdef USE_MPI
-			m->mothurOutJustToLog("Using MPI\tversion ");
-			int version, subversion;
-			MPI_Get_version(&version, &subversion);
-			m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
-		#endif
-		
-		//srand(54321);
-		srand( (unsigned)time( NULL ) );
-		
-		Engine* mothur;
-		bool bail = 0;
-		string input;
-
-		if(argc>1){
-			input = argv[1];
-
-			if (input[0] == '#') {
-				m->mothurOutJustToLog("Script Mode");
-				m->mothurOutEndLine(); m->mothurOutEndLine();
-
-				mothur = new ScriptEngine(argv[0], argv[1]);
-			}else{
-				m->mothurOutJustToLog("Batch Mode");
-				m->mothurOutEndLine(); m->mothurOutEndLine();
-				
-				mothur = new BatchEngine(argv[0], argv[1]);
-			}
-		}
-		else{
-			m->mothurOutJustToLog("Interactive Mode");
-			m->mothurOutEndLine(); m->mothurOutEndLine();
-			
-			mothur = new InteractEngine(argv[0]);	
-		}
-		
-		while(bail == 0)	{	bail = mothur->getInput();	}
-		
-		string outputDir = mothur->getOutputDir();
-		string newlogFileName = outputDir + logFileName;
-		
-		//closes logfile so we can rename
-		m->closeLog();
-	
-		//need this because m->mothurOut makes the logfile, but doesn't know where to put it
-		rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
-		
-		delete mothur;
-		
-		#ifdef USE_MPI
-			MPI_Finalize();
-		#endif
-		
-		return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "mothur", "main");
-		exit(1);
-	}
-}
-
-/**************************************************************************************************/
-
+/*
+ *  interface.cpp
+ *  
+ *
+ *  Created by Pat Schloss on 8/14/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+ 
+#include "mothur.h"
+#include "engine.hpp"
+#include "globaldata.hpp"
+#include "mothurout.h"
+
+
+/**************************************************************************************************/
+
+GlobalData* GlobalData::_uniqueInstance = 0;
+CommandFactory* CommandFactory::_uniqueInstance = 0;
+MothurOut* MothurOut::_uniqueInstance = 0;
+
+/***********************************************************************/
+volatile int ctrlc_pressed = 0;
+void ctrlc_handler ( int sig ) {
+	MothurOut* m = MothurOut::getInstance();
+    ctrlc_pressed = 1;
+	m->control_pressed = ctrlc_pressed;
+	
+	if (m->executing) { //if mid command quit execution, else quit mothur
+		m->mothurOutEndLine(); m->mothurOut("quitting command...");  m->mothurOutEndLine();
+	}else{
+		m->mothurOut("quitting mothur");  m->mothurOutEndLine();
+		exit(1);
+	}
+}
+/***********************************************************************/
+int main(int argc, char *argv[]){
+	MothurOut* m = MothurOut::getInstance();
+	try {
+		
+		signal(SIGINT, ctrlc_handler );
+				
+		time_t ltime = time(NULL); /* calendar time */  
+		string logFileName = "mothur." + toString(ltime) + ".logfile";
+		
+		#ifdef USE_MPI
+			MPI_Init(&argc, &argv); 
+		#endif
+
+		m->setFileName(logFileName);
+		
+				
+		//version
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			system("clear");
+			#if defined (__APPLE__) || (__MACH__)
+				m->mothurOutJustToLog("Mac version");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+			#else
+				m->mothurOutJustToLog("Linux version");
+				>m->mothurOutEndLine(); m->mothurOutEndLine();
+			#endif
+
+		#else
+			system("CLS");
+			m->mothurOutJustToLog("Windows version");
+			m->mothurOutEndLine(); m->mothurOutEndLine();
+		#endif		
+		
+		#ifdef USE_READLINE
+			m->mothurOutJustToLog("Using ReadLine");
+			m->mothurOutEndLine(); m->mothurOutEndLine();
+		#endif
+		
+		//header
+		m->mothurOut("mothur v.1.9");
+		m->mothurOutEndLine();		
+		m->mothurOut("Last updated: 4/16/2010");
+		m->mothurOutEndLine();	
+		m->mothurOutEndLine();		
+		m->mothurOut("by");
+		m->mothurOutEndLine();		
+		m->mothurOut("Patrick D. Schloss");
+		m->mothurOutEndLine();
+		m->mothurOutEndLine();			
+		m->mothurOut("Department of Microbiology & Immunology");
+		m->mothurOutEndLine();	
+		m->mothurOut("University of Michigan");
+		m->mothurOutEndLine();			
+		m->mothurOut("pschloss@umich.edu");
+		m->mothurOutEndLine();		
+		m->mothurOut("http://www.mothur.org");
+		m->mothurOutEndLine();
+		m->mothurOutEndLine();
+		m->mothurOut("When using, please cite:");
+		m->mothurOutEndLine();
+		m->mothurOut("Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.");
+		m->mothurOutEndLine();	
+		m->mothurOutEndLine();		
+		m->mothurOut("Distributed under the GNU General Public License");
+		m->mothurOutEndLine();
+		m->mothurOutEndLine();			
+		m->mothurOut("Type 'help()' for information on the commands that are available");
+		m->mothurOutEndLine();
+		m->mothurOutEndLine();			
+		m->mothurOut("Type 'quit()' to exit program");
+		m->mothurOutEndLine();	
+		
+		#ifdef USE_MPI
+			m->mothurOutJustToLog("Using MPI\tversion ");
+			int version, subversion;
+			MPI_Get_version(&version, &subversion);
+			m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
+		#endif
+		
+		//srand(54321);
+		srand( (unsigned)time( NULL ) );
+		
+		Engine* mothur;
+		bool bail = 0;
+		string input;
+
+		if(argc>1){
+			input = argv[1];
+
+			if (input[0] == '#') {
+				m->mothurOutJustToLog("Script Mode");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+
+				mothur = new ScriptEngine(argv[0], argv[1]);
+			}else{
+				m->mothurOutJustToLog("Batch Mode");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+				
+				mothur = new BatchEngine(argv[0], argv[1]);
+			}
+		}
+		else{
+			m->mothurOutJustToLog("Interactive Mode");
+			m->mothurOutEndLine(); m->mothurOutEndLine();
+			
+			mothur = new InteractEngine(argv[0]);	
+		}
+		
+		while(bail == 0)	{	bail = mothur->getInput();	}
+		
+		//closes logfile so we can rename
+		m->closeLog();
+		
+		string outputDir = mothur->getOutputDir();
+		string tempLog = mothur->getLogFileName();
+		bool append = mothur->getAppend();
+		
+		string newlogFileName;
+		if (tempLog != "") {
+			newlogFileName = outputDir + tempLog;
+			
+			if (!append) {	
+				//need this because m->mothurOut makes the logfile, but doesn't know where to put it
+				rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
+
+			}else {
+				ofstream outNewLog;
+				openOutputFileAppend(newlogFileName, outNewLog);
+				outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+				outNewLog.close();
+				
+				appendFiles(logFileName, newlogFileName);
+				remove(logFileName.c_str());
+			}
+		}else{  
+			newlogFileName = outputDir + logFileName;
+			//need this because m->mothurOut makes the logfile, but doesn't know where to put it
+			rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
+		}
+		
+				
+		delete mothur;
+		
+		#ifdef USE_MPI
+			MPI_Finalize();
+		#endif
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "mothur", "main");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+
diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
new file mode 100644
index 0000000..593664e
--- /dev/null
+++ b/setlogfilecommand.cpp
@@ -0,0 +1,84 @@
+/*
+ *  setlogfilecommand.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 4/27/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "setlogfilecommand.h"
+
+//**********************************************************************************************************************
+
+SetLogFileCommand::SetLogFileCommand(string option)  {
+	try {
+		abort = false;
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"name","append","outputdir","inputdir"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			OptionParser parser(option);
+			map<string, string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+			//check to make sure all parameters are valid for command
+			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+		
+			name = validParameter.validFile(parameters, "name", false);			
+			if (name == "not found") {  m->mothurOut("name is a required parameter for the set.logfile command."); abort = true; } 
+			
+			string temp = validParameter.validFile(parameters, "append", false);		if (temp == "not found") {  temp = "F";  }
+			append = isTrue(temp);
+		}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SetLogFileCommand", "SetLogFileCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+void SetLogFileCommand::help(){
+	try {
+		m->mothurOut("The set.logfile command can be used to provide a specific name for your logfile and/or to append the log generated by mothur to an existing file.\n");
+		m->mothurOut("The set.logfile command parameters are name and append, name is required. Append is set to false by default.\n");
+		m->mothurOut("The set.logfile command should be in the following format: set.logfile(name=yourLogFileName, append=T).\n");
+		m->mothurOut("Example set.logfile(name=/Users/lab/desktop/output.txt, append=T).\n");
+		m->mothurOut("Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourLogFileName).\n\n");
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SetLogFileCommand", "help");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+SetLogFileCommand::~SetLogFileCommand(){}
+
+//**********************************************************************************************************************
+
+int SetLogFileCommand::execute(){
+	try {
+		
+		if (abort == true) { return 0; }
+		
+		commandFactory = CommandFactory::getInstance();
+		
+		commandFactory->setLogfileName(name, append);
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SetLogFileCommand", "execute");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************/
diff --git a/setlogfilecommand.h b/setlogfilecommand.h
new file mode 100644
index 0000000..d16bcd6
--- /dev/null
+++ b/setlogfilecommand.h
@@ -0,0 +1,37 @@
+#ifndef SETLOGFILECOMMAND_H
+#define SETLOGFILECOMMAND_H
+
+/*
+ *  setlogfilecommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 4/27/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "commandfactory.hpp"
+
+/**********************************************************/
+
+class SetLogFileCommand : public Command {
+	
+public:
+	SetLogFileCommand(string);
+	~SetLogFileCommand();
+	int execute();
+	void help();
+	
+private:
+	CommandFactory* commandFactory;
+	string name;
+	bool abort, append;
+		
+};
+
+/**********************************************************/
+ 
+#endif
+
+