X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothur.cpp;h=accdb2962c198988c457dc8f837b8817dc2799f0;hp=43b838c2d94bad311204d26a82603901238687e1;hb=615301e57c25e241356a9c2380648d117709458d;hpb=4a2d841cb97fb02351022efe9d7068b1dc212bf9

diff --git a/mothur.cpp b/mothur.cpp
index 43b838c..accdb29 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -1,193 +1,255 @@
-/*
- *  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.1.10.0");
-		m->mothurOutEndLine();		
-		m->mothurOut("Last updated: 5/14/2010");
-		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);
-	}
-}
-
-/**************************************************************************************************/
-
+/*
+ *  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 "mothurout.h"
+#include "referencedb.h"
+
+/**************************************************************************************************/
+
+CommandFactory* CommandFactory::_uniqueInstance = 0;
+MothurOut* MothurOut::_uniqueInstance = 0;
+ReferenceDB* ReferenceDB::myInstance = 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);
+		
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+			system("clear");
+		#else
+			system("CLS");
+		#endif
+		
+		#ifdef MOTHUR_FILES
+			string temp = MOTHUR_FILES; 
+		
+			//add / to name if needed
+			string lastChar = temp.substr(temp.length()-1);
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+				if (lastChar != "/") { temp += "/"; }
+			#else
+				if (lastChar != "\\") { temp += "\\"; }	
+			#endif
+		
+			temp = m->getFullPathName(temp);
+			m->setDefaultPath(temp);
+		#endif
+		
+		#ifdef USE_MPI
+			int version, subversion;
+			MPI_Get_version(&version, &subversion);
+		#endif
+		
+		//get releaseDate from Make
+		string releaseDate = RELEASE_DATE; 
+		string mothurVersion = VERSION; 
+		m->setReleaseDate(releaseDate);
+		m->setVersion(mothurVersion);
+		
+		//will make the gui output "pretty"
+		bool outputHeader = true;
+		if (argc>1) {
+			string guiInput = argv[1];
+			if (guiInput[0] == '+') { outputHeader = false; }
+			if (guiInput[0] == '-') { outputHeader = false; }
+		}
+		
+		if (outputHeader)  {
+			//version
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+				#if defined (__APPLE__) || (__MACH__)
+					m->mothurOutJustToLog("Mac version");
+					m->mothurOutEndLine(); m->mothurOutEndLine();
+				#else
+					m->mothurOutJustToLog("Linux version");
+					m->mothurOutEndLine(); m->mothurOutEndLine();
+				#endif
+
+			#else
+				m->mothurOutJustToLog("Windows version");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+			#endif		
+			
+			#ifdef USE_READLINE
+				m->mothurOutJustToLog("Using ReadLine");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+			#endif
+			
+			#ifdef MOTHUR_FILES
+				m->mothurOutJustToLog("Using default file location " + temp);
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+			#endif
+			
+			#ifdef BIT_VERSION
+				m->mothurOutJustToLog("Running 64Bit Version");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+			#else
+				m->mothurOutJustToLog("Running 32Bit Version");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+			#endif
+			
+			//header
+			m->mothurOut("mothur v." + mothurVersion);
+			m->mothurOutEndLine();		
+			m->mothurOut("Last updated: " + releaseDate);
+			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 ");
+				m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
+			#endif
+		}
+		
+		//srand(54321);
+		srand( (unsigned)time( NULL ) );
+		
+		Engine* mothur = NULL;
+		bool bail = 0;
+		string input;
+ 
+		if(argc>1){
+			input = argv[1];
+			//m->mothurOut("input = " + input); m->mothurOutEndLine();
+
+			if (input[0] == '#') {
+				m->mothurOutJustToLog("Script Mode");
+				m->mothurOutEndLine(); m->mothurOutEndLine();
+
+				mothur = new ScriptEngine(argv[0], argv[1]);
+			}else if (input[0] == '+') {
+					mothur = new ScriptEngine(argv[0], argv[1]);
+					m->gui = true;
+			}else if (input == "-version") {
+				m->mothurOut("Mothur version=" + mothurVersion + "\nRelease Date=" + releaseDate); m->mothurOutEndLine(); m->mothurOutEndLine(); m->closeLog();
+				#ifdef USE_MPI
+					MPI_Finalize();
+				#endif
+				return 0;
+			}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;
+				m->openOutputFileAppend(newlogFileName, outNewLog);
+				
+				if (!m->gui) {
+					outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+				}else {
+					outNewLog << endl;
+				}
+				outNewLog.close();
+				
+				m->appendFiles(logFileName, newlogFileName);
+				m->mothurRemove(logFileName);
+			}
+		}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
+		}
+		
+				
+		if (mothur != NULL) { delete mothur; }
+		
+		#ifdef USE_MPI
+			MPI_Finalize();
+		#endif
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "mothur", "main");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+