-/*
- * 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.1.8");
- m->mothurOutEndLine();
- m->mothurOut("Last updated: 2/02/2010");
- 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;
-
- //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);
- }
-}
-
-/**************************************************************************************************/
-
+/*\r
+ * interface.cpp\r
+ * \r
+ *\r
+ * Created by Pat Schloss on 8/14/08.\r
+ * Copyright 2008 Patrick D. Schloss. All rights reserved.\r
+ *\r
+ */\r
+ \r
+#include "mothur.h"\r
+#include "engine.hpp"\r
+#include "globaldata.hpp"\r
+#include "mothurout.h"\r
+\r
+\r
+/**************************************************************************************************/\r
+\r
+GlobalData* GlobalData::_uniqueInstance = 0;\r
+CommandFactory* CommandFactory::_uniqueInstance = 0;\r
+MothurOut* MothurOut::_uniqueInstance = 0;\r
+\r
+/***********************************************************************/\r
+volatile int ctrlc_pressed = 0;\r
+void ctrlc_handler ( int sig ) {\r
+ MothurOut* m = MothurOut::getInstance();\r
+ ctrlc_pressed = 1;\r
+ m->control_pressed = ctrlc_pressed;\r
+ \r
+ if (m->executing) { //if mid command quit execution, else quit mothur\r
+ m->mothurOutEndLine(); m->mothurOut("quitting command..."); m->mothurOutEndLine();\r
+ }else{\r
+ m->mothurOut("quitting mothur"); m->mothurOutEndLine();\r
+ exit(1);\r
+ }\r
+}\r
+/***********************************************************************/\r
+int main(int argc, char *argv[]){\r
+ MothurOut* m = MothurOut::getInstance();\r
+ try {\r
+ \r
+ signal(SIGINT, ctrlc_handler );\r
+ \r
+ time_t ltime = time(NULL); /* calendar time */ \r
+ string logFileName = "mothur." + toString(ltime) + ".logfile";\r
+ \r
+ #ifdef USE_MPI\r
+ MPI_Init(&argc, &argv); \r
+ #endif\r
+\r
+ m->setFileName(logFileName);\r
+ \r
+ \r
+ //version\r
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
+ system("clear");\r
+ #if defined (__APPLE__) || (__MACH__)\r
+ m->mothurOutJustToLog("Mac version");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ #else\r
+ m->mothurOutJustToLog("Linux version");\r
+ >m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ #endif\r
+\r
+ #else\r
+ system("CLS");\r
+ m->mothurOutJustToLog("Windows version");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ #endif \r
+ \r
+ #ifdef USE_READLINE\r
+ m->mothurOutJustToLog("Using ReadLine");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ #endif\r
+ \r
+ //header\r
+ m->mothurOut("mothur v.1.9");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Last updated: 4/09/2010");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("by");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Patrick D. Schloss");\r
+ m->mothurOutEndLine();\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Department of Microbiology & Immunology");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("University of Michigan");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("pschloss@umich.edu");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("http://www.mothur.org");\r
+ m->mothurOutEndLine();\r
+ m->mothurOutEndLine();\r
+ m->mothurOut("When using, please cite:");\r
+ m->mothurOutEndLine();\r
+ 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.");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Distributed under the GNU General Public License");\r
+ m->mothurOutEndLine();\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Type 'help()' for information on the commands that are available");\r
+ m->mothurOutEndLine();\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Type 'quit()' to exit program");\r
+ m->mothurOutEndLine(); \r
+ \r
+ #ifdef USE_MPI\r
+ m->mothurOutJustToLog("Using MPI\tversion ");\r
+ int version, subversion;\r
+ MPI_Get_version(&version, &subversion);\r
+ m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");\r
+ #endif\r
+ \r
+ //srand(54321);\r
+ srand( (unsigned)time( NULL ) );\r
+ \r
+ Engine* mothur;\r
+ bool bail = 0;\r
+ string input;\r
+\r
+ if(argc>1){\r
+ input = argv[1];\r
+\r
+ if (input[0] == '#') {\r
+ m->mothurOutJustToLog("Script Mode");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+\r
+ mothur = new ScriptEngine(argv[0], argv[1]);\r
+ }else{\r
+ m->mothurOutJustToLog("Batch Mode");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ \r
+ mothur = new BatchEngine(argv[0], argv[1]);\r
+ }\r
+ }\r
+ else{\r
+ m->mothurOutJustToLog("Interactive Mode");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ \r
+ mothur = new InteractEngine(argv[0]); \r
+ }\r
+ \r
+ while(bail == 0) { bail = mothur->getInput(); }\r
+ \r
+ string outputDir = mothur->getOutputDir();\r
+ string newlogFileName = outputDir + logFileName;\r
+ \r
+ //closes logfile so we can rename\r
+ m->closeLog();\r
+ \r
+ //need this because m->mothurOut makes the logfile, but doesn't know where to put it\r
+ rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp\r
+ \r
+ delete mothur;\r
+ \r
+ #ifdef USE_MPI\r
+ MPI_Finalize();\r
+ #endif\r
+ \r
+ return 0;\r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "mothur", "main");\r
+ exit(1);\r
+ }\r
+}\r
+\r
+/**************************************************************************************************/\r
+\r
projects / mothur.git / blobdiff