5 * Created by Pat Schloss on 8/14/08.
6 * Copyright 2008 Patrick D. Schloss. All rights reserved.
12 #include "globaldata.hpp"
13 #include "mothurout.h"
16 /**************************************************************************************************/
18 GlobalData* GlobalData::_uniqueInstance = 0;
19 CommandFactory* CommandFactory::_uniqueInstance = 0;
20 MothurOut* MothurOut::_uniqueInstance = 0;
22 /***********************************************************************/
23 volatile int ctrlc_pressed = 0;
24 void ctrlc_handler ( int sig ) {
25 MothurOut* m = MothurOut::getInstance();
27 m->control_pressed = ctrlc_pressed;
29 if (m->executing) { //if mid command quit execution, else quit mothur
30 m->mothurOutEndLine(); m->mothurOut("quitting command..."); m->mothurOutEndLine();
32 m->mothurOut("quitting mothur"); m->mothurOutEndLine();
36 /***********************************************************************/
37 int main(int argc, char *argv[]){
38 MothurOut* m = MothurOut::getInstance();
41 signal(SIGINT, ctrlc_handler );
43 time_t ltime = time(NULL); /* calendar time */
44 string logFileName = "mothur." + toString(ltime) + ".logfile";
47 MPI_Init(&argc, &argv);
50 m->setFileName(logFileName);
54 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
56 #if defined (__APPLE__) || (__MACH__)
57 m->mothurOutJustToLog("Mac version");
58 m->mothurOutEndLine(); m->mothurOutEndLine();
60 m->mothurOutJustToLog("Linux version");
61 >m->mothurOutEndLine(); m->mothurOutEndLine();
66 m->mothurOutJustToLog("Windows version");
67 m->mothurOutEndLine(); m->mothurOutEndLine();
71 m->mothurOutJustToLog("Using ReadLine");
72 m->mothurOutEndLine(); m->mothurOutEndLine();
76 m->mothurOut("mothur v.1.9");
77 m->mothurOutEndLine();
78 m->mothurOut("Last updated: 4/16/2010");
79 m->mothurOutEndLine();
80 m->mothurOutEndLine();
82 m->mothurOutEndLine();
83 m->mothurOut("Patrick D. Schloss");
84 m->mothurOutEndLine();
85 m->mothurOutEndLine();
86 m->mothurOut("Department of Microbiology & Immunology");
87 m->mothurOutEndLine();
88 m->mothurOut("University of Michigan");
89 m->mothurOutEndLine();
90 m->mothurOut("pschloss@umich.edu");
91 m->mothurOutEndLine();
92 m->mothurOut("http://www.mothur.org");
93 m->mothurOutEndLine();
94 m->mothurOutEndLine();
95 m->mothurOut("When using, please cite:");
96 m->mothurOutEndLine();
97 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.");
98 m->mothurOutEndLine();
99 m->mothurOutEndLine();
100 m->mothurOut("Distributed under the GNU General Public License");
101 m->mothurOutEndLine();
102 m->mothurOutEndLine();
103 m->mothurOut("Type 'help()' for information on the commands that are available");
104 m->mothurOutEndLine();
105 m->mothurOutEndLine();
106 m->mothurOut("Type 'quit()' to exit program");
107 m->mothurOutEndLine();
110 m->mothurOutJustToLog("Using MPI\tversion ");
111 int version, subversion;
112 MPI_Get_version(&version, &subversion);
113 m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
117 srand( (unsigned)time( NULL ) );
126 if (input[0] == '#') {
127 m->mothurOutJustToLog("Script Mode");
128 m->mothurOutEndLine(); m->mothurOutEndLine();
130 mothur = new ScriptEngine(argv[0], argv[1]);
132 m->mothurOutJustToLog("Batch Mode");
133 m->mothurOutEndLine(); m->mothurOutEndLine();
135 mothur = new BatchEngine(argv[0], argv[1]);
139 m->mothurOutJustToLog("Interactive Mode");
140 m->mothurOutEndLine(); m->mothurOutEndLine();
142 mothur = new InteractEngine(argv[0]);
145 while(bail == 0) { bail = mothur->getInput(); }
147 //closes logfile so we can rename
150 string outputDir = mothur->getOutputDir();
151 string tempLog = mothur->getLogFileName();
152 bool append = mothur->getAppend();
154 string newlogFileName;
156 newlogFileName = outputDir + tempLog;
159 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
160 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
164 openOutputFileAppend(newlogFileName, outNewLog);
165 outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
168 appendFiles(logFileName, newlogFileName);
169 remove(logFileName.c_str());
172 newlogFileName = outputDir + logFileName;
173 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
174 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
186 catch(exception& e) {
187 m->errorOut(e, "mothur", "main");
192 /**************************************************************************************************/