5 * Created by Pat Schloss on 8/14/08.
6 * Copyright 2008 Patrick D. Schloss. All rights reserved.
12 #include "mothurout.h"
13 #include "referencedb.h"
15 /**************************************************************************************************/
17 CommandFactory* CommandFactory::_uniqueInstance = 0;
18 MothurOut* MothurOut::_uniqueInstance = 0;
19 ReferenceDB* ReferenceDB::myInstance = 0;
20 /***********************************************************************/
21 volatile int ctrlc_pressed = 0;
22 void ctrlc_handler ( int sig ) {
23 MothurOut* m = MothurOut::getInstance();
25 m->control_pressed = ctrlc_pressed;
27 if (m->executing) { //if mid command quit execution, else quit mothur
28 m->mothurOutEndLine(); m->mothurOut("quitting command..."); m->mothurOutEndLine();
30 m->mothurOut("quitting mothur"); m->mothurOutEndLine();
34 /***********************************************************************/
35 int main(int argc, char *argv[]){
36 MothurOut* m = MothurOut::getInstance();
38 signal(SIGINT, ctrlc_handler );
40 time_t ltime = time(NULL); /* calendar time */
41 string logFileName = "mothur." + toString(ltime) + ".logfile";
44 MPI_Init(&argc, &argv);
47 m->setFileName(logFileName);
49 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
56 string temp = MOTHUR_FILES;
58 //add / to name if needed
59 string lastChar = temp.substr(temp.length()-1);
60 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
61 if (lastChar != "/") { temp += "/"; }
63 if (lastChar != "\\") { temp += "\\"; }
66 temp = m->getFullPathName(temp);
67 m->setDefaultPath(temp);
71 int version, subversion;
72 MPI_Get_version(&version, &subversion);
75 //get releaseDate from Make
76 string releaseDate = RELEASE_DATE;
77 string mothurVersion = VERSION;
78 m->setReleaseDate(releaseDate);
79 m->setVersion(mothurVersion);
81 //will make the gui output "pretty"
82 bool outputHeader = true;
84 string guiInput = argv[1];
85 if (guiInput[0] == '+') { outputHeader = false; }
86 if (guiInput[0] == '-') { outputHeader = false; }
91 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
92 #if defined (__APPLE__) || (__MACH__)
93 m->mothurOutJustToLog("Mac version");
94 m->mothurOutEndLine(); m->mothurOutEndLine();
96 m->mothurOutJustToLog("Linux version");
97 m->mothurOutEndLine(); m->mothurOutEndLine();
101 m->mothurOutJustToLog("Windows version");
102 m->mothurOutEndLine(); m->mothurOutEndLine();
106 m->mothurOutJustToLog("Using ReadLine");
107 m->mothurOutEndLine(); m->mothurOutEndLine();
111 m->mothurOutJustToLog("Using default file location " + temp);
112 m->mothurOutEndLine(); m->mothurOutEndLine();
116 m->mothurOutJustToLog("Running 64Bit Version");
117 m->mothurOutEndLine(); m->mothurOutEndLine();
119 m->mothurOutJustToLog("Running 32Bit Version");
120 m->mothurOutEndLine(); m->mothurOutEndLine();
124 m->mothurOut("mothur v." + mothurVersion);
125 m->mothurOutEndLine();
126 m->mothurOut("Last updated: " + releaseDate);
127 m->mothurOutEndLine();
128 m->mothurOutEndLine();
130 m->mothurOutEndLine();
131 m->mothurOut("Patrick D. Schloss");
132 m->mothurOutEndLine();
133 m->mothurOutEndLine();
134 m->mothurOut("Department of Microbiology & Immunology");
135 m->mothurOutEndLine();
136 m->mothurOut("University of Michigan");
137 m->mothurOutEndLine();
138 m->mothurOut("pschloss@umich.edu");
139 m->mothurOutEndLine();
140 m->mothurOut("http://www.mothur.org");
141 m->mothurOutEndLine();
142 m->mothurOutEndLine();
143 m->mothurOut("When using, please cite:");
144 m->mothurOutEndLine();
145 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.");
146 m->mothurOutEndLine();
147 m->mothurOutEndLine();
148 m->mothurOut("Distributed under the GNU General Public License");
149 m->mothurOutEndLine();
150 m->mothurOutEndLine();
151 m->mothurOut("Type 'help()' for information on the commands that are available");
152 m->mothurOutEndLine();
153 m->mothurOutEndLine();
154 m->mothurOut("Type 'quit()' to exit program");
155 m->mothurOutEndLine();
158 m->mothurOutJustToLog("Using MPI\tversion ");
159 m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
164 srand( (unsigned)time( NULL ) );
166 Engine* mothur = NULL;
172 //m->mothurOut("input = " + input); m->mothurOutEndLine();
174 if (input[0] == '#') {
175 m->mothurOutJustToLog("Script Mode");
176 m->mothurOutEndLine(); m->mothurOutEndLine();
178 mothur = new ScriptEngine(argv[0], argv[1]);
179 }else if (input[0] == '+') {
180 mothur = new ScriptEngine(argv[0], argv[1]);
182 }else if (input == "-version") {
183 m->mothurOut("Mothur version=" + mothurVersion + "\nRelease Date=" + releaseDate); m->mothurOutEndLine(); m->mothurOutEndLine(); m->closeLog();
189 m->mothurOutJustToLog("Batch Mode");
190 m->mothurOutEndLine(); m->mothurOutEndLine();
192 mothur = new BatchEngine(argv[0], argv[1]);
196 m->mothurOutJustToLog("Interactive Mode");
197 m->mothurOutEndLine(); m->mothurOutEndLine();
199 mothur = new InteractEngine(argv[0]);
202 while(bail == 0) { bail = mothur->getInput(); }
204 //closes logfile so we can rename
207 string outputDir = mothur->getOutputDir();
208 string tempLog = mothur->getLogFileName();
209 bool append = mothur->getAppend();
211 string newlogFileName;
213 newlogFileName = outputDir + tempLog;
216 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
217 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
221 m->openOutputFileAppend(newlogFileName, outNewLog);
224 outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
230 m->appendFiles(logFileName, newlogFileName);
231 m->mothurRemove(logFileName);
234 newlogFileName = outputDir + logFileName;
235 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
236 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
240 if (mothur != NULL) { delete mothur; }
248 catch(exception& e) {
249 m->errorOut(e, "mothur", "main");
254 /**************************************************************************************************/