#include "mothur.h"
#include "engine.hpp"
-#include "globaldata.hpp"
#include "mothurout.h"
-
+#include "referencedb.h"
/**************************************************************************************************/
-GlobalData* GlobalData::_uniqueInstance = 0;
CommandFactory* CommandFactory::_uniqueInstance = 0;
MothurOut* MothurOut::_uniqueInstance = 0;
-
+ReferenceDB* ReferenceDB::myInstance = 0;
/***********************************************************************/
volatile int ctrlc_pressed = 0;
void ctrlc_handler ( int sig ) {
/***********************************************************************/
int main(int argc, char *argv[]){
MothurOut* m = MothurOut::getInstance();
- try {
-
+ try {
signal(SIGINT, ctrlc_handler );
time_t ltime = time(NULL); /* calendar time */
m->setFileName(logFileName);
-
- //version
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
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 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
- m->mothurOutJustToLog("Using MPI\tversion ");
int version, subversion;
MPI_Get_version(&version, &subversion);
- m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
#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;
+ 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();
while(bail == 0) { bail = mothur->getInput(); }
+ //closes logfile so we can rename
+ m->closeLog();
+
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
+ 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
+ }
- delete mothur;
+
+ if (mothur != NULL) { delete mothur; }
#ifdef USE_MPI
MPI_Finalize();
projects / mothur.git / blobdiff