+++ /dev/null
-/*
- * 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);
- }
-}
-
-/**************************************************************************************************/
-
projects / mothur.git / blobdiff