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/*
* interface.cpp
*
*
* Created by Pat Schloss on 8/14/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
#include "batchengine.hpp"
#include "scriptengine.hpp"
#include "interactengine.hpp"
#include "mothurout.h"
/**************************************************************************************************/
CommandFactory* CommandFactory::_uniqueInstance = 0;
MothurOut* MothurOut::_uniqueInstance = 0;
CurrentFile* CurrentFile::instance = 0;
/***********************************************************************/
volatile int ctrlc_pressed = 0;
void ctrlc_handler ( int sig ) {
MothurOut* m = MothurOut::getInstance();
ctrlc_pressed = 1;
m->setControl_pressed(ctrlc_pressed);
if (m->getExecuting()) { //if mid command quit execution, else quit mothur
m->mothurOut("\nquitting command...\n");
}else{
m->mothurOut("quitting mothur\n");
exit(1);
}
}
/***********************************************************************/
int main(int argc, char *argv[], char *envp[]){
MothurOut* m = MothurOut::getInstance();
try {
CurrentFile* current = CurrentFile::getInstance();
Utils util;
bool createLogFile = true;
signal(SIGINT, ctrlc_handler );
string mothurVersion, releaseDate, OS;
vector<string> defaultPath, toolsPath;
util.mothurInitialPrep(defaultPath, toolsPath, mothurVersion, releaseDate, OS);
current->setReleaseDate(releaseDate);
current->setVersion(mothurVersion);
#ifdef MOTHUR_FILES
current->setDefaultPath(defaultPath);
#endif
#ifdef MOTHUR_TOOLS
current->setToolsPath(toolsPath);
#endif
if (argc>1) {
if (argc > 2) { //is one of these -q for quiet mode?
if (argc > 3) { m->mothurOut("[ERROR]: mothur only allows command inputs and the -q command line options.\n i.e. ./mothur \"#summary.seqs(fasta=final.fasta);\" -q\n or ./mothur -q \"#summary.seqs(fasta=final.fasta);\"\n"); return 0; }
else {
string argv1 = argv[1];
string argv2 = argv[2];
if ((argv1 == "--quiet") || (argv1 == "-q")) {
m->setQuietMode(true);
argv[1] = argv[2];
}else if ((argv2 == "--quiet") || (argv2 == "-q")) {
m->setQuietMode(true);
}else {
m->mothurOut("[ERROR]: mothur only allows command inputs and the -q command line options.\n");
m->mothurOut("[ERROR]: Unrecognized options: " + argv1 + " " + argv2 + "\n");
return 0;
}
}
}
}
map<string, string> environmentalVariables;
for (char **env = envp; *env != 0; env++){
string thisEvn = *env;
string key, value; value = thisEvn;
util.splitAtEquals(key, value);
map<string, string>::iterator it = environmentalVariables.find(key);
if (it == environmentalVariables.end()) { environmentalVariables[key] = value; }
else { it->second = value; }
//m->mothurOut("[DEBUG]: Setting environment variable " + key + " to " + value + "\n");
if (m->getDebug()) { m->mothurOut("[DEBUG]: Setting environment variable " + key + " to " + value + "\n"); }
}
Engine* mothur = nullptr;
bool bail = false;
string input;
if(argc>1){
input = argv[1];
if (input[0] == '#') {
m->mothurOut("Script Mode\n\n");
mothur = new ScriptEngine(argv[0], argv[1], environmentalVariables);
}else if ((input == "--version") || (input == "-v")) {
cout << (OS + "\nMothur version=" + mothurVersion + "\nRelease Date=" + releaseDate + "\n\n"); return 0;
}else if ((input == "--help") || (input == "-h")) {
createLogFile = false;
m->mothurOut("Script Mode\n\n");
string helpQuit = "#help();quit();";
argv[1] = util.mothurConvert(helpQuit);
mothur = new ScriptEngine(argv[0], argv[1], environmentalVariables);
}else{
m->mothurOut("Batch Mode\n\n");
mothur = new BatchEngine(argv[0], argv[1], environmentalVariables);
}
}else{
m->mothurOut("Interactive Mode\n\n");
mothur = new InteractEngine(argv[0], environmentalVariables);
}
while(!bail) { bail = mothur->getInput(); }
string newlogFileName = mothur->getLogFileName();
if (!createLogFile) { util.mothurRemove(newlogFileName); }
if (mothur != nullptr) { delete mothur; }
int returnCode = 0;
if (m->getNumErrors() != 0) { returnCode = 1; }
m->closeLog();
return returnCode;
}
catch(exception& e) {
m->errorOut(e, "mothur", "main");
exit(1);
}
}
/**************************************************************************************************/
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