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#ifndef ENGINE_HPP
#define ENGINE_HPP
/*
* engine.hpp
*
*
* Created by Pat Schloss on 8/15/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
#include "commandoptionparser.hpp"
#include "command.hpp"
#include "commandfactory.hpp"
#include "mothurout.h"
class Engine {
public:
Engine(string tpath) {
try {
cFactory = CommandFactory::getInstance();
m = MothurOut::getInstance();
current = CurrentFile::getInstance();
m->resetCommandErrors();
string temppath = tpath.substr(0, (tpath.find_last_of("othur")-5));
//this will happen if you set the path variable to contain mothur's exe location
if (temppath == "") { path = util.findProgramPath("mothur"); }
else { path = temppath; }
if (path != "") {
string lastChar = path.substr(path.length()-1);
if (lastChar != PATH_SEPARATOR) { path += PATH_SEPARATOR; }
path = util.getFullPathName(path);
}
current->setProgramPath(util.getFullPathName(path));
//if you haven't set your own location
#ifdef MOTHUR_FILES
#else
//set default location to search for files to mothur's executable location. This will resolve issue of double-clicking on the executable which opens mothur and sets pwd to your home directory instead of the mothur directory and leads to "unable to find file" errors.
if (current->getProgramPath() != "") {
vector<string> temps; temps.push_back(current->getProgramPath());
current->setDefaultPath(temps);
}
#endif
start = time(nullptr);
numCommandsRun = 0;
noBufferNeeded = false;
}
catch(exception& e) {
m->errorOut(e, "Engine", "Engine");
exit(1);
}
}
virtual ~Engine(){}
virtual bool getInput() = 0;
virtual string getLogFileName() { return m->getLogFileName(); }
vector<string> getOptions() { return options; }
virtual void replaceVariables(string& nextCommand) {
for (map<string, string>::iterator it = environmentalVariables.begin(); it != environmentalVariables.end(); it++) {
int pos = nextCommand.find("$"+it->first);
while (pos != string::npos) { //allow for multiple uses of a environmental variable in a single command
nextCommand.replace(pos,it->first.length()+1,it->second); //-1 to grab $char
pos = nextCommand.find("$"+it->first);
}
}
//replace mothurhome with mothur executable location
int pos = nextCommand.find("mothurhome");
while (pos != string::npos) { //allow for multiple uses of mothurhome in a single command
nextCommand.replace(pos,10,current->getProgramPath()); //
pos = nextCommand.find("mothurhome");
}
}
virtual string findType(string nextCommand) {
string type = "command";
//determine if this is a command or batch file / environmental variable
//we know commands must include '(' characters for search for that
size_t openParen = nextCommand.find_first_of('(');
if (openParen == string::npos) { //no '(' character -> assume not a command, treat as new batchfile / environmental variable
//are you another batch file or an environmental variable
//if no '=' sign than not an environmental variable
size_t equalsSign = nextCommand.find_first_of('=');
if (equalsSign == string::npos) { //no '=' character -> assume not a environmental variable, treat as new batch
type = "batch";
}else { //assume environmental variable. filenames can contain '=' characters, but this is a rare case
type = "environment";
}
}
return type;
}
virtual void setEnvironmentVariables(map<string, string> ev) {
environmentalVariables = ev;
//set HOME path is present in environment variables
string homeEnvironmentTag = "HOMEPATH";
string homeEnvironmentValue = "";
#if defined NON_WINDOWS
homeEnvironmentTag = "HOME";
#endif
map<string, string>::iterator it = environmentalVariables.find(homeEnvironmentTag);
if (it != environmentalVariables.end()) { homeEnvironmentValue = it->second; }
//parse PATH to set search locations for mothur tools
//set HOME path is present in environment variables
string pathEnvironmentTag = "PATH";
string pathEnvironmentValue = "";
char delim = ';';
#if defined NON_WINDOWS
delim = ':';
#endif
it = environmentalVariables.find(pathEnvironmentTag);
if (it != environmentalVariables.end()) { pathEnvironmentValue = it->second; }
vector<string> pathDirs;
util.splitAtChar(pathEnvironmentValue, pathDirs, delim);
current->setPaths(pathDirs);
current->setHomePath(homeEnvironmentValue);
}
protected:
vector<string> options;
CommandFactory* cFactory;
MothurOut* m;
CurrentFile* current;
Utils util;
time_t start;
int numCommandsRun;
bool noBufferNeeded;
string path;
map<string, string> environmentalVariables;
};
#endif
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