#include "engine.hpp"
+/***********************************************************************/
+inline void terminateCommand(int dummy) {
+
+ //mothurOut("Stopping command....");
+ //CommandFactory* cFactory = CommandFactory::getInstance();
+ //cFactory->getCommand(); //deletes old command and makes new no command.
+ //this may cause memory leak if old commands execute function allocated memory
+ //that is freed in the execute function and not the deconstructor
+ //mothurOut("DONE."); mothurOutEndLine();
+}
+/***********************************************************************/
+Engine::Engine(){
+ try {
+ cFactory = CommandFactory::getInstance();
+ }
+ catch(exception& e) {
+ errorOut(e, "Engine", "Engine");
+ exit(1);
+ }
+}
+
/***********************************************************************/
InteractEngine::InteractEngine(string path){
globaldata = GlobalData::getInstance();
globaldata->argv = path;
- string logFileName = "mothur.logFile";
- remove(logFileName.c_str());
-
- system("clear");
}
/***********************************************************************/
-InteractEngine::~InteractEngine(){
- }
+InteractEngine::~InteractEngine(){}
/***********************************************************************/
//This function allows the user to input commands one line at a time until they quit.
string options = "";
int quitCommandCalled = 0;
- mothurOut("mothur v.1.4.1");
- mothurOutEndLine();
- mothurOut("Last updated: 6/23/2009");
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("by");
- mothurOutEndLine();
- mothurOut("Patrick D. Schloss");
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("Department of Microbiology");
- mothurOutEndLine();
- mothurOut("pschloss@micro.umass.edu");
- mothurOutEndLine();
- mothurOut("http://schloss.micro.umass.edu/mothur");
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("Distributed under the GNU General Public License");
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("Type 'help()' for information on the commands that are available");
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("Type 'quit()' to exit program");
- mothurOutEndLine();
-
while(quitCommandCalled != 1){
-
+
mothurOutEndLine();
- mothurOut("mothur > ");
- getline(cin, input);
- if (cin.eof()) { input = "quit()"; }
- mothurOutJustToLog(input);
- mothurOutEndLine();
+ input = getCommand();
//allow user to omit the () on the quit command
if (input == "quit") { input = "quit()"; }
CommandOptionParser parser(input);
commandName = parser.getCommandString();
+
options = parser.getOptionString();
if (commandName != "") {
//executes valid command
- CommandFactory cFactory;
- Command* command = cFactory.getCommand(commandName, options);
+ Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
}else {
exit(1);
}
}
-
+/***********************************************************************/
+string Engine::getCommand() {
+ try {
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #ifdef USE_READLINE
+ char* nextCommand = NULL;
+ nextCommand = readline("mothur > ");
+ if(nextCommand != NULL) { add_history(nextCommand); }
+ mothurOutJustToLog("mothur > " + toString(nextCommand));
+ return nextCommand;
+ #else
+ string nextCommand = "";
+ mothurOut("mothur > ");
+ getline(cin, nextCommand);
+ return nextCommand;
+ #endif
+ #else
+ string nextCommand = "";
+ mothurOut("mothur > ");
+ getline(cin, nextCommand);
+ return nextCommand;
+ #endif
+
+ mothurOutEndLine();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Engine", "getCommand");
+ exit(1);
+ }
+}
/***********************************************************************/
//This function opens the batchfile to be used by BatchEngine::getInput.
BatchEngine::BatchEngine(string path, string batchFileName){
openedBatch = openInputFile(batchFileName, inputBatchFile);
globaldata->argv = path;
- string logFileName = "mothur.logFile";
- remove(logFileName.c_str());
-
- system("clear");
-
- // char buffer = ' ';
- // ifstream header("introtext.txt");
- // while(!header.eof()){
- // cout << buffer;
- // buffer = header.get();
- // }
+
}
catch(exception& e) {
errorOut(e, "BatchEngine", "BatchEngine");
/***********************************************************************/
-BatchEngine::~BatchEngine(){
- }
+BatchEngine::~BatchEngine(){ }
/***********************************************************************/
//This Function allows the user to run a batchfile containing several commands on Dotur
while(quitCommandCalled == 0){
if (inputBatchFile.eof()) { input = "quit()"; }
- else { getline(inputBatchFile, input); }
-
-
+ else { input = getline(inputBatchFile); }
if (input[0] != '#') {
if (commandName != "") {
//executes valid command
- CommandFactory cFactory;
- Command* command = cFactory.getCommand(commandName, options);
+ Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
}else {
mothurOut("Invalid.");
listOfCommands = commandString.substr(1, (commandString.length()-1));
globaldata->argv = path;
- string logFileName = "mothur.logFile";
- remove(logFileName.c_str());
-
- system("clear");
-
+
}
catch(exception& e) {
errorOut(e, "ScriptEngine", "ScriptEngine");
/***********************************************************************/
-ScriptEngine::~ScriptEngine(){
- }
+ScriptEngine::~ScriptEngine(){ }
/***********************************************************************/
//This Function allows the user to run a batchfile containing several commands on mothur
if (commandName != "") {
//executes valid command
- CommandFactory cFactory;
- Command* command = cFactory.getCommand(commandName, options);
+ Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
}else {
mothurOut("Invalid.");
string ScriptEngine::getNextCommand(string& commandString) {
try {
string nextcommand = "";
+ int count = 0;
- nextcommand = commandString.substr(0,commandString.find_first_of(';'));
-
+ //go through string until you reach ; or end
+ while (count < commandString.length()) {
+
+ if (commandString[count] == ';') { break; }
+ else { nextcommand += commandString[count]; }
+
+ count++;
+ }
+
+ //if you are not at the end
+ if (count != commandString.length()) { commandString = commandString.substr(count+1, commandString.length()); }
+ else { commandString = ""; }
- if ((commandString.find_first_of(';')+1) <= commandString.length()) {
- commandString = commandString.substr(commandString.find_first_of(';')+1, commandString.length());
- }else { commandString = ""; } //you have reached the last command.
//get rid of spaces in between commands if any
if (commandString.length() > 0) {
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