globaldata = GlobalData::getInstance();
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();
-// }
}
/***********************************************************************/
string commandName = "";
string options = "";
int quitCommandCalled = 0;
- //bool errorFree;
- //ErrorCheck* errorCheckor = new ErrorCheck();
- cout << "mothur v.1.4.1" << endl;
- cout << "Last updated: 6/23/2009" << endl << endl;
- cout << "by" << endl;
- cout << "Patrick D. Schloss" << endl << endl;
- cout << "Department of Microbiology" << endl;
- cout << "The University of Massachusetts" << endl;
- cout << "pschloss@micro.umass.edu" << endl;
- cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl;
- cout << "Distributed under the GNU General Public License" << endl << endl;
- cout << "Type 'help()' for information on the commands that are available" << endl << endl;
- cout << "Type 'quit()' to exit program" << endl;
-
+ 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){
-
- cout << endl << "mothur > ";
+
+ mothurOutEndLine();
+ mothurOut("mothur > ");
getline(cin, input);
if (cin.eof()) { input = "quit()"; }
+ mothurOutJustToLog(input);
+ mothurOutEndLine();
+
//allow user to omit the () on the quit command
if (input == "quit") { input = "quit()"; }
- //errorFree = errorCheckor->checkInput(input);
- //if (errorFree == true) {
CommandOptionParser parser(input);
commandName = parser.getCommandString();
options = parser.getOptionString();
quitCommandCalled = command->execute();
}else {
- cout << "Your input contains errors. Please try again." << endl;
+ mothurOut("Your input contains errors. Please try again.");
+ mothurOutEndLine();
}
}
return 1;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "InteractEngine", "getInput");
exit(1);
}
-
}
/***********************************************************************/
openedBatch = openInputFile(batchFileName, inputBatchFile);
globaldata->argv = path;
-
+ string logFileName = "mothur.logFile";
+ remove(logFileName.c_str());
+
system("clear");
// char buffer = ' ';
// }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "BatchEngine", "BatchEngine");
exit(1);
}
}
bool BatchEngine::getInput(){
try {
//check if this is a valid batchfile
- if (openedBatch == 1) { cout << "unable to open batchfile" << endl; return 1; }
+ if (openedBatch == 1) {
+ mothurOut("unable to open batchfile");
+ mothurOutEndLine();
+ return 1;
+ }
string input = "";
string commandName = "";
string options = "";
- //int count = 1;
//CommandFactory cFactory;
int quitCommandCalled = 0;
if (inputBatchFile.eof()) { input = "quit()"; }
else { getline(inputBatchFile, input); }
- //cout << "command number" << count << endl; count++;
- if (input[0] != '#') {
- cout << endl << "mothur > " << input << endl;
+ if (input[0] != '#') {
+
+ mothurOutEndLine();
+ mothurOut("mothur > " + input);
+ mothurOutEndLine();
+
//allow user to omit the () on the quit command
if (input == "quit") { input = "quit()"; }
CommandFactory cFactory;
Command* command = cFactory.getCommand(commandName, options);
quitCommandCalled = command->execute();
- }else { cout << "Invalid." << endl; }
+ }else {
+ mothurOut("Invalid.");
+ mothurOutEndLine();
+ }
}
gobble(inputBatchFile);
return 1;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "BatchEngine", "getInput");
exit(1);
}
}
listOfCommands = commandString.substr(1, (commandString.length()-1));
globaldata->argv = path;
+ string logFileName = "mothur.logFile";
+ remove(logFileName.c_str());
system("clear");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function ScriptEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ScriptEngine class function ScriptEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ScriptEngine", "ScriptEngine");
exit(1);
}
}
}
/***********************************************************************/
-//This Function allows the user to run a batchfile containing several commands on Dotur
+//This Function allows the user to run a batchfile containing several commands on mothur
bool ScriptEngine::getInput(){
try {
string input = "";
string commandName = "";
string options = "";
- //int count = 1;
+
//CommandFactory cFactory;
int quitCommandCalled = 0;
input = getNextCommand(listOfCommands);
if (input == "") { input = "quit()"; }
- //cout << "command number" << count << endl; count++;
- cout << endl << "mothur > " << input << endl;
+
+ mothurOutEndLine();
+ mothurOut("mothur > " + input);
+ mothurOutEndLine();
+
//allow user to omit the () on the quit command
if (input == "quit") { input = "quit()"; }
CommandFactory cFactory;
Command* command = cFactory.getCommand(commandName, options);
quitCommandCalled = command->execute();
- }else { cout << "Invalid." << endl; }
+ }else {
+ mothurOut("Invalid.");
+ mothurOutEndLine();
+ }
}
return 1;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ScriptEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ScriptEngine", "getInput");
exit(1);
}
}
return nextcommand;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function getNextCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ScriptEngine class function getNextCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ScriptEngine", "getNextCommand");
exit(1);
}
}
projects / mothur.git / blobdiff