globaldata = GlobalData::getInstance();
globaldata->argv = path;
- 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;
-
+
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;
-
- system("clear");
-
- // char buffer = ' ';
- // ifstream header("introtext.txt");
- // while(!header.eof()){
- // cout << buffer;
- // buffer = header.get();
- // }
+
}
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;
while(quitCommandCalled == 0){
if (inputBatchFile.eof()) { input = "quit()"; }
- else { getline(inputBatchFile, input); }
-
- //cout << "command number" << count << endl; count++;
+ else { input = getline(inputBatchFile); }
if (input[0] != '#') {
-
- 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();
+ }
}
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;
-
- 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);
}
}
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) {
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