* Fix later, don't have time now.
*
*/
-using namespace std;
+
#include "engine.hpp"
try {
string input = "";
string commandName = "";
+ string options = "";
int quitCommandCalled = 0;
- bool errorFree;
- ErrorCheck* errorCheckor = new ErrorCheck();
+ //bool errorFree;
+ //ErrorCheck* errorCheckor = new ErrorCheck();
- cout << "mothur v1.2.0" << endl;
- cout << "Last updated: 4/14/2009" << endl << endl;
+ cout << "mothur v.1.4.0" << endl;
+ cout << "Last updated: 6/21/2009" << endl << endl;
cout << "by" << endl;
cout << "Patrick D. Schloss" << endl << endl;
cout << "Department of Microbiology" << endl;
getline(cin, input);
if (cin.eof()) { input = "quit()"; }
- errorFree = errorCheckor->checkInput(input);
- if (errorFree == true) {
- CommandOptionParser parser(input);
- commandName = parser.getCommandString();
+ //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();
+
+ if (commandName != "") {
//executes valid command
CommandFactory cFactory;
- Command* command = cFactory.getCommand(commandName);
+ Command* command = cFactory.getCommand(commandName, options);
quitCommandCalled = command->execute();
-
+
}else {
- cout << "Your input contains errors. Please try again." << endl;
+ cout << "Your input contains errors. Please try again." << endl;
}
}
return 1;
BatchEngine::BatchEngine(string path, string batchFileName){
try {
globaldata = GlobalData::getInstance();
+
openedBatch = openInputFile(batchFileName, inputBatchFile);
globaldata->argv = path;
string input = "";
string commandName = "";
- bool errorFree;
- ErrorCheck* errorCheckor = new ErrorCheck();
-
- CommandFactory cFactory;
+ string options = "";
+ //int count = 1;
+
+ //CommandFactory cFactory;
int quitCommandCalled = 0;
while(quitCommandCalled == 0){
-
- getline(inputBatchFile, input);
+
+ if (inputBatchFile.eof()) { input = "quit()"; }
+ else { getline(inputBatchFile, input); }
+
+ //cout << "command number" << count << endl; count++;
+
if (input[0] != '#') {
- if (inputBatchFile.eof()) { input = "quit()"; }
cout << endl << "mothur > " << input << endl;
- errorFree = errorCheckor->checkInput(input);
- if (errorFree == true) {
- CommandOptionParser parser(input);
- commandName = parser.getCommandString();
- ifstream filehandle;
-
- if (openedBatch == 0) { //able to open batchfile
- //executes valid command
- CommandFactory cFactory;
- Command* command = cFactory.getCommand(commandName);
- quitCommandCalled = command->execute();
- }
- else {
- cout << "Invalid." << endl;
- }
- }
- else {
- cout << "Unable to open batchfile." << endl;
- }
- }else { if (inputBatchFile.eof()) { input = "quit()"; } }
+
+ //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);
+ quitCommandCalled = command->execute();
+ }else { cout << "Invalid." << endl; }
+
+ }
+ gobble(inputBatchFile);
}
+
+ inputBatchFile.close();
return 1;
}
catch(exception& e) {
/***********************************************************************/
+/***********************************************************************/
+//This function opens the batchfile to be used by BatchEngine::getInput.
+ScriptEngine::ScriptEngine(string path, string commandString){
+ try {
+ globaldata = GlobalData::getInstance();
+
+ //remove quotes
+ 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";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+ScriptEngine::~ScriptEngine(){
+ }
+
+/***********************************************************************/
+//This Function allows the user to run a batchfile containing several commands on Dotur
+bool ScriptEngine::getInput(){
+ try {
+
+ string input = "";
+ string commandName = "";
+ string options = "";
+ //int count = 1;
+
+ //CommandFactory cFactory;
+ int quitCommandCalled = 0;
+
+ while(quitCommandCalled == 0){
+
+ input = getNextCommand(listOfCommands);
+
+ if (input == "") { input = "quit()"; }
+ //cout << "command number" << count << endl; count++;
+
+ cout << endl << "mothur > " << input << endl;
+
+ //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);
+ quitCommandCalled = command->execute();
+ }else { cout << "Invalid." << endl; }
+
+ }
+
+ 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";
+ exit(1);
+ }
+}
+/***********************************************************************/
+string ScriptEngine::getNextCommand(string& commandString) {
+ try {
+ string nextcommand = "";
+
+ nextcommand = commandString.substr(0,commandString.find_first_of(';'));
+
+ 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) {
+ while (commandString[0] == ' ') {
+ commandString = commandString.substr(1,commandString.length());
+ if (commandString.length() == 0) { break; }
+ }
+ }
+
+ 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";
+ exit(1);
+ }
+}
+/***********************************************************************/
projects / mothur.git / blobdiff