* Fix later, don't have time now.
*
*/
-using namespace std;
-
-#include <string>
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <vector>
-#include <set>
-#include <exception>
-
-#include "utilities.hpp"
-#include "globaldata.hpp"
-#include "commandoptionparser.hpp"
-#include "command.hpp"
-#include "commandfactory.hpp"
-#include "errorchecking.h"
+
+
#include "engine.hpp"
+/***********************************************************************/
+Engine::Engine(){
+ try {
+ cFactory = CommandFactory::getInstance();
+ mout = MothurOut::getInstance();
+ }
+ catch(exception& e) {
+ mout->errorOut(e, "Engine", "Engine");
+ exit(1);
+ }
+}
+
/***********************************************************************/
-InteractEngine::InteractEngine(){
+InteractEngine::InteractEngine(string path){
globaldata = GlobalData::getInstance();
-
- system("clear");
-// char buffer = ' ';
-// ifstream header("introtext.txt");
-// while(!header.eof()){
-// cout << buffer;
-// buffer = header.get();
-// }
+ globaldata->argv = path;
+
}
/***********************************************************************/
-InteractEngine::~InteractEngine(){
- }
+InteractEngine::~InteractEngine(){}
/***********************************************************************/
//This function allows the user to input commands one line at a time until they quit.
try {
string input = "";
string commandName = "";
+ string options = "";
int quitCommandCalled = 0;
- bool errorFree;
- ErrorCheck* errorCheckor = new ErrorCheck();
- cout << "MOTHUR v2.0 (Martha)" << endl;
- cout << "Last updated: 1/07/2009" << endl << endl;
- cout << "(Distance-based OTU and Richness)" << 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" << 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 > ";
- getline(cin, input);
- errorFree = errorCheckor->checkInput(input);
- if (errorFree == true) {
- CommandOptionParser parser(input);
- commandName = parser.getCommandString();
+ mout->mothurOutEndLine();
+
+ input = getCommand();
+ mout->mothurOutEndLine();
+
+ //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);
+ Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
-
+ mout->control_pressed = 0;
+
}else {
- cout << "Your input contains errors. Please try again." << endl;
+ mout->mothurOut("Your input contains errors. Please try again.");
+ mout->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";
+ mout->errorOut(e, "InteractEngine", "getInput");
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";
+}
+/***********************************************************************/
+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); }
+ else{ //^D causes null string and we want it to quit mothur
+ nextCommand = "quit";
+ cout << nextCommand << endl;
+ }
+
+ mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+ return nextCommand;
+ #else
+ string nextCommand = "";
+ mout->mothurOut("mothur > ");
+ getline(cin, nextCommand);
+ mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+ return nextCommand;
+ #endif
+ #else
+ string nextCommand = "";
+ mout->mothurOut("mothur > ");
+ getline(cin, nextCommand);
+ mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+ return nextCommand;
+ #endif
+
+ mout->mothurOutEndLine();
+
+ }
+ catch(exception& e) {
+ mout->errorOut(e, "Engine", "getCommand");
exit(1);
}
-
}
-
/***********************************************************************/
//This function opens the batchfile to be used by BatchEngine::getInput.
-BatchEngine::BatchEngine(string batchFileName){
+BatchEngine::BatchEngine(string path, string batchFileName){
try {
globaldata = GlobalData::getInstance();
- openedBatch = openInputFile(batchFileName, inputBatchFile);
-
- system("clear");
- // char buffer = ' ';
- // ifstream header("introtext.txt");
- // while(!header.eof()){
- // cout << buffer;
- // buffer = header.get();
- // }
+ openedBatch = openInputFile(batchFileName, inputBatchFile);
+ globaldata->argv = path;
+
}
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";
+ mout->errorOut(e, "BatchEngine", "BatchEngine");
exit(1);
}
}
/***********************************************************************/
-BatchEngine::~BatchEngine(){
- }
+BatchEngine::~BatchEngine(){ }
/***********************************************************************/
//This Function allows the user to run a batchfile containing several commands on Dotur
bool BatchEngine::getInput(){
try {
+ //check if this is a valid batchfile
+ if (openedBatch == 1) {
+ mout->mothurOut("unable to open batchfile");
+ mout->mothurOutEndLine();
+ return 1;
+ }
+
string input = "";
string commandName = "";
- bool errorFree;
- ErrorCheck* errorCheckor = new ErrorCheck();
-
- CommandFactory cFactory;
+ string options = "";
+
+ //CommandFactory cFactory;
int quitCommandCalled = 0;
while(quitCommandCalled == 0){
-
- getline(inputBatchFile, input);
- cout << endl << "dotur > " << input << endl;
- errorFree = errorCheckor->checkInput(input);
- if (errorFree == true) {
+
+ if (inputBatchFile.eof()) { input = "quit()"; }
+ else { input = getline(inputBatchFile); }
+
+ if (input[0] != '#') {
+
+ mout->mothurOutEndLine();
+ mout->mothurOut("mothur > " + input);
+ mout->mothurOutEndLine();
+
+
+ //allow user to omit the () on the quit command
+ if (input == "quit") { input = "quit()"; }
+
CommandOptionParser parser(input);
commandName = parser.getCommandString();
- ifstream filehandle;
-
- if (openedBatch == 0) { //able to open batchfile
+ options = parser.getOptionString();
+
+ if (commandName != "") {
+
//executes valid command
- CommandFactory cFactory;
- Command* command = cFactory.getCommand(commandName);
+ Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
+ mout->control_pressed = 0;
+ }else {
+ mout->mothurOut("Invalid.");
+ mout->mothurOutEndLine();
}
- else {
- cout << "Invalid." << endl;
- }
- }
- else {
- cout << "Unable to open batchfile." << endl;
+
}
+ gobble(inputBatchFile);
}
+
+ inputBatchFile.close();
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";
+ mout->errorOut(e, "BatchEngine", "getInput");
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";
+}
+
+
+/***********************************************************************/
+/***********************************************************************/
+//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;
+
+ }
+ catch(exception& e) {
+ mout->errorOut(e, "ScriptEngine", "ScriptEngine");
exit(1);
}
}
+/***********************************************************************/
+
+ScriptEngine::~ScriptEngine(){ }
/***********************************************************************/
+//This Function allows the user to run a batchfile containing several commands on mothur
+bool ScriptEngine::getInput(){
+ try {
+
+ string input = "";
+ string commandName = "";
+ string options = "";
+
+
+ //CommandFactory cFactory;
+ int quitCommandCalled = 0;
+
+ while(quitCommandCalled == 0){
+
+ input = getNextCommand(listOfCommands);
+
+ if (input == "") { input = "quit()"; }
+
+
+ mout->mothurOutEndLine();
+ mout->mothurOut("mothur > " + input);
+ mout->mothurOutEndLine();
+
+
+ //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
+ Command* command = cFactory->getCommand(commandName, options);
+ quitCommandCalled = command->execute();
+ mout->control_pressed = 0;
+ }else {
+ mout->mothurOut("Invalid.");
+ mout->mothurOutEndLine();
+ }
+
+ }
+
+ return 1;
+ }
+ catch(exception& e) {
+ mout->errorOut(e, "ScriptEngine", "getInput");
+ exit(1);
+ }
+}
+/***********************************************************************/
+string ScriptEngine::getNextCommand(string& commandString) {
+ try {
+ string nextcommand = "";
+ int count = 0;
+
+ //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 = ""; }
+
+
+ //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) {
+ mout->errorOut(e, "ScriptEngine", "getNextCommand");
+ exit(1);
+ }
+}
+/***********************************************************************/
projects / mothur.git / blobdiff