fixed some bugs

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index b0371378c29d72a7b37717e5c5d43cbc8f6ef23c..a2d525011ad2823d1c72e07e24a6c4974d98644c 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -47,8 +47,8 @@ bool InteractEngine::getInput(){
                //bool errorFree;
                //ErrorCheck* errorCheckor = new ErrorCheck();
                
-               cout << "mothur v.1.3.0" << endl;
-               cout << "Last updated: 5/29/2009" << 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;
@@ -103,6 +103,7 @@ bool InteractEngine::getInput(){
 BatchEngine::BatchEngine(string path, string batchFileName){
        try {
                globaldata = GlobalData::getInstance();
+       
                openedBatch = openInputFile(batchFileName, inputBatchFile);
                globaldata->argv = path;
 
@@ -140,15 +141,18 @@ bool BatchEngine::getInput(){
                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++;
+                       
                        if (input[0] != '#') {
                        
                                cout << endl << "mothur > " << input << endl;
@@ -169,7 +173,10 @@ bool BatchEngine::getInput(){
                                }else {         cout << "Invalid." << endl;             }
                                
                        }
+                       gobble(inputBatchFile);
                }
+               
+               inputBatchFile.close();
                return 1;
        }
        catch(exception& e) {
@@ -184,4 +191,114 @@ bool BatchEngine::getInput(){
 
 
 /***********************************************************************/
+/***********************************************************************/
+//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);
+       }
+}
+/***********************************************************************/
\ No newline at end of file