added ability to put # in front of any line in the batch file you don't want to use

diff --git a/engine.cpp b/engine.cpp
index 23e3f6e119af2add01b95aa0d8c41f710b9b0a96..ac49206040520592a212b68594305cf464494155 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -138,28 +138,30 @@ bool BatchEngine::getInput(){
                while(quitCommandCalled == 0){
                
                        getline(inputBatchFile, input);
-                       if (inputBatchFile.eof()) { input = "quit()"; }
+                       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;
+                               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();
+                                       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 << "Invalid." << endl;
+                                       cout << "Unable to open batchfile." << endl;
                                }
-                       }
-                       else {
-                               cout << "Unable to open batchfile." << endl;
-                       }
+                       }else { if (inputBatchFile.eof()) { input = "quit()"; } }
                }
                return 1;
        }

diff --git a/globaldata.cpp b/globaldata.cpp
index 16d434bcb47dbd18e91914214cd8fda032e9f47b..4005f40d8cb32bc5f293c97f32386029be08c1f3 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -198,7 +198,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                //input defaults for calculators
                if (commandName == "collect.single") {
 
-                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow-shen"; }
+                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
@@ -214,7 +214,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        splitAtDash(calc, Estimators); 
                }
                if (commandName == "summary.single") {
-                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow-shen"; }
+                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }