From b1ac9e686514752c0aa7df045a3b2ab70ceaec89 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Thu, 21 May 2009 14:44:28 +0000
Subject: [PATCH] added ability to put # in front of any line in the batch file
 you don't want to use

---
 engine.cpp     | 36 +++++++++++++++++++-----------------
 globaldata.cpp |  4 ++--
 2 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/engine.cpp b/engine.cpp
index 23e3f6e..ac49206 100644
--- 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 16d434b..4005f40 100644
--- 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); 
 		}
-- 
2.39.2