api: Convert TODOs to issues

See issues #302, #303, #304 on GitHub.

Also some code quality improvements.

Author: lorenzleutgeb

alpha-api/src/main/java/at/ac/tuwien/kr/alpha/api/config/SystemConfig.java

@@ -33,11 +33,6 @@
 import java.util.stream.Collectors;
 
 public class SystemConfig {
-
-	// TODO add validation on configs!
-	// TODO naive solver cannot print stats!
-	// TODO introduce debug levels (lvl 1 = print graphs and preprocessed, lvl 2 = same with debugInternalChecks)
-	
 	// Note: Defining constants for default values here rather than just
 	// initializing from those values in order to have the values accessible in
 	// contexts where no AlphaConfig instance exists (e.g. argument parsing from

alpha-commons/src/main/java/at/ac/tuwien/kr/alpha/commons/literals/BasicLiteralImpl.java

@@ -68,7 +68,7 @@ public BasicLiteralImpl negate() {
 	 */
 	@Override
 	public BasicLiteralImpl substitute(Substitution substitution) {
-		return new BasicLiteralImpl((BasicAtom) getAtom().substitute(substitution), positive);
+		return new BasicLiteralImpl(getAtom().substitute(substitution), positive);
 	}
 
 	/**

alpha-core/src/main/java/at/ac/tuwien/kr/alpha/core/parser/ParseTreeVisitor.java

@@ -271,7 +271,7 @@ public List<ChoiceElement> visitChoice_elements(ASPCore2Parser.Choice_elementsCo
 	@Override
 	public ChoiceHead.ChoiceElement visitChoice_element(ASPCore2Parser.Choice_elementContext ctx) {
 		// choice_element : classical_literal (COLON naf_literals?)?;
-		BasicAtom atom = (BasicAtom) visitClassical_literal(ctx.classical_literal());
+		BasicAtom atom = visitClassical_literal(ctx.classical_literal());
 		if (ctx.naf_literals() != null) {
 			return Heads.newChoiceElement(atom, visitNaf_literals(ctx.naf_literals()));
 		} else {

alpha-core/src/main/java/at/ac/tuwien/kr/alpha/core/solver/NoGoodStoreAlphaRoaming.java

@@ -820,15 +820,10 @@ private void clearAlphaWatchList(int literal) {
 
 	@Override
 	public int estimate(int atom, boolean truth, BinaryNoGoodPropagationEstimationStrategy strategy) {
-		switch (strategy) {
-			case BinaryNoGoodPropagation:
-				if (hasBinaryNoGoods) {
-					return estimateEffectsOfBinaryNoGoodPropagation(atom, truth) - 1;
-				}
-			case CountBinaryWatches:
-			default:
-				return getNumberOfBinaryWatches(atom, truth);
+		if (BinaryNoGoodPropagationEstimationStrategy.BinaryNoGoodPropagation.equals(strategy)) {
+			return estimateEffectsOfBinaryNoGoodPropagation(atom, truth) - 1;
 		}
+		return getNumberOfBinaryWatches(atom, truth);
 	}
 
 	private int getNumberOfBinaryWatches(int atom, boolean truth) {