Fix some code style issues

src/main/java/org/matsim/prepare/FilterRelevantAgents.java

@@ -41,11 +41,14 @@
 import java.util.concurrent.ConcurrentHashMap;
 
 
+/**
+ * Use {@link org.matsim.application.prepare.scenario.CreateScenarioCutOut} instead.
+ */
 @CommandLine.Command(
 	name = "filter-relevant-agents",
 	description = "Filter agents that have any activities or routes within the shp file."
 )
-@Deprecated
+@Deprecated(forRemoval = true, since = "6.4")
 public class FilterRelevantAgents implements MATSimAppCommand, PersonAlgorithm {
 
 	private static final Logger log = LogManager.getLogger(FilterRelevantAgents.class);

src/main/java/org/matsim/prepare/choices/ComputePlanChoices.java

@@ -74,8 +74,8 @@ public class ComputePlanChoices implements MATSimAppCommand, PersonAlgorithm {
 	@CommandLine.Option(names = "--calc-scores", description = "Perform pseudo scoring for each plan", defaultValue = "false")
 	private boolean calcScores;
 
-	@CommandLine.Option(names = "--plan-candidates", description = "Method to generate plan candidates", defaultValue = "bestK")
-	private PlanCandidates planCandidates = PlanCandidates.bestK;
+	@CommandLine.Option(names = "--plan-candidates", description = "Method to generate plan candidates", defaultValue = "subtour")
+	private PlanCandidates planCandidates = PlanCandidates.subtour;
 
 	@CommandLine.Option(names = "--max-plan-length", description = "Maximum plan length", defaultValue = "7")
 	private int maxPlanLength;

src/main/java/org/matsim/prepare/choices/RandomPlanGenerator.java

@@ -33,7 +33,7 @@ public List<PlanCandidate> generate(Plan plan, PlanModel planModel, @Nullable Se
 		PlanCandidate existing = gen.generatePredefined(planModel, chosen).get(0);
 
 		// This changes the internal state to randomize the estimates
-		// TODO random selection is biased because of mass conservation
+		// random selection is biased because of mass conservation
 		// due to that, this class should not be used
 		for (Map.Entry<String, List<ModeEstimate>> entry : planModel.getEstimates().entrySet()) {
 			for (ModeEstimate est : entry.getValue()) {

src/main/java/org/matsim/prepare/pt/CorrectRouteTypes.java

@@ -11,12 +11,12 @@
 @SuppressWarnings("unused")
 public class CorrectRouteTypes implements Consumer<Route> {
 
-	private static final Pattern ICE = Pattern.compile("ICE [0-9]+");
-	private static final Pattern IC = Pattern.compile("(IC|EC) [0-9]+");
-	private static final Pattern RE = Pattern.compile("((RE|RB[0-9]+)|FEX|^RE)");
+	private static final Pattern ICE = Pattern.compile("ICE \\d+");
+	private static final Pattern IC = Pattern.compile("(IC|EC) \\d+");
+	private static final Pattern RE = Pattern.compile("((RE|RB\\d+)|FEX|^RE)");
 
-	private static final Pattern S_BAHN = Pattern.compile("S[0-9]+");
-	private static final Pattern U_BAHN = Pattern.compile("U[0-9]+");
+	private static final Pattern S_BAHN = Pattern.compile("S\\d+");
+	private static final Pattern U_BAHN = Pattern.compile("U\\d+");
 
 	@Override
 	public void accept(Route route) {

src/main/java/org/matsim/run/OpenBerlinDrtScenario.java

@@ -139,10 +139,9 @@ private static void tagTransitStopsInServiceArea(TransitSchedule transitSchedule
 
 		for (TransitStopFacility stop : transitSchedule.getFacilities().values()) {
 			if (stop.getAttributes().getAttribute(oldFilterAttribute) != null) {
-				if (stop.getAttributes().getAttribute(oldFilterAttribute).equals(oldFilterValue)) {
-					if (serviceAreas.stream().anyMatch(geom -> geom.contains(MGC.coord2Point(stop.getCoord())))) {
-						stop.getAttributes().putAttribute(newAttributeName, newAttributeValue);
-					}
+				if (stop.getAttributes().getAttribute(oldFilterAttribute).equals(oldFilterValue) &&
+					serviceAreas.stream().anyMatch(geom -> geom.contains(MGC.coord2Point(stop.getCoord())))) {
+					stop.getAttributes().putAttribute(newAttributeName, newAttributeValue);
 				}
 			}
 		}

src/main/java/org/matsim/run/scoring/IndividualPersonScoringParameters.java

@@ -92,12 +92,12 @@ public IndividualPersonScoringParameters(Scenario scenario) {
 		this.cache = new IdMap<>(Person.class, scenario.getPopulation().getPersons().size());
 
 		// Create uncorrelated seed from the global seed
-		SplittableRandom rnd = new SplittableRandom(scenario.getConfig().global().getRandomSeed());
-		for (int i = 0; i < rnd.nextInt(); i++) {
-			rnd.nextLong();
+		SplittableRandom rng = new SplittableRandom(scenario.getConfig().global().getRandomSeed());
+		for (int i = 0; i < rng.nextInt(); i++) {
+			rng.nextLong();
 		}
 
-		byte[] seed = Longs.toByteArray(rnd.nextLong());
+		byte[] seed = Longs.toByteArray(rng.nextLong());
 		this.rnd = ThreadLocal.withInitial(() -> new Context(seed));
 	}