Fix two PMD issues, but comment others where if's were added for readability

src/main/java/org/apache/commons/collections4/functors/PrototypeFactory.java

@@ -193,12 +193,12 @@ public class PrototypeFactory {
                     if (bais != null) {
                         bais.close();
                     }
-                } catch (final IOException ex) {
+                } catch (final IOException ex) { //NOPMD
                     // ignore
                 }
                 try {
                     baos.close();
-                } catch (final IOException ex) {
+                } catch (final IOException ex) { //NOPMD
                     // ignore
                 }
             }

src/main/java/org/apache/commons/collections4/iterators/FilterIterator.java

@@ -96,10 +96,8 @@ public class FilterIterator<E> implements Iterator<E> {
      */
     @Override
     public E next() {
-        if (!nextObjectSet) {
-            if (!setNextObject()) {
-                throw new NoSuchElementException();
-            }
+        if (!nextObjectSet && !setNextObject()) {
+            throw new NoSuchElementException();
         }
         nextObjectSet = false;
         return nextObject;

src/main/java/org/apache/commons/collections4/iterators/FilterListIterator.java

@@ -132,10 +132,8 @@ public class FilterListIterator<E> implements ListIterator<E> {
 
     @Override
     public E next() {
-        if (!nextObjectSet) {
-            if (!setNextObject()) {
-                throw new NoSuchElementException();
-            }
+        if (!nextObjectSet && !setNextObject()) {
+            throw new NoSuchElementException();
         }
         nextIndex++;
         final E temp = nextObject;
@@ -150,10 +148,8 @@ public class FilterListIterator<E> implements ListIterator<E> {
 
     @Override
     public E previous() {
-        if (!previousObjectSet) {
-            if (!setPreviousObject()) {
-                throw new NoSuchElementException();
-            }
+        if (!previousObjectSet && !setPreviousObject()) {
+            throw new NoSuchElementException();
         }
         nextIndex--;
         final E temp = previousObject;

src/main/java/org/apache/commons/collections4/iterators/PermutationIterator.java

@@ -116,7 +116,7 @@ public class PermutationIterator<E> implements Iterator<List<E>> {
         for (int i = 0; i < keys.length; i++) {
             if ((direction[i] && i < keys.length - 1 && keys[i] > keys[i + 1]) ||
                 (!direction[i] && i > 0 && keys[i] > keys[i - 1])) {
-                if (keys[i] > largestKey) {
+                if (keys[i] > largestKey) { // NOPMD
                     largestKey = keys[i];
                     indexOfLargestMobileInteger = i;
                 }

src/main/java/org/apache/commons/collections4/keyvalue/AbstractMapEntry.java

@@ -48,7 +48,7 @@ public abstract class AbstractMapEntry<K, V> extends AbstractKeyValue<K, V> impl
      * @return the previous value
      */
     @Override
-    public V setValue(final V value) {
+    public V setValue(final V value) { // NOPMD
         return super.setValue(value);
     }
 

src/main/java/org/apache/commons/collections4/map/AbstractReferenceMap.java

@@ -291,7 +291,8 @@ public abstract class AbstractReferenceMap<K, V> extends AbstractHashedMap<K, V>
     @Override
     public void clear() {
         super.clear();
-        while (queue.poll() != null) {} // drain the queue
+        // drain the queue
+        while (queue.poll() != null) {} // NOPMD
     }
 
     //-----------------------------------------------------------------------

src/main/java/org/apache/commons/collections4/map/MultiValueMap.java

@@ -309,7 +309,7 @@ public class MultiValueMap<K, V> extends AbstractMapDecorator<K, Object> impleme
      * @see #iterator()
      */
     @Override
-    public Set<Entry<K, Object>> entrySet() {
+    public Set<Entry<K, Object>> entrySet() { // NOPMD
         return super.entrySet();
     }
 

src/main/java/org/apache/commons/collections4/sequence/SequencesComparator.java

@@ -201,7 +201,7 @@ public class SequencesComparator<T> {
                 }
                 // Second step
                 if (delta % 2 != 0 && delta - d <= k && k <= delta + d) {
-                    if (vUp[i-delta] <= vDown[i]) {
+                    if (vUp[i-delta] <= vDown[i]) { // NOPMD
                         return buildSnake(vUp[i-delta], k + start1 - start2, end1, end2);
                     }
                 }
@@ -227,7 +227,7 @@ public class SequencesComparator<T> {
                 }
                 // Second step
                 if (delta % 2 == 0 && -d <= k && k <= d ) {
-                    if (vUp[i] <= vDown[i + delta]) {
+                    if (vUp[i] <= vDown[i + delta]) { // NOPMD
                         return buildSnake(vUp[i], k + start1 - start2, end1, end2);
                     }
                 }

src/main/java/org/apache/commons/collections4/trie/AbstractPatriciaTrie.java

@@ -177,7 +177,7 @@ abstract class AbstractPatriciaTrie<K, V> extends AbstractBitwiseTrie<K, V> {
                 // This is a very special and rare case.
 
                 /* REPLACE OLD KEY+VALUE */
-                if (found != root) {
+                if (found != root) { // NOPMD
                     incrementModCount();
                     return found.setKeyValue(key, value);
                 }