Addressing review comments

josemduarte · josemduarte · commit 95c0ffc8cd2c · 2021-10-12T13:41:06.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java
@@ -28,6 +28,7 @@
 import java.io.Serializable;
 import java.util.Arrays;
 import java.util.Locale;
+import java.util.Objects;
 
 
 /**
@@ -73,9 +74,12 @@ public BoundingBox(BoundingBox bb) {
 	 * Constructs a BoundingBox by calculating maxs and mins of given array of atoms.
 	 * @param atoms the atom array
 	 * @throws IllegalArgumentException if atom array is empty
+	 * @throws NullPointerException if input is null
 	 */
 	public BoundingBox (Point3d[] atoms) {
 
+		Objects.requireNonNull(atoms);
+
 		if (atoms.length==0)
 			throw new IllegalArgumentException("Empty list of atoms is not allowed for BoundingBox construction");
 
@@ -103,9 +107,12 @@ public BoundingBox (Point3d[] atoms) {
 	 * Given a set of bounding boxes returns a bounding box that bounds all of them.
 	 * @param boxes an array of bounding boxes
 	 * @throws IllegalArgumentException if input array is empty
+	 * @throws NullPointerException if input is null
 	 */
 	public BoundingBox(BoundingBox[] boxes) {
 
+		Objects.requireNonNull(boxes);
+
 		if (boxes.length==0)
 			throw new IllegalArgumentException("Empty list of bounding boxes is not allowed for BoundingBox construction");
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/InterfaceFinder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/InterfaceFinder.java
@@ -1,14 +1,18 @@
 package org.biojava.nbio.structure.contact;
 
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Calc;
+import org.biojava.nbio.structure.Chain;
+import org.biojava.nbio.structure.Group;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.xtal.CrystalTransform;
 import org.biojava.nbio.structure.xtal.SpaceGroup;
 
 import javax.vecmath.Point3d;
 import java.util.ArrayList;
-import java.util.Iterator;
+import java.util.Collection;
 import java.util.List;
-import java.util.stream.IntStream;
 
 /**
  * A class containing methods to find interfaces in a given structure.
@@ -37,11 +41,10 @@ public InterfaceFinder(Structure structure) {
      * Remove polymer chains with 0 atoms.
      */
     private void trimPolyChains() {
-        Iterator<Chain> it = polyChains.iterator();
-        while (it.hasNext()) {
-            int count = it.next().getAtomGroups().stream().flatMapToInt(g-> IntStream.of(g.getAtoms().size())).sum();
-            if (count==0) it.remove();
-        }
+        polyChains.removeIf(chain -> {
+            int count = chain.getAtomGroups().stream().map(Group::getAtoms).mapToInt(Collection::size).sum();
+            return count == 0;
+        });
     }
 
     /**
