Refactoring : Extract method changes to reduce the cyclomatic complexity of getBackboneAtomArray

Sreejith Nair · Sreejith Nair · commit bf40264a472d · 2023-04-04T21:38:15.000-03:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -1128,65 +1128,39 @@ public static Atom[] getRepresentativeAtomArray(Structure s) {
 	 * @return an Atom[] array
 	 */
 	public static Atom[] getBackboneAtomArray(Structure s) {
-
 		List<Atom> atoms = new ArrayList<>();
+		Set<String> nucleotideAtomNames = new HashSet<>(Arrays.asList(C1_ATOM_NAME, C2_ATOM_NAME, C3_ATOM_NAME, C4_ATOM_NAME, O2_ATOM_NAME, O3_ATOM_NAME, O4_ATOM_NAME, O5_ATOM_NAME, OP1_ATOM_NAME, OP2_ATOM_NAME, P_ATOM_NAME));
+		Set<String> aminoAcidAtomNames = new HashSet<>(Arrays.asList(CA_ATOM_NAME, C_ATOM_NAME, N_ATOM_NAME, O_ATOM_NAME));
 
 		for (Chain c : s.getChains()) {
 			for (Group g : c.getAtomGroups()) {
 				if (g.hasAminoAtoms()) {
-					// this means we will only take atoms grom groups that have
-					// complete backbones
-					for (Atom a : g.getAtoms()) {
-						switch (g.getType()) {
-						case NUCLEOTIDE:
-							// Nucleotide backbone
-							if (a.getName().equals(C1_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(C2_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(C3_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(C4_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(O2_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(O3_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(O4_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(O5_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(OP1_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(OP2_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(P_ATOM_NAME))
-								atoms.add(a);
-							// TODO Allow C4* names as well as C4'? -SB 3/2015
-							break;
-						case AMINOACID:
-						default:
-							// we do it this way instead of with g.getAtom() to
-							// be sure we always use the same order as original
-							if (a.getName().equals(CA_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(C_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(N_ATOM_NAME))
-								atoms.add(a);
-							if (a.getName().equals(O_ATOM_NAME))
-								atoms.add(a);
-							break;
-						}
+					if (g.getType() == GroupType.NUCLEOTIDE) {
+						addNucleotideAndAminoAtoms(atoms, g, nucleotideAtomNames);
+					} else {
+						addNucleotideAndAminoAtoms(atoms, g, aminoAcidAtomNames);
 					}
 				}
 			}
-
 		}
-
 		return atoms.toArray(new Atom[0]);
 	}
 
+	/**
+	 * This method will be used to add the Nucleotide and Amino atoms to the backbone Atom arrays based on the pre-defined Atom names.
+	 * @param atoms
+	 * @param g
+	 * @param atomNames
+	 */
+	private static void addNucleotideAndAminoAtoms(List<Atom> atoms, Group g, Set<String> atomNames) {
+		for (Atom a : g.getAtoms()) {
+			if (atomNames.contains(a.getName())) {
+				atoms.add(a);
+			}
+		}
+	}
+
+
 	/**
 	 * Convert three character amino acid codes into single character e.g.
 	 * convert CYS to C. Valid 3-letter codes will be those of the standard 20
