Cosmetics and possible bugfix

josemduarte · josemduarte · commit 706a60a23f77 · 2021-06-25T10:22:13.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java
@@ -51,7 +51,7 @@
  *
  * @author Andreas Prlic
  * @author Aleix Lafita
- * @autho Anthony Bradley
+ * @author Anthony Bradley
  *
  */
 public class SecStrucCalc {
@@ -83,7 +83,8 @@ public class SecStrucCalc {
 	/** higher limit for H-bond energy */
 	public static final double HBONDHIGHENERGY = -500.0;
 
-	/** constant for electrostatic energy
+	/**
+	 * constant for electrostatic energy
 	 * <pre>
 	 *      f  *  q1 *   q2  *  scale
 	 * Q = -332 * 0.42 * 0.20 * 1000.0
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucElement.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucElement.java
@@ -37,9 +37,9 @@ public class SecStrucElement implements Serializable  {
 
 	private static final long serialVersionUID = -8485685793171396131L;
 
-	private SecStrucType type;
-	private ResidueRangeAndLength range;
-	private int index;
+	private final SecStrucType type;
+	private final ResidueRangeAndLength range;
+	private final int index;
 
 	/**
 	 * Create a new SSE object. The start and end residue numbers cannot be the
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucGroup.java
@@ -53,7 +53,7 @@ public SecStrucGroup() {
 	@Override
 	public String toString() {
 
-		StringBuffer str = new StringBuffer("SecStrucGroup ");
+		StringBuilder str = new StringBuilder("SecStrucGroup ");
 		str.append(residueNumber);
 		str.append(" ");
 		str.append(pdb_name);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
@@ -50,7 +50,7 @@ public class SecStrucTools {
 	 */
 	public static List<SecStrucInfo> getSecStrucInfo(Structure s) {
 
-		List<SecStrucInfo> listSSI = new ArrayList<SecStrucInfo>();
+		List<SecStrucInfo> listSSI = new ArrayList<>();
 		GroupIterator iter = new GroupIterator(s);
 
 		while (iter.hasNext()) {
@@ -88,7 +88,7 @@ public static void assignSecStruc( Structure s,List<SecStrucInfo> listSSI){
 	 */
 	public static List<SecStrucElement> getSecStrucElements(Structure s) {
 
-		List<SecStrucElement> listSSE = new ArrayList<SecStrucElement>();
+		List<SecStrucElement> listSSE = new ArrayList<>();
 		GroupIterator iter = new GroupIterator(s);
 
 		// SecStruc information - initialize
@@ -114,7 +114,7 @@ public static List<SecStrucElement> getSecStrucElements(Structure s) {
 
 				if (count > 0) {
 					// If chain and type are equal increment counter
-					if (ss.type == type && chainId == g.getChainId()) {
+					if (ss.type == type && chainId.equals(g.getChainId())) {
 						previous = g.getResidueNumber();
 						count++;
 						continue;
@@ -161,7 +161,7 @@ public static List<SecStrucElement> getSecStrucElements(Structure s) {
 	 */
 	public static List<SecStrucElement> getSecStrucElements(List<Group> groups) {
 
-		List<SecStrucElement> listSSE = new ArrayList<SecStrucElement>();
+		List<SecStrucElement> listSSE = new ArrayList<>();
 
 		// SecStruc information - initialize
 		SecStrucType type = SecStrucType.coil;
@@ -171,7 +171,7 @@ public static List<SecStrucElement> getSecStrucElements(List<Group> groups) {
 		int count = 0; // counts the number of residues in SSE
 
 		// Create a map for the IDs of the SSE in the structure
-		Map<SecStrucType, Integer> ids = new TreeMap<SecStrucType, Integer>();
+		Map<SecStrucType, Integer> ids = new TreeMap<>();
 		for (SecStrucType t : SecStrucType.values())
 			ids.put(t, 1);
 
@@ -185,7 +185,7 @@ public static List<SecStrucElement> getSecStrucElements(List<Group> groups) {
 
 				if (count > 0) {
 					// If chain and type are equal increment counter
-					if (ss.type == type && chainId == g.getChainId()) {
+					if (ss.type == type && chainId.equals(g.getChainId())) {
 						previous = g.getResidueNumber();
 						count++;
 						continue;
