Correct JavaDoc with refactor

Author: AndrewQuijano

src/main/java/edu/fiu/adwise/ciphercraft/dgk/DGKPrivateKey.java

@@ -13,6 +13,7 @@
 import edu.fiu.adwise.ciphercraft.misc.KeyFunctions;
 import edu.fiu.adwise.ciphercraft.misc.NTL;
 import edu.fiu.adwise.ciphercraft.misc.ObjectIdentifier;
+import edu.fiu.adwise.ciphercraft.paillier.PaillierPublicKey;
 import org.bouncycastle.asn1.*;
 import org.bouncycastle.asn1.pkcs.PrivateKeyInfo;
 import org.bouncycastle.asn1.x509.AlgorithmIdentifier;
@@ -112,6 +113,13 @@ public DGKPrivateKey (BigInteger p, BigInteger q, BigInteger vp,
 		this.generategLUT();
 	}
 
+    /**
+     * Loads a DGK private key from a PEM-encoded file.
+     *
+     * @param keyFile the path to the PEM file containing the private key
+     * @return a {@link DGKPrivateKey} instance parsed from the file
+     * @throws IOException if an error occurs while reading or parsing the file
+     */
     public static DGKPrivateKey fromFile(String keyFile) throws IOException {
         byte[] encoded = KeyFunctions.readPemFile(keyFile, PRIVATE_KEY_START, PRIVATE_KEY_END);
         return fromEncoded(encoded);

src/main/java/edu/fiu/adwise/ciphercraft/dgk/DGKPublicKey.java

@@ -88,6 +88,13 @@ public DGKPublicKey(BigInteger n, BigInteger g, BigInteger h, BigInteger u,
 		this.k = k;
 	}
 
+    /**
+     * Loads a DGK public key from a PEM-encoded file.
+     *
+     * @param keyFile the path to the PEM file containing the public key
+     * @return a {@link DGKPublicKey} instance parsed from the file
+     * @throws IOException if an error occurs while reading or parsing the file
+     */
     public static DGKPublicKey fromFile(String keyFile) throws IOException {
         byte[] encoded = KeyFunctions.readPemFile(keyFile, PUBLIC_KEY_START, PUBLIC_KEY_END);
         return fromEncoded(encoded);

src/main/java/edu/fiu/adwise/ciphercraft/misc/KeyFunctions.java

@@ -1,3 +1,7 @@
+/*
+ * Copyright (c) 2025 ADWISE Lab, Florida International University (FIU), AndrewQuijano
+ * Licensed under the MIT License. See LICENSE file in the project root for details.
+ */
 package edu.fiu.adwise.ciphercraft.misc;
 
 import java.io.BufferedReader;
@@ -11,6 +15,15 @@
 import static edu.fiu.adwise.ciphercraft.misc.CipherConstants.*;
 import static edu.fiu.adwise.ciphercraft.misc.CipherConstants.PRIVATE_KEY_END;
 
+/**
+ * Utility class for reading and writing cryptographic keys in PEM format.
+ * <p>
+ * Provides methods to serialize {@link java.security.Key} objects to PEM files
+ * and to parse PEM-encoded key files into byte arrays.
+ * <p>
+ * This class supports both public and private keys, automatically handling
+ * the appropriate PEM headers and footers.
+ */
 public class KeyFunctions {
 
     /**
@@ -33,6 +46,15 @@ public static void writeKey(Key key, String key_file) throws IOException {
         }
     }
 
+    /**
+     * Reads a PEM-encoded key from a file and decodes its Base64 content.
+     *
+     * @param filePath the path to the PEM file
+     * @param beginMarker the string marking the beginning of the key section (e.g., "-----BEGIN PUBLIC KEY-----")
+     * @param endMarker the string marking the end of the key section (e.g., "-----END PUBLIC KEY-----")
+     * @return a byte array containing the decoded key data
+     * @throws IOException if an I/O error occurs while reading the file
+     */
     public static byte[] readPemFile(String filePath, String beginMarker, String endMarker) throws IOException {
         StringBuilder pemContent = new StringBuilder();
         try (BufferedReader br = new BufferedReader(new FileReader(filePath))) {

src/main/java/edu/fiu/adwise/ciphercraft/misc/ObjectIdentifier.java

@@ -1,3 +1,7 @@
+/*
+ * Copyright (c) 2025 ADWISE Lab, Florida International University (FIU), AndrewQuijano
+ * Licensed under the MIT License. See LICENSE file in the project root for details.
+ */
 package edu.fiu.adwise.ciphercraft.misc;
 
 import edu.fiu.adwise.ciphercraft.dgk.DGK_Key;
@@ -8,28 +12,40 @@
 
 import java.security.Key;
 
+/**
+ * Utility class for mapping cryptographic key instances to their corresponding
+ * ASN.1 Object Identifiers (OIDs) for VCU-specific algorithms.
+ * <p>
+ * Supports DGK, ElGamal, Goldwasser-Micali, and Paillier algorithms, assigning
+ * each a unique OID under the Virginia Commonwealth University (VCU) Private Enterprise Number (PEN)
+ * as registered with IANA.
+ * <p>
+ * The OIDs are used for identifying algorithms in cryptographic protocols and data formats.
+ */
 public class ObjectIdentifier {
 
     /**
      * The Object Identifier (OID) for a VCU-specific cryptographic algorithm.
      * <p>
      * An OID is a globally unique identifier with a hierarchical structure.
-     * The prefix {@code 1.3.6.1.4.1} is the globally recognized path for **Private Enterprise Numbers (PENs)**.
+     * The prefix {@code 1.3.6.1.4.1} is the globally recognized path for <b>Private Enterprise Numbers (PENs)</b>.
      * <ul>
-     * <li>{@code 1}: Refers to ISO (International Organization for Standardization).</li>
-     * <li>{@code 3}: A sub-tree for "identified-organization."</li>
-     * <li>{@code 6}: A sub-tree for the U.S. Department of Defense (DoD).</li>
-     * <li>{@code 1}: The "internet" branch under the DoD.</li>
-     * <li>{@code 4}: The "private" branch for privately assigned numbers.</li>
-     * <li>{@code 1}: The "enterprise" branch, which IANA manages for PENs.</li>
+     *   <li>{@code 1}: Refers to ISO (International Organization for Standardization).</li>
+     *   <li>{@code 3}: A sub-tree for "identified-organization."</li>
+     *   <li>{@code 6}: A sub-tree for the U.S. Department of Defense (DoD).</li>
+     *   <li>{@code 1}: The "internet" branch under the DoD.</li>
+     *   <li>{@code 4}: The "private" branch for privately assigned numbers.</li>
+     *   <li>{@code 1}: The "enterprise" branch, which IANA manages for PENs.</li>
      * </ul>
      * <p>
      * The number {@code 10384} is the specific PEN assigned to Virginia Commonwealth University (VCU)
      * by the Internet Assigned Numbers Authority (IANA). The final number, {@code 1}, is a
      * sub-identifier defined by VCU for DGK, and the sequence continues for ElGamal, Goldwasser-Micali and Paillier.
      * <p>
      * You can verify this assignment on the official IANA registry here:
-     * {@link <a href="https://www.iana.org/assignments/enterprise-numbers">IANA Link</a>}.
+     * <a href="https://www.iana.org/assignments/enterprise-numbers">IANA Link</a>
+     * <a href="https://michaelwaterman.nl/2025/05/10/part-5-pki-best-practices-creating-unique-object-identifiers-oids/">Best Practices Guide</a>
+     *
      * @param key the cryptographic key instance
      * @return the corresponding ASN1ObjectIdentifier for the algorithm, or {@code null} if unknown
      */

src/main/java/edu/fiu/adwise/ciphercraft/paillier/PaillierKeyPairGenerator.java

@@ -30,6 +30,7 @@ public class PaillierKeyPairGenerator extends KeyPairGeneratorSpi implements Cip
 	 * Main method to generate and save Paillier public and private keys to files.
 	 *
 	 * @param args Command-line arguments (not used).
+     * @throws IOException If an I/O error occurs during key file writing.
 	 */
 	public static void main(String []  args) throws IOException {
 		String paillier_private_key_file = "paillier.priv";

src/main/java/edu/fiu/adwise/ciphercraft/paillier/PaillierPrivateKey.java

@@ -74,6 +74,13 @@ public PaillierPrivateKey(int key_size, BigInteger n, BigInteger mod,
 		this.rho = PaillierCipher.L(this.g.modPow(this.lambda, this.modulus), this.n).modInverse(this.modulus);
 	}
 
+    /**
+     * Loads a Paillier private key from a PEM-encoded file.
+     *
+     * @param keyFile the path to the PEM file containing the private key
+     * @return a {@link PaillierPrivateKey} instance parsed from the file
+     * @throws IOException if an error occurs while reading or parsing the file
+     */
     public static PaillierPrivateKey fromFile(String keyFile) throws IOException {
         byte[] encoded = KeyFunctions.readPemFile(keyFile, PRIVATE_KEY_START, PRIVATE_KEY_END);
         return fromEncoded(encoded);

src/main/java/edu/fiu/adwise/ciphercraft/paillier/PaillierPublicKey.java

@@ -57,12 +57,18 @@ public PaillierPublicKey(int key_size, BigInteger n, BigInteger modulus, BigInte
 		this.g = g;
 	}
 
+    /**
+     * Loads a Paillier public key from a PEM-encoded file.
+     *
+     * @param keyFile the path to the PEM file containing the public key
+     * @return a {@link PaillierPublicKey} instance parsed from the file
+     * @throws IOException if an error occurs while reading or parsing the file
+     */
     public static PaillierPublicKey fromFile(String keyFile) throws IOException {
         byte[] encoded = KeyFunctions.readPemFile(keyFile, PUBLIC_KEY_START, PUBLIC_KEY_END);
         return fromEncoded(encoded);
     }
 
-
     /**
 	 * Retrieves the encryption of zero using this public key.
 	 *