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The Bouncy Castle Java APIs for CMS, PKCS, EAC, TSP, CMP, CRMF, OCSP, and certificate generation. This jar contains APIs for JDK 1.5 to JDK 1.8. The APIs can be used in conjunction with a JCE/JCA provider such as the one provided with the Bouncy Castle Cryptography APIs.
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package org.bouncycastle.cert;

import java.math.BigInteger;
import java.util.Date;

import org.bouncycastle.asn1.ASN1Encodable;
import org.bouncycastle.asn1.ASN1Integer;
import org.bouncycastle.asn1.ASN1ObjectIdentifier;
import org.bouncycastle.asn1.x500.X500Name;
import org.bouncycastle.asn1.x509.Certificate;
import org.bouncycastle.asn1.x509.Extension;
import org.bouncycastle.asn1.x509.ExtensionsGenerator;
import org.bouncycastle.asn1.x509.SubjectPublicKeyInfo;
import org.bouncycastle.asn1.x509.Time;
import org.bouncycastle.asn1.x509.V3TBSCertificateGenerator;
import org.bouncycastle.operator.ContentSigner;


/**
 * class to produce an X.509 Version 3 certificate.
 */
public class X509v3CertificateBuilder
{
    private V3TBSCertificateGenerator   tbsGen;
    private ExtensionsGenerator extGenerator;

    /**
     * Create a builder for a version 3 certificate.
     *
     * @param issuer the certificate issuer
     * @param serial the certificate serial number
     * @param notBefore the date before which the certificate is not valid
     * @param notAfter the date after which the certificate is not valid
     * @param subject the certificate subject
     * @param publicKeyInfo the info structure for the public key to be associated with this certificate.
     */
    public X509v3CertificateBuilder(X500Name issuer, BigInteger serial, Date notBefore, Date notAfter, X500Name subject, SubjectPublicKeyInfo publicKeyInfo)
    {
        tbsGen = new V3TBSCertificateGenerator();
        tbsGen.setSerialNumber(new ASN1Integer(serial));
        tbsGen.setIssuer(issuer);
        tbsGen.setStartDate(new Time(notBefore));
        tbsGen.setEndDate(new Time(notAfter));
        tbsGen.setSubject(subject);
        tbsGen.setSubjectPublicKeyInfo(publicKeyInfo);

        extGenerator = new ExtensionsGenerator();
    }

    /**
     * Set the subjectUniqueID - note: it is very rare that it is correct to do this.
     *
     * @param uniqueID a boolean array representing the bits making up the subjectUniqueID.
     * @return this builder object.
     */
    public X509v3CertificateBuilder setSubjectUniqueID(boolean[] uniqueID)
    {
        tbsGen.setSubjectUniqueID(CertUtils.booleanToBitString(uniqueID));

        return this;
    }

    /**
     * Set the issuerUniqueID - note: it is very rare that it is correct to do this.
     *
     * @param uniqueID a boolean array representing the bits making up the issuerUniqueID.
     * @return this builder object.
     */
    public X509v3CertificateBuilder setIssuerUniqueID(boolean[] uniqueID)
    {
        tbsGen.setIssuerUniqueID(CertUtils.booleanToBitString(uniqueID));

        return this;
    }

    /**
     * Add a given extension field for the standard extensions tag (tag 3)
     *
     * @param oid the OID defining the extension type.
     * @param isCritical true if the extension is critical, false otherwise.
     * @param value the ASN.1 structure that forms the extension's value.
     * @return this builder object.
     */
    public X509v3CertificateBuilder addExtension(
        ASN1ObjectIdentifier oid,
        boolean isCritical,
        ASN1Encodable value)
        throws CertIOException
    {
        CertUtils.addExtension(extGenerator, oid, isCritical, value);

        return this;
    }

    /**
     * Add a given extension field for the standard extensions tag (tag 3)
     * copying the extension value from another certificate.
     *
     * @param oid the OID defining the extension type.
     * @param isCritical true if the copied extension is to be marked as critical, false otherwise.
     * @param certHolder the holder for the certificate that the extension is to be copied from.
     * @return this builder object.
     */
    public X509v3CertificateBuilder copyAndAddExtension(
        ASN1ObjectIdentifier oid,
        boolean isCritical,
        X509CertificateHolder certHolder)
    {
        Certificate cert = certHolder.toASN1Structure();

        Extension extension = cert.getTBSCertificate().getExtensions().getExtension(oid);

        if (extension == null)
        {
            throw new NullPointerException("extension " + oid + " not present");
        }

        extGenerator.addExtension(oid, isCritical, extension.getExtnValue().getOctets());

        return this;
    }

    /**
     * Generate an X.509 certificate, based on the current issuer and subject
     * using the passed in signer.
     *
     * @param signer the content signer to be used to generate the signature validating the certificate.
     * @return a holder containing the resulting signed certificate.
     */
    public X509CertificateHolder build(
        ContentSigner signer)
    {
        tbsGen.setSignature(signer.getAlgorithmIdentifier());

        if (!extGenerator.isEmpty())
        {
            tbsGen.setExtensions(extGenerator.generate());
        }

        return CertUtils.generateFullCert(signer, tbsGen.generateTBSCertificate());
    }
}