■ 注意

 * X509Certificate は、2種類ある
  （１） javax.security.cert.X509Certificate
  （２） java.security.cert.X509Certificate

■ サンプル

（１） javax.security.cert.X509Certificate編

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Base64;
import java.util.Base64.Encoder;

import javax.security.cert.CertificateEncodingException;
import javax.security.cert.CertificateException;
import javax.security.cert.X509Certificate;

public class Main {
  private static final String BEGIN_CERT = "-----BEGIN CERTIFICATE-----\n";
  private static final String END_CERT = "\n-----END CERTIFICATE-----";
  
  public static void main(String[] args) {
    try {
      X509Certificate certificate = loadCertificate("./etc/cacert.crt");
      String contentInPem = toPem(certificate);
      outputFile("./etc/cacertOutput.pem", contentInPem);
      
      System.out.println("See ./etc/cacertOutput.pem");
      System.out.println("Done...");
    } catch (Exception ex) {
      ex.printStackTrace();
    }
  }

  // 証明書ファイル→X509Certificate を変換
  private static X509Certificate loadCertificate(String certificatePath)
      throws FileNotFoundException, IOException, CertificateException {
    try (FileInputStream inputStream = new FileInputStream(new File(certificatePath))) {
      X509Certificate returnValue = X509Certificate.getInstance(inputStream);
      returnValue.checkValidity();
      return returnValue;
    }
  }

  // X509Certificate→ 証明書ファイル（公開鍵） を変換
  private static String toPem(X509Certificate certificate) throws CertificateEncodingException {
    Encoder encoder = Base64.getEncoder();
    byte[] derCertificate = certificate.getEncoded();
    return BEGIN_CERT + new String(encoder.encode(derCertificate)) + END_CERT;
  }

  // ファイル出力
  private static void outputFile(String outputFilePath, String fileContent) throws IOException {
    try (FileWriter fileWriter = new FileWriter(outputFilePath)) {
      fileWriter.write(fileContent);
    }
  }
}

（２） java.security.cert.X509Certificate編

以下の関連記事のサンプルで使用している。

https://blogs.yahoo.co.jp/dk521123/37097725.html
一部抜粋

  private static final String CERTIFICATE_TYPE = "X.509";

  // X509Certificate→ 証明書ファイル を変換
  // エクスポート機能
  public void exportCertificate(String alias, String exportFilePath)
      throws CertificateEncodingException, IOException, KeyStoreException {
    try (FileOutputStream outputStream = new FileOutputStream(new File(exportFilePath))) {
      X509Certificate x509Certificate = this.getCertificatesByAlias(alias);
      outputStream.write(x509Certificate.getEncoded());
    }
  }

  // 証明書ファイル→X509Certificate を変換
  private static X509Certificate getX509Certificate(String certificateFilePath)
      throws IOException, CertificateException {
    try (InputStream inputStream = new FileInputStream(new File(certificateFilePath))) {
      CertificateFactory certificateFactory = CertificateFactory.getInstance(CERTIFICATE_TYPE);
      return (X509Certificate) certificateFactory.generateCertificate(inputStream);
    }
  }

  // 証明書(byte[])→X509Certificate を変換
  private static X509Certificate getX509Certificate(byte[] certificates)
      throws IOException, CertificateException {
    try (InputStream inputStream = new ByteArrayInputStream(certificates)) {
      CertificateFactory certificateFactory = CertificateFactory.getInstance(CERTIFICATE_TYPE);
      return (X509Certificate) certificateFactory.generateCertificate(inputStream);
    }
  }