import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.OutputStream;

import org.apache.fop.apps.Driver;
import org.apache.fop.apps.TraxInputHandler;
import org.xml.sax.InputSource;

…

File xmlFile = new File("projectteam.xml"); // XMLファイル
File xslFile = new File("projectteam2fo.xsl"); // XSLファイル
File pdfFile = new File("projectteam.pdf"); // PDFの出力ファイル

InputStream xmlIn = new BufferedInputStream(new FileInputStream(xmlFile));
InputStream xslIn = new BufferedInputStream(new FileInputStream(xslFile));
OutputStream pdfOut = new BufferedOutputStream(new FileOutputStream(pdfFile));

TraxInputHandler inputHandler = new TraxInputHandler(new InputSource(xmlIn),
new InputSource(xslIn));

Driver driver = new Driver();
driver.setRenderer(Driver.RENDER_PDF); // PDF形式でレンダリング
driver.setOutputStream(pdfOut);

inputHandler.run(driver); // レンダリング開始

xmlIn.close();
xslIn.close();
pdfOut.close();