Why can't my code see annotations in a class file?

Question

So I have a JAR file with some classes in it. I have used DJ Java Decompiler to inspect the class in question and I can definitely see the annotations in it.
I'm working on a Maven MOJO that reads the JAR files to find the annotations, but for some reason my code does not find any annotations at all. Does anyone have any ideas what the problem might be?
The StreamLoader seems to be working because when I load the classes, their names get logged properly. Could there be something in the StreamLoader that is stripping off the annotations?
Cheers, Eric
try
    JarFile jarFile = new JarFile(artifact.getFile());
    Enumeration<JarEntry> jarEntries = jarFile.entries();
    while (jarEntries.hasMoreElements())
        JarEntry jarEntry = jarEntries.nextElement();
         if (!jarEntry.isDirectory() && jarEntry.getName().endsWith(".class"))
            getLog().info("jarEntry.getName() = " + jarEntry.getName());
            try
             Class<?> entry = streamLoader.loadClass(jarFile.getInputStream(jarEntry));
             getLog().info("entry " + entry.getName());
             if (entry.isAnnotationPresent(DotNet.class))
                 getLog().info("including " + entry.getName());
             DotNet dotNet = entry.getAnnotation(net.sf.jni4net.annotations.DotNet.class);
             if (dotNet == null)
                 Annotation [] annotations = entry.getAnnotations();
                 for (Annotation annotation : annotations)
                     getLog().info("annotation " + annotation.toString());
             else
                 getLog().info("including " + entry.getName());
         catch (Throwable t)
             getLog().warn("can't find class " + jarEntry.getName());
catch (IOException e)
    getLog().error(e.getMessage(), e);
class StreamLoader extends ClassLoader
    public StreamLoader(ClassLoader parent)
        super(parent);
    public Class<?> loadClass(InputStream input) throws ClassNotFoundException
        try
            ByteArrayOutputStream buffer = new ByteArrayOutputStream();
            int data = input.read();
            while(data != -1)
                buffer.write(data);
                data = input.read();
            input.close();
            byte[] classData = buffer.toByteArray();
            return defineClass(null, classData, 0, classData.length);
        catch (MalformedURLException e)
            e.printStackTrace();
        catch (IOException e)
            e.printStackTrace();
        return null;
}

Answer 1

Yes.
@Retention(value=java.lang.annotation.RetentionPolicy.RUNTIME)
public @interface DotNet { }I am assuming that if it were not set that way then it would not show up in the class file at all - but I could be wrong.
There are also other annotations with RetentionPolicy.RUNTIME, i.e. @ThreadSafe, but my code cannot see them either, even though the disassembler can see them.
Cheers, Eric