Specification for javax.smartcardio.CommandAPDU.CommandAPDU(ByteBuffer apdu) is insufficient because it says nothing about the required state of ByteBuffer object passed to the constructor. Current implementation requires ByteBuffer object with a buffer's position pointed to the start of APDU array in the ByteBuffer.
We believe that this should be specified in javadoc explicitly.

Minimized test:
--- Test.java ---
import java.nio.ByteBuffer;
import javax.smartcardio.CommandAPDU;

public class Test {

    public static void main(String[] args) {
        byte[] apdu_array = {0,0,0,0};//case 1 APDU
        ByteBuffer buffer = ByteBuffer.allocate(apdu_array.length);
        buffer.put(apdu_array); // putting apdu data
        //buffer.position(0);
        CommandAPDU cAPDU = new CommandAPDU(buffer);
    }
}
--- Test.java ---

Minimized test output:
>java Test
Exception in thread "main" java.lang.IllegalArgumentException: apdu must be at least 4 bytes long
    at javax.smartcardio.CommandAPDU.parse(CommandAPDU.java:301)
    at javax.smartcardio.CommandAPDU.<init>(CommandAPDU.java:188)
    at Test.main(Test.java:11)


The IllegalArgumentException is thrown because the buffer's position pointed to the end of data.
It's required to uncomment commented string to make it work.