We present Java Sensei, an Intelligent Learning Environment (ILE) for learning Java programming. The ILE is formed by an affective tutoring system working in a Web environment. The tutoring system was implemented under different learning methodologies like problem-solving for the pedagogical module, knowledge space for the expert module, and overlays for the student module. The main contribution of this work was the integration of cognitive and affective information in a behavior graph which is used by the pedagogical agent to show emotion and empathy to the student.