A Java compiler is a compiler for the Java programming language. The most common form of output from a Java compiler is Java class files containing platform-neutral Java bytecode. There exist also compilers emitting optimized native machine code for a particular hardware/operating system combination.
Most Java-to-bytecode compilers, Jikes being a well known exception, do virtually no optimization, leaving this until run time to be done by the JRE.
The Java Virtual Machine (JVM) loads the class files and either interprets the bytecode or just-in-time compiles it to machine code and then possibly optimizes it using dynamic compilation.
A standard on how to interact with Java compilers programmatically was specified in JSR 199.
Read more about Java Compiler: Major Java Compilers, Java Decompilers