The paper presents extensions to Bell Canada source code quality assessment suite (DATRIX tm) for handling Java language systems. Such extensions are based on source code object metrics, including Java interface metrics, which are presented and explained in detail. The assessment suite helps to evaluate the quality of medium-large software systems identifying parts of the system which have unusual characteristics. The paper also studies and reports the occurrence of clones in medium-large Java software systems. Clone presence affects quality since it increases a system size and often leads to higher maintenance costs. The clone identification process uses Java specific metrics to determine similarities between methods throughout a system. The results obtained from experiments with software evaluation and clone detection techniques, on over 500 KLOC of Java source code, are presented.