Quality assurance (QA) tools are receiving more and more attention and are widely used by developers. Given the wide range of solutions for QA technology, it is still a question of evaluating QA tools. Most existing research is limited in the following ways: \textit{(i)} They compare tools without considering scanning rules analysis. \textit{(ii)} They disagree on the effectiveness of tools due to the study methodology and benchmark dataset. \textit{(iii)} They do not separately analyze the role of the warnings. \textit{(iv)} There is no large-scale study on the analysis of time performance. To address these problems, in the paper, we systematically select 6 free or open-source tools for a comprehensive study from a list of 148 existing Java QA tools. To carry out a comprehensive study and evaluate tools in multi-level dimensions, we first mapped the scanning rules to the CWE and analyze the coverage and granularity of the scanning rules. Then we conducted an experiment on 5 benchmarks, including 1,425 bugs, to investigate the effectiveness of these tools. Furthermore, we took substantial effort to investigate the effectiveness of warnings by comparing the real labeled bugs with the warnings and investigating their role in bug detection. Finally, we assessed these tools' time performance on 1,049 projects. The useful findings based on our comprehensive study can help developers improve their tools and provide users with suggestions for selecting QA tools.