| Element | Missed Instructions | Cov. | Missed Branches | Cov. | Missed | Cxty | Missed | Lines | Missed | Methods |
| Total | 237 of 282 | 15% | 6 of 6 | 0% | 15 | 18 | 51 | 62 | 12 | 15 |
| writeStats(int, STmap, MaximaFinder, TrackCollection) | | 0% | n/a | 1 | 1 | 15 | 15 | 1 | 1 | |
| Prot_Analysis(String) | | 0% | n/a | 1 | 1 | 9 | 9 | 1 | 1 | |
| createUIInstance() | | 0% | n/a | 1 | 1 | 4 | 4 | 1 | 1 | |
| getImage() | | 0% | | 0% | 3 | 3 | 5 | 5 | 1 | 1 |
| validate() | | 0% | n/a | 1 | 1 | 5 | 5 | 1 | 1 | |
| runFromQconf() | | 0% | n/a | 1 | 1 | 6 | 6 | 1 | 1 | |
| showUi(boolean) | | 0% | | 0% | 2 | 2 | 4 | 4 | 1 | 1 |
| parseArgumentString(String) | | 0% | n/a | 1 | 1 | 2 | 2 | 1 | 1 | |
| runFromPaqp() | | 0% | n/a | 1 | 1 | 1 | 1 | 1 | 1 | |
| run(String) | | 0% | n/a | 1 | 1 | 2 | 2 | 1 | 1 | |
| getGui() | | 0% | n/a | 1 | 1 | 1 | 1 | 1 | 1 | |
| about() | | 0% | n/a | 1 | 1 | 1 | 1 | 1 | 1 | |
| Prot_Analysis() | | 100% | n/a | 0 | 1 | 0 | 8 | 0 | 1 | |
| static {...} | | 100% | n/a | 0 | 1 | 0 | 2 | 0 | 1 | |
| getSink() | | 100% | n/a | 0 | 1 | 0 | 1 | 0 | 1 |