| readOptions() |   | 53% |   | 45% | 9 | 12 | 22 | 49 | 0 | 1 |
| setChadoOptions() |   | 45% |   | 40% | 5 | 6 | 5 | 14 | 0 | 1 |
| getDefaultSequenceFileName() |  | 0% |  | 0% | 6 | 6 | 10 | 10 | 1 | 1 |
| getDefaultFeatureFileName() |  | 0% |  | 0% | 6 | 6 | 10 | 10 | 1 | 1 |
| resetCachedValues() |   | 72% |   | 70% | 3 | 6 | 7 | 31 | 0 | 1 |
| static {...} |   | 56% | | n/a | 0 | 1 | 8 | 20 | 0 | 1 |
| isBuggyLinuxVM() |  | 0% |  | 0% | 4 | 4 | 9 | 9 | 1 | 1 |
| getInvisibleQualifiers(boolean) |  | 0% |  | 0% | 4 | 4 | 7 | 7 | 1 | 1 |
| setDirectEdit(boolean) |  | 0% |  | 0% | 4 | 4 | 8 | 8 | 1 | 1 |
| setEukaryoticMode(boolean) |  | 0% |  | 0% | 4 | 4 | 8 | 8 | 1 | 1 |
| setHighlightActiveEntryFlag(boolean) |  | 0% |  | 0% | 4 | 4 | 8 | 8 | 1 | 1 |
| getColorFromColourNumber(int) |   | 46% |   | 37% | 4 | 5 | 5 | 9 | 0 | 1 |
| isEukaryoticMode() |   | 36% |   | 12% | 4 | 5 | 4 | 7 | 0 | 1 |
| getAllGeneNames() |  | 0% |  | 0% | 2 | 2 | 4 | 4 | 1 | 1 |
| getMinimumORFSize() |  | 0% |  | 0% | 2 | 2 | 4 | 4 | 1 | 1 |
| setDisplayNameQualifiers(String) |  | 0% | | n/a | 1 | 1 | 4 | 4 | 1 | 1 |
| setSystematicQualifierNames(String) |  | 0% | | n/a | 1 | 1 | 4 | 4 | 1 | 1 |
| getStartCodons() |   | 78% |   | 66% | 2 | 4 | 2 | 9 | 0 | 1 |
| getDisplayQualifierNames() |   | 59% |   | 75% | 1 | 3 | 2 | 7 | 0 | 1 |
| getSystematicQualifierNames() |   | 59% |   | 75% | 1 | 3 | 2 | 8 | 0 | 1 |
| canDirectEdit() |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
| highlightActiveEntryFlag() |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
| isUnixHost() |   | 41% |   | 25% | 2 | 3 | 2 | 4 | 0 | 1 |
| readWritePossible() |   | 71% |  | 100% | 0 | 2 | 2 | 7 | 0 | 1 |
| isNoddyMode() |  | 0% |  | 0% | 2 | 2 | 1 | 1 | 1 | 1 |
| getUndoLevels() |   | 75% |   | 50% | 2 | 3 | 2 | 6 | 0 | 1 |
| parseColour(String) |   | 91% | | n/a | 0 | 1 | 2 | 11 | 0 | 1 |
| Options() |   | 91% | | n/a | 0 | 1 | 2 | 13 | 0 | 1 |
| getDBEntryInformation() |  | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| setDefaultFeatureColours() |  | 100% |  | 100% | 0 | 2 | 0 | 4 | 0 | 1 |
| readQualifierInfo(InputStream, InputStream) |  | 100% |  | 100% | 0 | 6 | 0 | 41 | 0 | 1 |
| getExternalPrograms() |  | 100% |   | 78% | 3 | 8 | 0 | 30 | 0 | 1 |
| getNCBIPrograms() |  | 100% |   | 70% | 3 | 6 | 0 | 23 | 0 | 1 |
| makeArtemisEntryInformation(EntryInformation) |  | 100% |  | 100% | 0 | 6 | 0 | 19 | 0 | 1 |
| setDefaultColourMap() |  | 100% | | n/a | 0 | 1 | 0 | 14 | 0 | 1 |
| getExtraQualifiers(String) |  | 100% |  | 100% | 0 | 2 | 0 | 10 | 0 | 1 |
| makeEntryInformation() |  | 100% |  | 100% | 0 | 2 | 0 | 13 | 0 | 1 |
| getPropertyTruthValueInternal(String) |  | 100% |   | 70% | 3 | 6 | 0 | 8 | 0 | 1 |
| readSystemOptions() |  | 100% |   | 66% | 2 | 4 | 0 | 10 | 0 | 1 |
| fireChangeEvent(String) |  | 100% |  | 100% | 0 | 2 | 0 | 8 | 0 | 1 |
| getDefaultFeatureColour(Key) |  | 100% |  | 100% | 0 | 2 | 0 | 4 | 0 | 1 |
| reset() |  | 100% | | n/a | 0 | 1 | 0 | 8 | 0 | 1 |
| getPropertyValues(Properties, String) |  | 100% |  | 100% | 0 | 2 | 0 | 4 | 0 | 1 |
| getIntegerProperty(String) |  | 100% |  | 100% | 0 | 2 | 0 | 4 | 0 | 1 |
| setGeneticCode(String) |  | 100% | | n/a | 0 | 1 | 0 | 3 | 0 | 1 |
| addOptionChangeListener(OptionChangeListener) |  | 100% | | n/a | 0 | 1 | 0 | 2 | 0 | 1 |
| getPropertyTruthValue(String) |  | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| load(InputStream) |  | 100% | | n/a | 0 | 1 | 0 | 3 | 0 | 1 |
| getFontUIResource() |  | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| removeOptionChangeListener(OptionChangeListener) |  | 100% | | n/a | 0 | 1 | 0 | 2 | 0 | 1 |
| isBlackBeltMode() |  | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getOptionValues(String) |  | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getExtraQualifiers() |  | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getExtraGffQualifiers() |  | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getFont() |  | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getOptions() |  | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getArtemisEntryInformation() |  | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |