| combineGeneFeatures(FeatureVector) |  | 0% |  | 0% | 27 | 27 | 70 | 70 | 1 | 1 |
| mergeFeatures(List, List, String) |  | 0% |  | 0% | 12 | 12 | 66 | 66 | 1 | 1 |
| mergeGtfFeatures(FeatureVector, String) |  | 0% |  | 0% | 8 | 8 | 38 | 38 | 1 | 1 |
| IndexedGFFDocumentEntry(Document) |  | 0% |  | 0% | 6 | 6 | 38 | 38 | 1 | 1 |
| indexOf(Feature) |  | 0% |  | 0% | 15 | 15 | 35 | 35 | 1 | 1 |
| getFeaturesInRange(IndexedGFFDocumentEntry.IndexContig, Range, FeatureVector) |  | 0% |  | 0% | 8 | 8 | 30 | 30 | 1 | 1 |
| getFeatureAtIndex(int) |  | 0% |  | 0% | 10 | 10 | 32 | 32 | 1 | 1 |
| getContigsInRange(Range) |  | 0% |  | 0% | 13 | 13 | 17 | 17 | 1 | 1 |
| combineChadoExons(ChadoCanonicalGene, FeatureVector) |  | 0% |  | 0% | 7 | 7 | 25 | 25 | 1 | 1 |
| contains(Feature, String, String, String, String) |  | 0% |  | 0% | 18 | 18 | 21 | 21 | 1 | 1 |
| mergeQualifiers(QualifierVector, boolean) |  | 0% |  | 0% | 10 | 10 | 23 | 23 | 1 | 1 |
| checkOffset() |  | 0% |  | 0% | 7 | 7 | 15 | 15 | 1 | 1 |
| iterate(IndexedGFFDocumentEntry.IndexContig, int, int, TabixReader.Iterator, FeatureVector) |  | 0% |  | 0% | 9 | 9 | 18 | 18 | 1 | 1 |
| initContig() |  | 0% |  | 0% | 7 | 7 | 17 | 17 | 1 | 1 |
| getGffInArtemisCoordinates(String, StringVector, IndexedGFFDocumentEntry.IndexContig) |  | 0% |  | 0% | 5 | 5 | 15 | 15 | 1 | 1 |
| getFeatureCount() |  | 0% |  | 0% | 6 | 6 | 19 | 19 | 1 | 1 |
| getFeaturesInRange(Range) |  | 0% |  | 0% | 5 | 5 | 19 | 19 | 1 | 1 |
| truncate(Range, Entry) |  | 0% |  | 0% | 2 | 2 | 12 | 12 | 1 | 1 |
| getListOfContigs() |  | 0% |  | 0% | 4 | 4 | 7 | 7 | 1 | 1 |
| contains(Feature, FeatureVector) |  | 0% |  | 0% | 3 | 3 | 8 | 8 | 1 | 1 |
| isTranscript(Key) |  | 0% |  | 0% | 4 | 4 | 6 | 6 | 1 | 1 |
| getStartInArtemisCoords(StringVector, IndexedGFFDocumentEntry.IndexContig) |  | 0% |  | 0% | 2 | 2 | 4 | 4 | 1 | 1 |
| getEndInArtemisCoords(StringVector, IndexedGFFDocumentEntry.IndexContig) |  | 0% |  | 0% | 2 | 2 | 4 | 4 | 1 | 1 |
| getCoordInContigCoords(int, IndexedGFFDocumentEntry.IndexContig) |  | 0% |  | 0% | 3 | 3 | 5 | 5 | 1 | 1 |
| updateReference(String, boolean) |  | 0% | | n/a | 1 | 1 | 5 | 5 | 1 | 1 |
| save(Document) |  | 0% | | n/a | 1 | 1 | 7 | 7 | 1 | 1 |
| contains(Feature) |  | 0% |  | 0% | 2 | 2 | 1 | 1 | 1 | 1 |
| setName(String) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| features() |  | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getAllFeatures() |  | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| save() |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| setEntryGroup(EntryGroup) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| getName() |  | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getDocument() |  | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getEntryInformation() |  | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| hasUnsavedChanges() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| isReadOnly() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getHeaderText() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| setHeaderText(String) | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| createFeature(Key, Location, QualifierVector) | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| add(Feature) | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| forcedAdd(Feature) | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| remove(Feature) | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getSequence() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getLastChangeTime() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| dispose() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| writeToStream(Writer) | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| setDirtyFlag() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| isIndexed(File) |  | 100% | | n/a | 0 | 1 | 0 | 2 | 0 | 1 |
| static {...} |  | 100% | | n/a | 0 | 1 | 0 | 2 | 0 | 1 |