| drawLabels(Graphics) |  | 0% |  | 0% | 13 | 13 | 78 | 78 | 1 | 1 |
| splitMatches(boolean, int, int, int) |  | 0% |  | 0% | 23 | 23 | 60 | 60 | 1 | 1 |
| getDifferenceCoords(boolean) |  | 0% |  | 0% | 22 | 22 | 61 | 61 | 1 | 1 |
| drawAlignments(Graphics) |  | 0% |  | 0% | 18 | 18 | 60 | 60 | 1 | 1 |
| popupMenu(MouseEvent) |  | 0% |  | 0% | 2 | 2 | 46 | 46 | 1 | 1 |
| flippingContig(boolean, int, int) |  | 0% |  | 0% | 20 | 20 | 29 | 29 | 1 | 1 |
| reorder(boolean, int, int, int) |  | 0% |  | 0% | 18 | 18 | 26 | 26 | 1 | 1 |
| AlignmentViewer(FeatureDisplay, FeatureDisplay, ComparisonData) |  | 0% | | n/a | 1 | 1 | 46 | 46 | 1 | 1 |
| getAlignMatchFromPosition(Point) |  | 0% |  | 0% | 8 | 8 | 31 | 31 | 1 | 1 |
| getMatchCoords(int, AlignMatch, int, int, boolean, boolean, float, float, int, int, boolean, boolean, boolean) |  | 0% |  | 0% | 19 | 19 | 38 | 38 | 1 | 1 |
| selectFromSubjectRanges(RangeVector) |  | 0% |  | 0% | 14 | 14 | 36 | 36 | 1 | 1 |
| selectFromQueryRanges(RangeVector) |  | 0% |  | 0% | 14 | 14 | 36 | 36 | 1 | 1 |
| selectionChanged() |  | 0% |  | 0% | 9 | 9 | 23 | 23 | 1 | 1 |
| paintComponentForPrint(Graphics, boolean) |  | 0% |  | 0% | 7 | 7 | 20 | 20 | 1 | 1 |
| paintComponent(Graphics) |  | 0% |  | 0% | 5 | 5 | 17 | 17 | 1 | 1 |
| removeMatches(Vector) |  | 0% |  | 0% | 4 | 4 | 14 | 14 | 1 | 1 |
| isVisible(AlignMatch) |  | 0% |  | 0% | 10 | 10 | 14 | 14 | 1 | 1 |
| createColours(String, Color) |  | 0% |  | 0% | 2 | 2 | 9 | 9 | 1 | 1 |
| makeColours() |  | 0% |  | 0% | 2 | 2 | 7 | 7 | 1 | 1 |
| toggleSelection(Point) |  | 0% |  | 0% | 5 | 5 | 13 | 13 | 1 | 1 |
| alignAt(AlignMatch) |  | 0% |  | 0% | 2 | 2 | 7 | 7 | 1 | 1 |
| getScreenPosition(float, int, int) |  | 0% |  | 0% | 3 | 3 | 6 | 6 | 1 | 1 |
| handleCanvasMousePress(MouseEvent) |  | 0% |  | 0% | 3 | 3 | 7 | 7 | 1 | 1 |
| subjectIsRevComp() |  | 0% |  | 0% | 3 | 3 | 5 | 5 | 1 | 1 |
| queryIsRevComp() |  | 0% |  | 0% | 3 | 3 | 5 | 5 | 1 | 1 |
| handleCanvasSingleClick(MouseEvent) |  | 0% |  | 0% | 3 | 3 | 6 | 6 | 1 | 1 |
| modifiersForLockToggle(MouseEvent) |  | 0% |  | 0% | 3 | 3 | 2 | 2 | 1 | 1 |
| setSelection(AlignMatch) |  | 0% | | n/a | 1 | 1 | 4 | 4 | 1 | 1 |
| isMenuTrigger(MouseEvent) |  | 0% |  | 0% | 3 | 3 | 4 | 4 | 1 | 1 |
| getRealSubjectSequenceStart(AlignMatch, int, boolean) |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
| getRealSubjectSequenceEnd(AlignMatch, int, boolean) |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
| getRealQuerySequenceStart(AlignMatch, int, boolean) |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
| getRealQuerySequenceEnd(AlignMatch, int, boolean) |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
| toggleDisplayLock() |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
| handleCanvasDoubleClick(MouseEvent) |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
| setSubjectSequencePosition(DisplayAdjustmentEvent) |  | 0% | | n/a | 1 | 1 | 3 | 3 | 1 | 1 |
| setQuerySequencePosition(DisplayAdjustmentEvent) |  | 0% | | n/a | 1 | 1 | 3 | 3 | 1 | 1 |
| removeAlignmentSelectionChangeListener(AlignmentSelectionChangeListener) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| removeAlignmentListener(AlignmentListener) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| invalidate() |  | 0% | | n/a | 1 | 1 | 3 | 3 | 1 | 1 |
| lockDisplays() |  | 0% | | n/a | 1 | 1 | 3 | 3 | 1 | 1 |
| unlockDisplays() |  | 0% | | n/a | 1 | 1 | 3 | 3 | 1 | 1 |
| addAlignmentSelectionChangeListener(AlignmentSelectionChangeListener) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| addAlignmentListener(AlignmentListener) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| getSubjectForwardStrand() |  | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getQueryForwardStrand() |  | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| disableSelection() | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| enableSelection() | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| sequenceChanged(SequenceChangeEvent) | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| offerToFlip() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getSubjectEntryGroup() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getQueryEntryGroup() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getSubjectDisplay() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getQueryDisplay() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getOrigSubjectForwardStrand() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getOrigQueryForwardStrand() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| displaysAreLocked() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getComparisonData() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| static {...} | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |