| createMenus(JComponent) |  | 0% |  | 0% | 7 | 7 | 140 | 140 | 1 | 1 |
| drawPairedStackView(Graphics2D, int, float, int, int) |  | 0% |  | 0% | 32 | 32 | 94 | 94 | 1 | 1 |
| drawSequence(Graphics2D, BamViewRecord, int, String, int) |  | 0% |  | 0% | 32 | 32 | 85 | 85 | 1 | 1 |
| appendToDetailView(SAMRecord, SAMRecord, FileViewer, List) |  | 0% |  | 0% | 23 | 23 | 58 | 58 | 1 | 1 |
| main(String[]) |  | 0% |  | 0% | 41 | 41 | 105 | 105 | 1 | 1 |
| drawLineView(Graphics2D, int, float, int, int) |  | 0% |  | 0% | 21 | 21 | 56 | 56 | 1 | 1 |
| drawBaseAlignment(Graphics2D, int, float, int, int) |  | 0% |  | 0% | 19 | 19 | 59 | 59 | 1 | 1 |
| drawRead(Graphics2D, BamViewRecord, float, int, int, List, int) |  | 0% |  | 0% | 17 | 17 | 41 | 41 | 1 | 1 |
| paintComponent(Graphics) |   | 52% |   | 41% | 33 | 36 | 39 | 100 | 0 | 1 |
| iterateOverBam(SamReader, String, int, int, short, float, String) |   | 23% |   | 10% | 22 | 24 | 49 | 68 | 0 | 1 |
| getSequenceOffset(String) |  | 2% |   | 5% | 9 | 10 | 27 | 29 | 0 | 1 |
| drawStrand(Graphics2D, boolean, int, int, int, float) |  | 0% |  | 0% | 17 | 17 | 40 | 40 | 1 | 1 |
| bamTopPanel(JFrame) |   | 47% |   | 54% | 10 | 12 | 37 | 66 | 0 | 1 |
| drawStackView(Graphics2D, int, float, int, int) |   | 27% |   | 11% | 17 | 18 | 34 | 49 | 0 | 1 |
| getToolTipText() |   | 5% |   | 8% | 12 | 13 | 21 | 24 | 0 | 1 |
| drawLoneRead(Graphics2D, BamViewRecord, int, float, int, int, List, int) |  | 0% |  | 0% | 10 | 10 | 34 | 34 | 1 | 1 |
| setZoomLevel(int) |  | 0% |  | 0% | 12 | 12 | 35 | 35 | 1 | 1 |
| getSNPs(SAMRecord) |  | 0% |  | 0% | 8 | 8 | 28 | 28 | 1 | 1 |
| addBamToPanel(JFrame) |   | 53% |   | 25% | 8 | 9 | 15 | 41 | 0 | 1 |
| drawTicks(Graphics2D, int, int, float, int, int) |  | 0% |  | 0% | 6 | 6 | 18 | 18 | 1 | 1 |
| drawCoverage(Graphics2D, int, int, float) |  | 0% |  | 0% | 5 | 5 | 16 | 16 | 1 | 1 |
| drawScale(Graphics2D, int, int, float, int) |  | 0% |  | 0% | 6 | 6 | 16 | 16 | 1 | 1 |
| BamView(List, String, int, FeatureDisplay, Bases, JPanel, JFrame) |   | 84% |   | 38% | 11 | 14 | 26 | 132 | 0 | 1 |
| openBamView(List) |  | 0% |  | 0% | 5 | 5 | 18 | 18 | 1 | 1 |
| highlightRange(MouseEvent, int) |  | 0% |  | 0% | 7 | 7 | 20 | 20 | 1 | 1 |
| getSAMFileReader(String) |   | 50% |   | 37% | 7 | 9 | 14 | 32 | 0 | 1 |
| drawYScale(Graphics2D, int) |  | 0% |  | 0% | 6 | 6 | 18 | 18 | 1 | 1 |
| drawStrandStackView(Graphics2D, int, float, int, int) |  | 0% |  | 0% | 2 | 2 | 12 | 12 | 1 | 1 |
| readFromAlignmentFile(int, int, short, float) |   | 27% |   | 6% | 8 | 9 | 14 | 20 | 0 | 1 |
| drawArrow(Graphics2D, SAMRecord, int, int, float, int, int) |  | 0% |  | 0% | 3 | 3 | 11 | 11 | 1 | 1 |
| getEntry(String, EntryGroup) |  | 0% |  | 0% | 4 | 4 | 19 | 19 | 1 | 1 |
| getMate(BamViewRecord) |  | 0% |  | 0% | 4 | 4 | 14 | 14 | 1 | 1 |
| showSNPsOnReads(List, Graphics2D, float, int) |  | 0% |  | 0% | 2 | 2 | 8 | 8 | 1 | 1 |
| readsOverlap(SAMRecord, SAMRecord) |  | 0% |  | 0% | 9 | 9 | 11 | 11 | 1 | 1 |
| closeBamPanel() |  | 0% |  | 0% | 4 | 4 | 12 | 12 | 1 | 1 |
| drawSelectionRange(Graphics2D, float, int, int, Color) |   | 19% |   | 25% | 4 | 5 | 8 | 12 | 0 | 1 |
| wrapReadBases(SAMRecord, FileViewer) |  | 0% |  | 0% | 3 | 3 | 8 | 8 | 1 | 1 |
| getSelectedCheckBoxMenuItem() |  | 0% |  | 0% | 7 | 7 | 13 | 13 | 1 | 1 |
| getVersion() |  | 0% |  | 0% | 3 | 3 | 11 | 11 | 1 | 1 |
| refreshColourOfBamMenu() |  | 0% |  | 0% | 4 | 4 | 8 | 8 | 1 | 1 |
| displayAdjustmentWork(DisplayAdjustmentEvent) |  | 0% |  | 0% | 2 | 2 | 12 | 12 | 1 | 1 |
| drawTranslucentJointedLine(Graphics2D, int, int, int) |  | 0% | | n/a | 1 | 1 | 7 | 7 | 1 | 1 |
| getColorByJCheckBoxMenuItem(JCheckBoxMenuItem) |  | 0% |  | 0% | 3 | 3 | 6 | 6 | 1 | 1 |
| addToViewMenu(short) |  | 0% | | n/a | 1 | 1 | 7 | 7 | 1 | 1 |
| displayAdjustmentValueChanged(DisplayAdjustmentEvent) |  | 0% |  | 0% | 4 | 4 | 9 | 9 | 1 | 1 |
| isFromSameBamFile(BamViewRecord, BamViewRecord, List) |  | 0% |  | 0% | 6 | 6 | 8 | 8 | 1 | 1 |
| getSequenceLength() |   | 34% |   | 25% | 2 | 3 | 4 | 6 | 0 | 1 |
| setColourByBaseQuality(Graphics2D, byte) |  | 0% |  | 0% | 4 | 4 | 8 | 8 | 1 | 1 |
| handleFatalError(String) |  | 0% |  | 0% | 2 | 2 | 5 | 5 | 1 | 1 |
| getYPos(int, int) |  | 0% |  | 0% | 2 | 2 | 4 | 4 | 1 | 1 |
| getImageIcon(Color) |  | 0% | | n/a | 1 | 1 | 5 | 5 | 1 | 1 |
| setViewportMidPoint() |  | 0% | | n/a | 1 | 1 | 4 | 4 | 1 | 1 |
| handleCanvasMouseDrag(MouseEvent) |  | 0% |  | 0% | 4 | 4 | 8 | 8 | 1 | 1 |
| isNegativeStrand(SAMRecord, boolean) |  | 20% |   | 16% | 3 | 4 | 5 | 7 | 0 | 1 |
| drawTranslucentLine(Graphics2D, int, int, int) |  | 0% | | n/a | 1 | 1 | 5 | 5 | 1 | 1 |
| close() |  | 0% |  | 0% | 2 | 2 | 6 | 6 | 1 | 1 |
| getMaxBasesInPanel(int) |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
| openFileViewer(SAMRecord, SAMRecord, List) |  | 0% | | n/a | 1 | 1 | 3 | 3 | 1 | 1 |
| setDisplay(int, int, DisplayAdjustmentEvent) |   | 82% |   | 50% | 3 | 4 | 2 | 16 | 0 | 1 |
| getReadGroupFrame() |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
| getColourByCoverageColour(BamViewRecord) |  | 0% |  | 0% | 2 | 2 | 4 | 4 | 1 | 1 |
| isThisBamRecordHighlighted(BamViewRecord) |  | 0% |  | 0% | 2 | 2 | 3 | 3 | 1 | 1 |
| getColourByCoverageColour(short) |  | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| setSamRecordMapQPredicate(SAMRecordMapQPredicate) |  | 0% | | n/a | 1 | 1 | 4 | 4 | 1 | 1 |
| setViewportBtm() |  | 0% | | n/a | 1 | 1 | 3 | 3 | 1 | 1 |
| setVisible(boolean) |  | 0% | | n/a | 1 | 1 | 3 | 3 | 1 | 1 |
| repaintBamView() | | 0% | | n/a | 1 | 1 | 3 | 3 | 1 | 1 |
| isCoverageView(float) |  | 81% |   | 50% | 4 | 5 | 1 | 3 | 0 | 1 |
| getBaseAtStartOfView() |  | 63% |   | 50% | 1 | 2 | 1 | 3 | 0 | 1 |
| isPairedStackView() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| isStrandStackView() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| isIsizeStackView() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| setHighlightSAMRecord(BamViewRecord) | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| setMaxBases(int) | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| getReadsInView() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getBasesInView() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getHighlightSAMRecord() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getFeatureDisplay() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| selectionChanged(SelectionChangeEvent) | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| setStandaloneMode(boolean) | | 0% | | n/a | 1 | 1 | 2 | 2 | 1 | 1 |
| isBaseAlignmentView(float) |  | 83% |   | 50% | 1 | 2 | 1 | 3 | 0 | 1 |
| isShowScale() | | 71% |   | 50% | 1 | 2 | 0 | 1 | 0 | 1 |
| getMaxBases() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| isStandaloneMode() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| static {...} |  | 100% | | n/a | 0 | 1 | 0 | 10 | 0 | 1 |
| readAlignmentFileHeader() |  | 100% |  | 100% | 0 | 2 | 0 | 8 | 0 | 1 |
| BamView(List, String, int, EntryEdit, FeatureDisplay, Bases, JPanel, JFrame) |  | 100% | | n/a | 0 | 1 | 0 | 3 | 0 | 1 |
| setSamRecordFlagPredicate(SAMRecordPredicate) |  | 100% | | n/a | 0 | 1 | 0 | 4 | 0 | 1 |
| getPixPerBaseByWidth() |  | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| isStackView() | | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getJspView() | | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getSelection() | | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getCombo() | | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getSamFileReaderHash() | | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getSeqNames() | | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getSeqLengths() | | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getOffsetLengths() | | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getSamRecordFlagPredicate() | | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| getSamRecordMapQPredicate() | | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |
| isConcatSequences() | | 100% | | n/a | 0 | 1 | 0 | 1 | 0 | 1 |