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Make frame row order consistent in LinearApolloSixFrameDisplay #754

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Make frame row order consistent in LinearApolloSixFrameDisplay #754

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14 changes: 9 additions & 5 deletions ...-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,6 @@ export const LinearApolloSixFrameDisplay = observer(
contextMenuItems: getContextMenuItems,
cursor,
featuresHeight,
featureLabelSpacer,
geneTrackRowNums,
isShown,
onMouseDown,
Expand All @@ -55,6 +54,7 @@ export const LinearApolloSixFrameDisplay = observer(
setOverlayCanvas,
setTheme,
showCheckResults,
showFeatureLabels,
} = model
const { classes } = useStyles()
const lgv = getContainingView(model) as unknown as LinearGenomeViewModel
Expand Down Expand Up @@ -188,15 +188,19 @@ export const LinearApolloSixFrameDisplay = observer(
let row
for (const loc of feature.cdsLocations) {
for (const cds of loc) {
let rowNum: number = getFrame(
const frame = getFrame(
cds.min,
cds.max,
feature.strand ?? 1,
cds.phase,
)
rowNum = featureLabelSpacer(
rowNum < 0 ? -1 * rowNum + 5 : rowNum,
)
const frameOffsets = showFeatureLabels
? [0, 5, 3, 1, 15, 13, 11]
: [0, 2, 1, 0, 8, 7, 6]
const rowNum = frameOffsets.at(frame)
if (!rowNum) {
continue
}
if (
checkResult.start >= cds.min &&
checkResult.start <= cds.max
Expand Down
35 changes: 24 additions & 11 deletions packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -347,9 +347,14 @@ function draw(
cdsStartPx = reversed ? minX - cdsWidthPx : minX
ctx.fillStyle = theme.palette.text.primary
const frame = getFrame(cds.min, cds.max, child.strand ?? 1, cds.phase)
const frameAdjust =
(frame < 0 ? -1 * frame + 5 : frame) * featureLabelSpacer
cdsTop = (frameAdjust - featureLabelSpacer) * rowHeight
const frameOffsets = showFeatureLabels
? [0, 4, 2, 0, 14, 12, 10]
: [0, 2, 1, 0, 7, 6, 5]
const row = frameOffsets.at(frame)
if (row === undefined) {
continue
}
cdsTop = row * rowHeight
ctx.fillRect(cdsStartPx, cdsTop, cdsWidthPx, cdsHeight)

// Draw lines to connect CDS features with shared mRNA parent
Expand Down Expand Up @@ -525,9 +530,14 @@ function drawHover(
})?.offsetPx ?? 0) - offsetPx
const cdsStartPx = reversed ? minX - cdsWidthPx : minX
const frame = getFrame(cds.min, cds.max, strand ?? 1, cds.phase)
const frameAdjust =
(frame < 0 ? -1 * frame + 5 : frame) * featureLabelSpacer
const cdsTop = (frameAdjust - featureLabelSpacer) * rowHeight
const frameOffsets = showFeatureLabels
? [0, 4, 2, 0, 14, 12, 10]
: [0, 2, 1, 0, 7, 6, 5]
const row = frameOffsets.at(frame)
if (row === undefined) {
continue
}
const cdsTop = row * rowHeight
if (counter > 1) {
// Mid-point for intron line "hat"
const midPoint: [number, number] = [
Expand Down Expand Up @@ -759,8 +769,6 @@ function drawTooltip(
const displayedRegion = displayedRegions[layoutIndex]
const { refName, reversed } = displayedRegion
const rowHeight = apolloRowHeight
const cdsHeight = Math.round(0.7 * rowHeight)
const featureLabelSpacer = showFeatureLabels ? 2 : 1
let location = 'Loc: '
let cds: TranscriptPartCoding | undefined = undefined
for (const loc of feature.cdsLocations) {
Expand All @@ -784,9 +792,14 @@ function drawTooltip(
regionNumber: layoutIndex,
})?.offsetPx ?? 0) - offsetPx
const frame = getFrame(min, max, strand ?? 1, phase)
const frameAdjust = (frame < 0 ? -1 * frame + 5 : frame) * featureLabelSpacer
const cdsTop =
(frameAdjust - featureLabelSpacer) * rowHeight + (rowHeight - cdsHeight) / 2
const frameOffsets = showFeatureLabels
? [0, 4, 2, 0, 14, 12, 10]
: [0, 2, 1, 0, 7, 6, 5]
const row = frameOffsets.at(frame)
if (row === undefined) {
return
}
const cdsTop = row * rowHeight
const cdsWidthPx = (max - min) / bpPerPx

const featureType = `Type: ${cds.type}`
Expand Down
12 changes: 8 additions & 4 deletions packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -159,15 +159,19 @@ export function layoutsModelFactory(
}
for (const cdsRow of cdsLocations) {
for (const cds of cdsRow) {
let rowNum: number = getFrame(
const frame = getFrame(
cds.min,
cds.max,
strand ?? 1,
cds.phase,
)
rowNum = self.featureLabelSpacer(
rowNum < 0 ? -1 * rowNum + 5 : rowNum,
)
const frameOffsets = self.showFeatureLabels
? [0, 5, 3, 1, 15, 13, 11]
: [0, 2, 1, 0, 8, 7, 6]
const rowNum = frameOffsets.at(frame)
if (!rowNum) {
continue
}
if (!featureLayout.get(rowNum)) {
featureLayout.set(rowNum, [])
}
Expand Down
9 changes: 5 additions & 4 deletions packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -86,15 +86,16 @@ export function mouseEventsModelIntermediateFactory(
}
for (const loc of feature.cdsLocations) {
for (const cds of loc) {
let rowNum: number = getFrame(
const frame = getFrame(
cds.min,
cds.max,
feature.strand ?? 1,
cds.phase,
)
rowNum = self.featureLabelSpacer(
rowNum < 0 ? -1 * rowNum + 5 : rowNum,
)
const frameOffsets = self.showFeatureLabels
? [0, 5, 3, 1, 15, 13, 11]
: [0, 2, 1, 0, 8, 7, 6]
const rowNum = frameOffsets.at(frame)
if (row === rowNum && bp >= cds.min && bp <= cds.max) {
return (
featureID === undefined ||
Expand Down