From 9fbc5cf6791ac2485d5bbe815e98ccc45ec87e1b Mon Sep 17 00:00:00 2001
From: Julien Touchais <5978-julien.touchais@users.noreply.forgemia.inra.fr>
Date: Thu, 25 Apr 2024 09:33:17 +0200
Subject: [PATCH 1/9] feat(base-components): :sparkles: add a lockable (in
place) tooltip component
---
src/components/BaseLockableTooltip.vue | 115 +++++++++++++++++++++++++
1 file changed, 115 insertions(+)
create mode 100644 src/components/BaseLockableTooltip.vue
diff --git a/src/components/BaseLockableTooltip.vue b/src/components/BaseLockableTooltip.vue
new file mode 100644
index 0000000..52fb6f1
--- /dev/null
+++ b/src/components/BaseLockableTooltip.vue
@@ -0,0 +1,115 @@
+<script setup lang="ts">
+/**
+ * Vue imports
+ */
+import { computed, ref } from 'vue'
+/**
+ * Components imports
+ */
+import BaseTooltip from '@/components/BaseTooltip.vue'
+/**
+ * Other 3rd-party imports
+ */
+import { useMouse, onClickOutside } from '@vueuse/core'
+
+/**
+ * Component props.
+ */
+defineProps<{
+ /** Show the tooltip (even if not locked). */
+ show?: boolean
+}>()
+
+/**
+ * Component slots.
+ */
+defineSlots<{
+ /** Custom tooltip template. */
+ default: (props: {}) => any
+}>()
+
+/**
+ * Component events.
+ */
+const emit = defineEmits<{
+ /** Emitted when locking the tooltip. */
+ lock: []
+ /** Emitted when unlocking the tooltip. */
+ unlock: []
+}>()
+
+/**
+ * Reactive position of the mouse in the document.
+ */
+const mouse = useMouse({ type: 'client' })
+
+/**
+ * Location of the tooltip when locked in place, undefined if not locked.
+ */
+const lockedTooltipPosition = ref<{ bottom: number; left: number }>()
+
+/**
+ * Locks the tooltip in its place and add a scroll listener.
+ */
+const lockTooltipIfUnlocked = () => {
+ if (lockedTooltipPosition.value) return
+ // Set locked position
+ lockedTooltipPosition.value = {
+ bottom: tooltipComponentPositions.value.bottom,
+ left: tooltipComponentPositions.value.left
+ }
+ // Add scroll event listener to unlock if scroll
+ document.addEventListener('scroll', unlockTooltipIfLocked)
+ emit('lock')
+}
+
+/**
+ * Unlocks the tooltip when clicking out of it.
+ */
+const unlockTooltipIfLocked = () => {
+ if (!lockedTooltipPosition.value) return
+ // Reset position
+ lockedTooltipPosition.value = undefined
+ // Remove scroll event listener
+ document.removeEventListener('scroll', unlockTooltipIfLocked)
+ emit('unlock')
+}
+
+/**
+ * Ref to the tooltip component.
+ */
+const tooltipComponent = ref<InstanceType<typeof BaseTooltip>>()
+
+/**
+ * Position of the tooltip component relative to the viewport.
+ */
+const tooltipComponentPositions = computed(() => ({
+ bottom:
+ lockedTooltipPosition.value?.bottom ||
+ window.innerHeight - mouse.y.value + 10,
+ left: lockedTooltipPosition.value?.left || mouse.x.value
+}))
+
+/**
+ * Adds a listener to unlock the tooltip when clicking outside of it.
+ */
+onClickOutside(tooltipComponent, unlockTooltipIfLocked)
+
+/**
+ * Exposes methods to un/lock the tooltip.
+ */
+defineExpose({ unlockTooltipIfLocked, lockTooltipIfUnlocked })
+</script>
+
+<template>
+ <BaseTooltip
+ v-show="show || lockedTooltipPosition"
+ ref="tooltipComponent"
+ :style="{
+ bottom: `${tooltipComponentPositions.bottom}px`,
+ left: `${tooltipComponentPositions.left}px`
+ }"
+ >
+ <slot />
+ </BaseTooltip>
+</template>
--
GitLab
From c00c26c0ab7434edcf937e763c394d97bcbdf69b Mon Sep 17 00:00:00 2001
From: Julien Touchais <5978-julien.touchais@users.noreply.forgemia.inra.fr>
Date: Thu, 25 Apr 2024 09:51:53 +0200
Subject: [PATCH 2/9] refactor(karyotype): :coffin: remove unused code & update
comments
---
src/components/ChromosomeMagnify.vue | 65 +++++++++-------------------
1 file changed, 21 insertions(+), 44 deletions(-)
diff --git a/src/components/ChromosomeMagnify.vue b/src/components/ChromosomeMagnify.vue
index eeac915..78a8152 100644
--- a/src/components/ChromosomeMagnify.vue
+++ b/src/components/ChromosomeMagnify.vue
@@ -18,12 +18,12 @@ import { G, Rect, SVG, type Svg } from '@svgdotjs/svg.js'
import type { ChromosomeModel, GenomeObjectModel } from './KaryotypeBoard.vue'
/**
- * In pixels, the minimal unzoomed size at which to draw karyotype objects
+ * In pixels, the minimal unzoomed size at which to draw karyotype objects.
*/
const MIN_BASE_OBJECT_LENGTH_PX = 4
/**
- * Component props
+ * Component props.
*/
const props = withDefaults(
defineProps<{
@@ -50,7 +50,7 @@ const props = withDefaults(
/**
* Dimensions of the base chromosome element, position of the mouse relative to
- * the top left of the client, and to the chromosome element
+ * the top left of the client, and to the chromosome element.
*/
const { chromosomeDimensions, mouseClient, mouseChromosome } = (() => {
const { elementHeight, elementWidth, elementX, elementY, isOutside, x, y } =
@@ -75,12 +75,12 @@ const { chromosomeDimensions, mouseClient, mouseChromosome } = (() => {
})()
/**
- * Ref to the div containing the chromosome SVG
+ * Ref to the div containing the chromosome SVG.
*/
const magnifiedChromosome = ref<HTMLDivElement>()
/**
- * Position of the magnify div relative to the viewport
+ * Position of the magnify div relative to the viewport.
*/
const magnifyElementPositions = computed(() => ({
top: mouseClient.y.value,
@@ -93,17 +93,18 @@ const lockedTooltipPosition = ref<{ bottom: number; left: number }>()
const lockOffset = ref(0)
/**
- * DOM elements of objects currently hovered
+ * DOM elements of objects currently hovered, to display in the tooltip when
+ * not locked.
*/
const hoveredObjectsElements = ref<SVGElement[]>([])
/**
- * DOM elements corresponding to objects to display in the tooltip when locked
+ * DOM elements of objects to display in the tooltip when locked.
*/
const lockedTooltipObjectsElements = ref<SVGElement[]>([])
/**
- * DOM elements corresponding to objects to display in the tooltip
+ * DOM elements of objects to display in the tooltip.
*/
const tooltipObjectsElements = computed(() =>
lockedTooltipPosition.value
@@ -156,7 +157,7 @@ const tooltipComponentPositions = computed(() => ({
}))
/**
- * Normalised position of the mouse on the chromosome (between 0 & 1)
+ * Normalised position of the mouse on the chromosome (between 0 & 1).
*/
const mousePositionNormalised = computed(() => ({
x: mouseChromosome.x.value / chromosomeDimensions.width.value,
@@ -164,37 +165,7 @@ const mousePositionNormalised = computed(() => ({
}))
/**
- * Position of the mouse in terms of chromosome coordinate
- */
-const mousePositionChromosomeCoordinate = computed(() =>
- Math.round(mousePositionNormalised.value.x * props.chromosome.length)
-)
-
-/**
- * Length (in bp) of the magnified portion, w/ respect to the zoom factor
- */
-const magnifiedPortionLengthBP = computed(() =>
- Math.round(
- ((props.radius / chromosomeDimensions.width.value) *
- props.chromosome.length) /
- props.zoomFactor
- )
-)
-
-/**
- * Coordinates of the magnified chromosome portion
- */
-const magnifiedPortionCoordinates = computed(() => ({
- start:
- mousePositionChromosomeCoordinate.value -
- Math.floor(magnifiedPortionLengthBP.value / 2),
- end:
- mousePositionChromosomeCoordinate.value +
- Math.floor(magnifiedPortionLengthBP.value / 2)
-}))
-
-/**
- * Dimensions (in px) of the entire magnified chromosome
+ * Dimensions (in px) of the entire magnified chromosome.
*/
const magnifiedChromosomeDimensionsPX = computed(() => ({
length: chromosomeDimensions.width.value * props.zoomFactor,
@@ -202,7 +173,7 @@ const magnifiedChromosomeDimensionsPX = computed(() => ({
}))
/**
- * Translation applied to the magnified chromosome
+ * Translation applied to the magnified chromosome.
*/
const magnifiedChromosomeTranslate = computed(() => ({
x:
@@ -215,12 +186,12 @@ const magnifiedChromosomeTranslate = computed(() => ({
}))
/**
- * Ref to the SVG representation of the chromosome
+ * Ref to the SVG representation of the chromosome.
*/
const draw = ref<Svg>()
/**
- * Creates the elements forming the chromosome SVG
+ * Creates the elements forming the chromosome SVG.
*/
const createChromosomeSVG = () => {
if (!magnifiedChromosome.value) {
@@ -291,6 +262,8 @@ const createChromosomeSVG = () => {
})
hoveredObjectsElements.value = hoveredObjectsElementsNew
})
+
+ // Clear style of no-longer-hovered elements
objectsGroup.mouseleave(() => {
hoveredObjectsElements.value.forEach((objectElement) => {
objectElement.setAttribute(
@@ -304,6 +277,7 @@ const createChromosomeSVG = () => {
hoveredObjectsElements.value = []
})
+ // Lock the tooltip when clicking on any chromosome object
objectsGroup.click(lockTooltipIfUnlocked)
// Create the clip of the object's group, by cloning the chromosome body,
@@ -316,7 +290,7 @@ const createChromosomeSVG = () => {
}
/**
- * Updates the size & position of the elements in the chromosome SVG
+ * Updates the size & position of the elements in the chromosome SVG.
*/
const updateChromosomeSVG = () => {
if (!draw.value) {
@@ -439,6 +413,9 @@ const updateChromosomeSVG = () => {
objectsGroup.transform(groupsTransforms)
}
+/**
+ * Creates and updates the SVG elements of the chromosome on mount.
+ */
onMounted(() => {
createChromosomeSVG()
updateChromosomeSVG()
--
GitLab
From 02db6cd5d75c48570dd4cf915c1f7028f04028dd Mon Sep 17 00:00:00 2001
From: Julien Touchais <5978-julien.touchais@users.noreply.forgemia.inra.fr>
Date: Thu, 25 Apr 2024 09:53:29 +0200
Subject: [PATCH 3/9] refactor(karyotype): :recycle: use lockable tooltip
component
---
src/components/ChromosomeMagnify.vue | 76 ++++++----------------------
1 file changed, 16 insertions(+), 60 deletions(-)
diff --git a/src/components/ChromosomeMagnify.vue b/src/components/ChromosomeMagnify.vue
index 78a8152..0c339e8 100644
--- a/src/components/ChromosomeMagnify.vue
+++ b/src/components/ChromosomeMagnify.vue
@@ -6,11 +6,11 @@ import { computed, onMounted, ref } from 'vue'
/**
* Components imports
*/
-import BaseTooltip from './BaseTooltip.vue'
+import BaseLockableTooltip from '@/components/BaseLockableTooltip.vue'
/**
* Other 3rd-party imports
*/
-import { onClickOutside, useMouseInElement } from '@vueuse/core'
+import { useMouseInElement } from '@vueuse/core'
import { G, Rect, SVG, type Svg } from '@svgdotjs/svg.js'
/**
* Types imports
@@ -86,11 +86,6 @@ const magnifyElementPositions = computed(() => ({
top: mouseClient.y.value,
left: mouseClient.x.value
}))
-/**
- * Location of the tooltip when locked in place, undefined if not locked
- */
-const lockedTooltipPosition = ref<{ bottom: number; left: number }>()
-const lockOffset = ref(0)
/**
* DOM elements of objects currently hovered, to display in the tooltip when
@@ -101,61 +96,28 @@ const hoveredObjectsElements = ref<SVGElement[]>([])
/**
* DOM elements of objects to display in the tooltip when locked.
*/
-const lockedTooltipObjectsElements = ref<SVGElement[]>([])
+const lockedTooltipObjectsElements = ref<SVGElement[]>()
/**
* DOM elements of objects to display in the tooltip.
*/
-const tooltipObjectsElements = computed(() =>
- lockedTooltipPosition.value
- ? lockedTooltipObjectsElements.value
- : hoveredObjectsElements.value
+const tooltipObjectsElements = computed(
+ () => lockedTooltipObjectsElements.value || hoveredObjectsElements.value
)
/**
- * Lock the tooltip in its place and add a scroll listener
+ * Ref to the tooltip component.
*/
-const lockTooltipIfUnlocked = () => {
- if (lockedTooltipPosition.value) return
- lockedTooltipObjectsElements.value = hoveredObjectsElements.value
- // Set locked position
- lockedTooltipPosition.value = {
- bottom: tooltipComponentPositions.value.bottom,
- left: tooltipComponentPositions.value.left
- }
- // Save lock offset
- lockOffset.value = magnifiedChromosomeTranslate.value.x
- // Add scroll event listener to unlock if scroll
- document.addEventListener('scroll', unlockTooltipIfLocked)
-}
+const tooltipComponent = ref<InstanceType<typeof BaseLockableTooltip>>()
/**
- * Unlock the tooltip when clicking out of it
+ * Locks the tooltip and the values to display in it.
*/
-const unlockTooltipIfLocked = () => {
- if (!lockedTooltipPosition.value) return
- // Reset position
- lockedTooltipPosition.value = undefined
- // Remove scroll event listener
- document.removeEventListener('scroll', unlockTooltipIfLocked)
+const lockTooltip = () => {
+ lockedTooltipObjectsElements.value = hoveredObjectsElements.value
+ tooltipComponent.value?.lockTooltipIfUnlocked()
}
-/**
- * Ref to the tooltip component
- */
-const tooltipComponent = ref()
-
-/**
- * Position of the tooltip component relative to the viewport
- */
-const tooltipComponentPositions = computed(() => ({
- bottom:
- lockedTooltipPosition.value?.bottom ||
- window.innerHeight - mouseClient.y.value + 10,
- // bottom: objectsGroupTop.value.value - mouseClient.y.value,
- left: lockedTooltipPosition.value?.left || mouseClient.x.value
-}))
-
/**
* Normalised position of the mouse on the chromosome (between 0 & 1).
*/
@@ -278,7 +240,7 @@ const createChromosomeSVG = () => {
})
// Lock the tooltip when clicking on any chromosome object
- objectsGroup.click(lockTooltipIfUnlocked)
+ objectsGroup.click(lockTooltip)
// Create the clip of the object's group, by cloning the chromosome body,
// and apply the clip
@@ -420,9 +382,6 @@ onMounted(() => {
createChromosomeSVG()
updateChromosomeSVG()
})
-
-// Add a listener to unlock the tooltip when clicking outside of it
-onClickOutside(tooltipComponent, unlockTooltipIfLocked)
</script>
<template>
@@ -443,13 +402,10 @@ onClickOutside(tooltipComponent, unlockTooltipIfLocked)
}"
></div>
</div>
- <BaseTooltip
- v-show="hoveredObjectsElements.length || lockedTooltipPosition"
+ <BaseLockableTooltip
ref="tooltipComponent"
- :style="{
- bottom: `${tooltipComponentPositions.bottom}px`,
- left: `${tooltipComponentPositions.left}px`
- }"
+ :show="!!hoveredObjectsElements.length"
+ @unlock="lockedTooltipObjectsElements = undefined"
>
<div class="flex flex-col gap-2">
<RouterLink
@@ -464,5 +420,5 @@ onClickOutside(tooltipComponent, unlockTooltipIfLocked)
{{ objectElement.dataset.name }}
</RouterLink>
</div>
- </BaseTooltip>
+ </BaseLockableTooltip>
</template>
--
GitLab
From 661ffe884f4c8187d89ad865d782bee3f6907893 Mon Sep 17 00:00:00 2001
From: Julien Touchais <5978-julien.touchais@users.noreply.forgemia.inra.fr>
Date: Thu, 25 Apr 2024 17:11:25 +0200
Subject: [PATCH 4/9] feat(base-components): :lipstick: add a border to legend
component to be consistent with tooltips
---
src/components/BaseLegendButtonOverlay.vue | 1 +
1 file changed, 1 insertion(+)
diff --git a/src/components/BaseLegendButtonOverlay.vue b/src/components/BaseLegendButtonOverlay.vue
index 346c550..5eef2a5 100644
--- a/src/components/BaseLegendButtonOverlay.vue
+++ b/src/components/BaseLegendButtonOverlay.vue
@@ -101,6 +101,7 @@ const toggleLegend = (event: Event) => {
:style="{
opacity: opacity && 0 <= opacity && opacity <= 1 ? opacity : 1
}"
+ class="!border !border-solid !border-slate-200"
>
<slot name="legend">
<ul class="flex max-w-lg flex-col gap-3">
--
GitLab
From dd8b7841dee6a552cd24127331082a34bf9adddd Mon Sep 17 00:00:00 2001
From: Julien Touchais <5978-julien.touchais@users.noreply.forgemia.inra.fr>
Date: Thu, 25 Apr 2024 17:12:22 +0200
Subject: [PATCH 5/9] fix(base-components): :adhesive_bandage: tooltip arrow
was above the tooltip content
---
src/components/BaseTooltip.vue | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/components/BaseTooltip.vue b/src/components/BaseTooltip.vue
index 1da727a..b3cdb78 100644
--- a/src/components/BaseTooltip.vue
+++ b/src/components/BaseTooltip.vue
@@ -78,7 +78,7 @@ const tooltipAfterStyle = computed(() => {
:class="[
'tooltip fixed flex flex-col items-center rounded border bg-white p-2 transition-all duration-500',
showArrow &&
- 'after:absolute after:h-4 after:w-4 after:rounded-sm after:border-b after:border-r after:bg-white'
+ 'after:absolute after:-z-10 after:h-4 after:w-4 after:rounded-sm after:border-b after:border-r after:bg-white'
]"
:style="tooltipStyle"
>
--
GitLab
From d54cf3ab7843b2ad06ccf52391182093a57fced3 Mon Sep 17 00:00:00 2001
From: Julien Touchais <5978-julien.touchais@users.noreply.forgemia.inra.fr>
Date: Thu, 25 Apr 2024 17:29:18 +0200
Subject: [PATCH 6/9] feat(linear-sequence): :sparkles: add a tooltip to show
info on hover highlighted groups
---
src/components/SequenceBoard.vue | 115 ++++++++++++++++++++++++++++++-
1 file changed, 113 insertions(+), 2 deletions(-)
diff --git a/src/components/SequenceBoard.vue b/src/components/SequenceBoard.vue
index 5583f97..d7dbfe7 100644
--- a/src/components/SequenceBoard.vue
+++ b/src/components/SequenceBoard.vue
@@ -7,6 +7,7 @@ import { ref, computed, onMounted, watch } from 'vue'
* Components imports
*/
import BaseLegendButtonOverlay from '@/components/BaseLegendButtonOverlay.vue'
+import BaseLockableTooltip from '@/components/BaseLockableTooltip.vue'
import Dropdown from 'primevue/dropdown'
import Button from 'primevue/button'
import Toolbar from 'primevue/toolbar'
@@ -28,6 +29,7 @@ import { inRange as _inRange } from 'lodash-es'
*/
import type { TailwindDefaultColorNameModel } from '@/typings/styleTypes'
import type { LegendItemModel } from '@/components/BaseLegendButtonOverlay.vue'
+import type { RouteLocationRaw } from 'vue-router'
/**
* Utils imports
*/
@@ -48,6 +50,10 @@ export interface highlightGroupModel {
name?: string
/** Group type. */
type?: string
+ /** Link to go to when clicking on the group. */
+ link?: RouteLocationRaw
+ /** Wether to show a tooltip on hover on this group. */
+ shouldTooltip?: boolean
}
/**
@@ -96,6 +102,13 @@ defineSlots<{
'legend-item-description': (props: {
/** The item of which to customise the description. */ item: LegendItemModel
}) => any
+ /** Custom tooltip group items template */
+ 'tooltip-item': (props: {
+ /** The group of the item to customise */
+ group: highlightGroupModel
+ /** The ID of the group of the item to customise */
+ groupId: string
+ }) => any
}>()
/**
@@ -561,6 +574,47 @@ watch(isSequenceContainerElementVisible, (visibility) => {
updateAndRedraw()
}
})
+
+/**
+ * The highlighted boxes currently being hovered.
+ */
+const hoveredHighlightedGroups = ref(new Set<[string, highlightGroupModel]>())
+
+/**
+ * The highlighted boxes currently being hovered.
+ */
+const lockedTooltipHighlightedGroups = ref<Set<[string, highlightGroupModel]>>()
+
+/**
+ * DOM elements of objects to display in the tooltip.
+ */
+const tooltipHighlightedGroups = computed(
+ () => lockedTooltipHighlightedGroups.value || hoveredHighlightedGroups.value
+)
+
+/**
+ * Lockable tooltip component.
+ */
+const tooltipComponent = ref<InstanceType<typeof BaseLockableTooltip>>()
+
+/**
+ * Locks the tooltip and the values to display in it.
+ */
+const lockTooltip = () => {
+ lockedTooltipHighlightedGroups.value = new Set(hoveredHighlightedGroups.value)
+ tooltipComponent.value?.lockTooltipIfUnlocked()
+}
+
+const deleteHoveredHighlightedGroup = (
+ highlightedGroupTuple: [string, highlightGroupModel]
+) => {
+ const hoveredHighlightedGroupTuple = [...hoveredHighlightedGroups.value].find(
+ ([hoveredHighlightedGroupId]) =>
+ hoveredHighlightedGroupId === highlightedGroupTuple[0]
+ )
+ hoveredHighlightedGroupTuple &&
+ hoveredHighlightedGroups.value.delete(hoveredHighlightedGroupTuple)
+}
</script>
<template>
@@ -674,6 +728,7 @@ watch(isSequenceContainerElementVisible, (visibility) => {
{{ nucleotide }}
</span>
</span>
+
<span
v-for="(_sequenceGroup, groupIndex) in splitSequence"
:key="groupIndex"
@@ -683,6 +738,7 @@ watch(isSequenceContainerElementVisible, (visibility) => {
>
{{ groupIndex * nucleotideGroupsSize + 1 }}
</span>
+
<span
v-for="[highlightedGroupId, highlightedGroup] in Object.entries(
highlightedGroups || {}
@@ -692,6 +748,14 @@ watch(isSequenceContainerElementVisible, (visibility) => {
:data-start="highlightedGroup.start"
:data-end="highlightedGroup.end"
class="highlight-group"
+ @mouseenter="
+ highlightedGroup.shouldTooltip &&
+ hoveredHighlightedGroups.add([highlightedGroupId, highlightedGroup])
+ "
+ @mouseleave="
+ deleteHoveredHighlightedGroup([highlightedGroupId, highlightedGroup])
+ "
+ @click="lockTooltip"
>
<span
v-for="highlightedGroupLine in range(
@@ -709,11 +773,58 @@ watch(isSequenceContainerElementVisible, (visibility) => {
'rounded-r-xl border-r-2':
highlightedGroupsLineCount &&
highlightedGroupLine + 1 ===
- highlightedGroupsLineCount[highlightedGroupId]
+ highlightedGroupsLineCount[highlightedGroupId],
+ 'z-10 hover:cursor-help': highlightedGroup.shouldTooltip
}
]"
- ></span>
+ />
</span>
+
+ <BaseLockableTooltip
+ ref="tooltipComponent"
+ :show="!!hoveredHighlightedGroups.size"
+ class="z-20 max-w-min font-sans text-base shadow-xl"
+ @unlock="lockedTooltipHighlightedGroups = undefined"
+ >
+ <ul>
+ <li
+ v-for="(highlightedGroup, index) in tooltipHighlightedGroups"
+ :key="index"
+ >
+ <RouterLink
+ v-if="highlightedGroup[1].link"
+ :to="highlightedGroup[1].link"
+ :class="[
+ `text-${highlightedGroup[1].color}-600`,
+ 'whitespace-nowrap'
+ ]"
+ >
+ <slot
+ name="tooltip-item"
+ :group="highlightedGroup[1]"
+ :group-id="highlightedGroup[0]"
+ >
+ {{ highlightedGroup[1].name || highlightedGroup[1].link }}
+ {{
+ highlightedGroup[1].type && ` - ${highlightedGroup[1].type}`
+ }}
+ </slot>
+ </RouterLink>
+ <span v-else>
+ <slot
+ name="tooltip-item"
+ :group="highlightedGroup[1]"
+ :group-id="highlightedGroup[0]"
+ >
+ {{ highlightedGroup[1].name || highlightedGroup[1].link }}
+ {{
+ highlightedGroup[1].type && ` - ${highlightedGroup[1].type}`
+ }}
+ </slot>
+ </span>
+ </li>
+ </ul>
+ </BaseLockableTooltip>
</div>
<span class="absolute italic text-slate-400" :style="threePrimeLabelStyle"
>→ 3'</span
--
GitLab
From 3888f35b45045ad2eeb212da9cadd8e0cf69d116 Mon Sep 17 00:00:00 2001
From: Julien Touchais <5978-julien.touchais@users.noreply.forgemia.inra.fr>
Date: Fri, 26 Apr 2024 09:12:11 +0200
Subject: [PATCH 7/9] feat(utils): :sparkles: add util to check if value is in
an enum (& narrow)
---
src/typings/typeUtils.ts | 43 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/src/typings/typeUtils.ts b/src/typings/typeUtils.ts
index 3829cb3..717ecb3 100644
--- a/src/typings/typeUtils.ts
+++ b/src/typings/typeUtils.ts
@@ -33,10 +33,53 @@ export type DeepDefined<T> = T extends object
}>
: T
+/**
+ * Checks if a value is defined, narrowing by excluding `undefined` if yes.
+ * @param value The value to check.
+ */
export const isDefined = <T>(value: T): value is Exclude<T, undefined> =>
typeof value !== 'undefined'
+/**
+ * Checks if a value is a key of an object, narrowing its type to object
+ * properties' one if yes.
+ * @param value The value to check if it is a key of the object.
+ * @param object The object in which to check properties.
+ */
export const isIn = <T extends object>(
value: any,
object: T
): value is keyof T => value in object
+
+/**
+ * Checks if a value is present in a string enum, narrowing its type to enum's
+ * one if yes.
+ * @param value The value to check if it is present in enum.
+ * @param enumType The enum to check into.
+ */
+export function isInEnum<T extends Record<string, string>>(
+ value: string,
+ enumType: T
+): value is T[keyof T]
+/**
+ * Checks if a value is present in a numeric enum, narrowing its type to enum's
+ * one if yes.
+ * @param value The value to check if it is present in enum.
+ * @param enumType The enum to check into.
+ */
+export function isInEnum<T extends Record<string, string | number>>(
+ value: string | number,
+ enumType: T
+): value is T[keyof T]
+export function isInEnum<T extends Record<string, string | number>>(
+ value: string | number,
+ enumType: T
+): value is T[keyof T] {
+ if (typeof value === 'string') {
+ return Object.values(enumType).includes(value)
+ } else {
+ return Object.values(enumType)
+ .filter((v) => typeof v === 'number')
+ .includes(value)
+ }
+}
--
GitLab
From 2df7e1bca78d1ff168ab068ee0db348d5dc26017 Mon Sep 17 00:00:00 2001
From: Julien Touchais <5978-julien.touchais@users.noreply.forgemia.inra.fr>
Date: Fri, 26 Apr 2024 09:17:55 +0200
Subject: [PATCH 8/9] feat(target-view): :sparkles: add tooltip & links on
modifs in sequence
---
src/views/TargetView.vue | 41 ++++++++++++++++++++++++++++++++--------
1 file changed, 33 insertions(+), 8 deletions(-)
diff --git a/src/views/TargetView.vue b/src/views/TargetView.vue
index b93eadb..d027676 100644
--- a/src/views/TargetView.vue
+++ b/src/views/TargetView.vue
@@ -28,7 +28,7 @@ import IconFa6SolidCircleXmark from '~icons/fa6-solid/circle-xmark'
/**
* Other 3rd-party imports
*/
-import { uniq as _uniq, omit as _omit, find as _find } from 'lodash-es'
+import { omit as _omit, find as _find } from 'lodash-es'
import { useQuery } from '@urql/vue'
import { useFetch, useTitle } from '@vueuse/core'
/**
@@ -44,7 +44,7 @@ import { FeatureType, ModifType, Strand } from '@/gql/codegen/graphql'
*/
import { formatSpeciesName, separateThousands } from '@/utils/textFormatting'
import { targetByIdQuery } from '@/gql/queries'
-import { isDefined } from '@/typings/typeUtils'
+import { isDefined, isInEnum } from '@/typings/typeUtils'
import { getModificationColor } from '@/utils/colors'
import type { LegendItemModel } from '@/components/BaseLegendButtonOverlay.vue'
@@ -256,12 +256,11 @@ const interactionList = computed<InteractionCardModel[] | undefined>(() => {
/**
* Target modifications, filtered by keeping only ones with positive position
*/
-const filteredModifications = computed(() =>
- _uniq(
+const filteredModifications = computed(
+ () =>
target.value?.modifications.filter(
(modification) => modification.position >= 0
- )
- )
+ ) || []
)
/**
@@ -281,7 +280,14 @@ const sequenceChunks = computed(() =>
? getModificationColor(modification.type)
: ('slate' as TailwindDefaultColorNameModel),
name: modification.name,
- type: modification.type || undefined
+ type: modification.type || undefined,
+ link: {
+ name: 'modificationDetails',
+ params: {
+ id: modification.id
+ }
+ },
+ shouldTooltip: true
}
}),
{}
@@ -604,6 +610,22 @@ const ontologyLinks = computed(() => ({
long-format
/>
</template>
+
+ <template #tooltip-item="{ group }">
+ <Chip
+ v-if="group.type && isInEnum(group.type, ModifType)"
+ :class="[
+ 'border-2 !font-semibold',
+ `!border-${getModificationColor(
+ group.type
+ )}-600 !bg-${getModificationColor(
+ group.type
+ )}-100 !text-${getModificationColor(group.type)}-600`
+ ]"
+ >
+ {{ group.name }}
+ </Chip>
+ </template>
</SequenceBoard>
</Panel>
@@ -633,7 +655,10 @@ const ontologyLinks = computed(() => ({
>
<template #item-label-1="{ currentValue }">
<strong>{{ currentValue.modification.name }}</strong>
- <em v-if="currentValue.modification.type" class="italic text-slate-400">
+ <em
+ v-if="currentValue.modification.type"
+ class="italic text-slate-400"
+ >
{{ ' - ' }}
<FormattedModificationType
:type-code="currentValue.modification.type"
--
GitLab
From 30a5d5010d0afc44afbbd2da9c94a11070f6d582 Mon Sep 17 00:00:00 2001
From: Julien Touchais <5978-julien.touchais@users.noreply.forgemia.inra.fr>
Date: Fri, 26 Apr 2024 09:18:26 +0200
Subject: [PATCH 9/9] feat(guide-view): :sparkles: add tooltip & link on
modifications & boxes on sequence
---
src/views/GuideView.vue | 142 +++++++++++++++++++++++++++-------------
1 file changed, 96 insertions(+), 46 deletions(-)
diff --git a/src/views/GuideView.vue b/src/views/GuideView.vue
index 4cab84f..75ad379 100644
--- a/src/views/GuideView.vue
+++ b/src/views/GuideView.vue
@@ -27,7 +27,7 @@ import IconFa6SolidCircleXmark from '~icons/fa6-solid/circle-xmark'
/**
* Other 3rd-party imports
*/
-import { omit as _omit } from 'lodash-es'
+import { omit as _omit, uniq as _uniq } from 'lodash-es'
import { useQuery } from '@urql/vue'
import { useTitle } from '@vueuse/core'
/**
@@ -40,6 +40,7 @@ import {
FeatureType,
GuideType,
SequenceType,
+ ModifType,
Strand
} from '@/gql/codegen/graphql'
import type { LegendItemModel } from '@/components/BaseLegendButtonOverlay.vue'
@@ -52,8 +53,8 @@ import {
separateThousands
} from '@/utils/textFormatting'
import { guideByIdQuery } from '@/gql/queries'
-import { isDefined } from '@/typings/typeUtils'
-import { getBoxColor } from '@/utils/colors'
+import { isDefined, isInEnum } from '@/typings/typeUtils'
+import { getBoxColor, getModificationColor } from '@/utils/colors'
/**
* Utility constant to get the icon component corresponding to each strand value.
@@ -192,35 +193,41 @@ const interactionList = computed<InteractionCardModel[] | undefined>(() => {
})
/**
- * Positions of the modifications, relative to the guide sequence.
+ * Guide modifications, filtered by keeping only ones with positive position, relative to the guide sequence.
*/
-const onGuideModificationPositions = computed(() =>
- interactionList.value?.reduce(
- (
- onGuideModificationPositions: { [modificationId: string]: number },
- interaction
- ) => {
- const position =
- interaction.duplexes[0] &&
- interaction.duplexes[0].primaryFragment.onParentPosition?.start &&
- interaction.duplexes[0].secondaryFragment.onParentPosition?.end
- ? interaction.duplexes[0].primaryFragment.onParentPosition.start +
- (interaction.duplexes[0].secondaryFragment.start -
- interaction.duplexes[0].primaryFragment.start) +
- (interaction.duplexes[0].secondaryFragment.onParentPosition.end -
- interaction.modification.position) +
- 1
+const filteredFacingModifications = computed(() =>
+ _uniq(
+ interactionList.value
+ ?.map((interaction) => {
+ // Start coordinate of the guide fragment on the guide
+ const guideFragmentStart =
+ interaction.duplexes[0]?.primaryFragment.onParentPosition?.start ||
+ NaN
+ // End coordinate of the target fragment on the target
+ const targetFragmentEnd =
+ interaction.duplexes[0]?.secondaryFragment.onParentPosition?.end ||
+ NaN
+ // Start coordinate of the binding on the guide fragment
+ const bindingGuideStart =
+ interaction.duplexes[0]?.primaryFragment.start || NaN
+ // End coordinate of the binding on the target fragment
+ const bindingTargetEnd =
+ interaction.duplexes[0]?.secondaryFragment.end || NaN
+ // Length of the target fragment
+ const targetFragmentLength =
+ interaction.duplexes[0]?.secondaryFragment.seq.length || NaN
+
+ const position =
+ guideFragmentStart +
+ (bindingGuideStart - 1) +
+ (targetFragmentEnd -
+ (targetFragmentLength - bindingTargetEnd) -
+ interaction.modification.position)
+ return position && position >= 0
+ ? { ...interaction.modification, facingPosition: position }
: undefined
- // Only keep modification position if positive (! on the guide, this is
- // why we can't filter before computing it)
- return position && position >= 0
- ? {
- ...onGuideModificationPositions,
- [interaction.modification.id]: position
- }
- : onGuideModificationPositions
- },
- {}
+ })
+ .filter(isDefined)
)
)
@@ -236,27 +243,36 @@ const sequenceChunks = computed(() => ({
[featureEdge.node.id]: {
start: Math.max(featureEdge.start, 1),
end: Math.min(featureEdge.end, guide.value?.length || featureEdge.end),
- color: getBoxColor(featureEdge.node.type)
+ color: getBoxColor(featureEdge.node.type),
+ type: featureEdge.node.type,
+ shouldTooltip: true
}
}),
{}
),
- ...(onGuideModificationPositions.value
- ? Object.entries(onGuideModificationPositions.value).reduce(
- (
- sequenceChunks: { [groupId: string]: highlightGroupModel },
- [modificationId, modificationPosition]
- ) => ({
- ...sequenceChunks,
- [modificationId]: {
- start: modificationPosition,
- end: modificationPosition,
- color: 'slate' as TailwindDefaultColorNameModel
+ ...filteredFacingModifications.value?.reduce(
+ (
+ sequenceChunks: { [groupId: string]: highlightGroupModel },
+ facingModification
+ ) => ({
+ ...sequenceChunks,
+ [facingModification.id]: {
+ start: facingModification.facingPosition,
+ end: facingModification.facingPosition,
+ color: 'slate' as TailwindDefaultColorNameModel,
+ name: facingModification.name,
+ type: facingModification.type,
+ link: {
+ name: 'modificationDetails',
+ params: {
+ id: facingModification.id
}
- }),
- {}
- )
- : undefined)
+ },
+ shouldTooltip: true
+ }
+ }),
+ {}
+ )
}))
/**
@@ -669,6 +685,40 @@ const ontologyLinks = computed(() => ({
>{{ item.title.slice(1) }}
</span>
</template>
+
+ <template #tooltip-item="{ group }">
+ <Chip
+ v-if="group.type && isInEnum(group.type, ModifType)"
+ :class="[
+ 'border-2 !font-semibold',
+ `!border-${getModificationColor(
+ group.type
+ )}-600 !bg-${getModificationColor(
+ group.type
+ )}-100 !text-${getModificationColor(group.type)}-600`
+ ]"
+ >
+ {{ group.name }}
+ </Chip>
+ <span
+ v-else-if="group.type === SequenceType.CBox"
+ :class="[
+ 'whitespace-nowrap font-bold not-italic',
+ `text-${getBoxColor(group.type)}-600`
+ ]"
+ >
+ <em>C</em> box
+ </span>
+ <span
+ v-else-if="group.type === SequenceType.DBox"
+ :class="[
+ 'whitespace-nowrap font-bold not-italic',
+ `text-${getBoxColor(group.type)}-600`
+ ]"
+ >
+ <em>D</em> box
+ </span>
+ </template>
</SequenceBoard>
</Panel>
--
GitLab