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post rebase clean up
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@turner
turner committed Aug 5, 2024
1 parent e257765 commit 5c62980
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Showing 3 changed files with 839 additions and 1,054 deletions.
102 changes: 48 additions & 54 deletions js/feature/segTrack.js
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Original file line number Diff line number Diff line change
@@ -1,16 +1,14 @@
import $ from "../vendor/jquery-3.3.1.slim.js"
import FeatureSource from './featureSource.js'
import TrackBase from "../trackBase.js"
import IGVGraphics from "../igv-canvas.js"
import {IGVMath} from "../../node_modules/igv-utils/src/index.js"
import {createCheckbox} from "../igv-icons.js"
import {GradientColorScale} from "../util/colorScale.js"
import {ColorTable} from "../util/colorPalletes.js"
import { IGVMath } from "../../node_modules/igv-utils/src/index.js"
import { createCheckbox } from "../igv-icons.js"
import { GradientColorScale } from "../util/colorScale.js"
import { ColorTable } from "../util/colorPalletes.js"
import SampleInfo from "../sample/sampleInfo.js"
import HicColorScale from "../hic/hicColorScale.js"
import ShoeboxSource from "../hic/shoeboxSource.js"
import {doSortByAttributes} from "../sample/sampleUtils.js"

import { doSortByAttributes } from "../sample/sampleUtils.js"

class SegTrack extends TrackBase {

Expand All @@ -31,7 +29,7 @@ class SegTrack extends TrackBase {
this.maxHeight = config.maxHeight || 500
this.squishedRowHeight = config.sampleSquishHeight || config.squishedRowHeight || 2
this.expandedRowHeight = config.sampleExpandHeight || config.expandedRowHeight || 13
this.sampleHeight = this.squishedRowHeight // Initial value, will get overwritten when rendered
this.sampleHeight = this.squishedRowHeight // Initial value, will get overwritten when rendered

// Explicitly set samples -- used to select a subset of samples from a dataset
this.sampleKeys = []
Expand All @@ -45,7 +43,7 @@ class SegTrack extends TrackBase {

// Color settings
if (config.color) {
this.color = config.color // Overrides defaults, can be a function
this.color = config.color // Overrides defaults, can be a function
} else if (config.colorTable) {
this.colorTable = new ColorTable(config.colorTable)
} else {
Expand All @@ -63,7 +61,6 @@ class SegTrack extends TrackBase {
}
}


// Create featureSource
// Disable whole genome downsampling unless explicitly.
const configCopy = Object.assign({}, this.config)
Expand All @@ -87,15 +84,14 @@ class SegTrack extends TrackBase {
async postInit() {
if (typeof this.featureSource.getHeader === "function") {
this.header = await this.featureSource.getHeader()
if (this.disposed) return // This track was removed during async load
if (this.disposed) return // This track was removed during async load
}
// Set properties from track line
if (this.header) {
this.setTrackProperties(this.header)
}
}


menuItemList() {

const menuItems = []
Expand All @@ -111,10 +107,10 @@ class SegTrack extends TrackBase {
return attrs && attrs[attribute]
})) {

const object = $('<div>')
object.html(`&nbsp;&nbsp;${attribute.split(SampleInfo.emptySpaceReplacement).join(' ')}`)
const object = document.createElement('div')
object.innerHTML = `&nbsp;&nbsp;${attribute.split(SampleInfo.emptySpaceReplacement).join(' ')}`

function attributeSort() {
object.addEventListener('click', () => {
const sortDirection = this.#sortDirections.get(attribute) || 1
this.sortByAttribute(attribute, sortDirection)
this.#sortDirections.set(attribute, sortDirection * -1)
Expand All @@ -124,19 +120,18 @@ class SegTrack extends TrackBase {
attribute: attribute,
direction: sortDirection === 1 ? "ASC" : "DESC"
}
}
})

menuItems.push({object, click: attributeSort})
menuItems.push({ object })
}
}
}

const lut =
{
"SQUISHED": "Squish",
"EXPANDED": "Expand",
"FILL": "Fill"
}
const lut = {
"SQUISHED": "Squish",
"EXPANDED": "Expand",
"FILL": "Fill"
}

if (this.type === 'shoebox' && this.sbColorScale) {
menuItems.push('<hr/>')
Expand All @@ -155,33 +150,36 @@ class SegTrack extends TrackBase {
}, e)
}

menuItems.push({object: $('<div>Set color scale threshold</div>'), dialog: dialogPresentationHandler})
const divElement = document.createElement('div');
divElement.textContent = 'Set color scale threshold';
divElement.addEventListener('click', dialogPresentationHandler.bind(this));
menuItems.push({ object: divElement });
}

menuItems.push('<hr/>')
menuItems.push("DisplayMode:")
const displayOptions = this.type === 'seg' || this.type === 'shoebox' ? ["SQUISHED", "EXPANDED", "FILL"] : ["SQUISHED", "EXPANDED"]
for (let displayMode of displayOptions) {
const checkBox = createCheckbox(lut[displayMode], displayMode === this.displayMode)
menuItems.push(
{
object: $(checkBox),
click: function displayModeHandler() {
this.displayMode = displayMode
this.config.displayMode = displayMode
this.trackView.checkContentHeight()
this.trackView.repaintViews()
this.trackView.moveScroller(this.trackView.sampleNameViewport.trackScrollDelta)
}
})
const object = document.createElement('div');
object.appendChild(checkBox);
object.addEventListener('click', () => {
this.displayMode = displayMode
this.config.displayMode = displayMode
this.trackView.checkContentHeight()
this.trackView.repaintViews()
this.trackView.moveScroller(this.trackView.sampleNameViewport.trackScrollDelta)
})

menuItems.push({ object })
}

return menuItems

}

hasSamples() {
return true // SEG, MUT, and MAF tracks have samples by definition
return true // SEG, MUT, and MAF tracks have samples by definition
}

getSamples() {
Expand All @@ -193,7 +191,7 @@ class SegTrack extends TrackBase {
}

async getFeatures(chr, start, end) {
const features = await this.featureSource.getFeatures({chr, start, end})
const features = await this.featureSource.getFeatures({ chr, start, end })
// New segments could conceivably add new samples
this.updateSampleKeys(features)

Expand All @@ -205,23 +203,22 @@ class SegTrack extends TrackBase {
const sortDirection = "DESC" === sort.direction ? 1 : -1
this.sortByAttribute(sort.attribute, sortDirection)
}
this.initialSort = undefined // Sample order is sorted,
this.initialSort = undefined // Sample order is sorted,
}
return features
}

draw({ context, pixelTop, pixelWidth, pixelHeight, features, bpPerPixel, bpStart }) {

draw({context, pixelTop, pixelWidth, pixelHeight, features, bpPerPixel, bpStart}) {

IGVGraphics.fillRect(context, 0, pixelTop, pixelWidth, pixelHeight, {'fillStyle': "rgb(255, 255, 255)"})
IGVGraphics.fillRect(context, 0, pixelTop, pixelWidth, pixelHeight, { 'fillStyle': "rgb(255, 255, 255)" })

if (features && features.length > 0) {

this.checkForLog(features)

if (this.type === "shoebox" && !this.sbColorScale) {
const threshold = this.featureSource.hicFile.percentile95 || 2000
this.sbColorScale = new HicColorScale({threshold, r: 0, g: 0, b: 255})
this.sbColorScale = new HicColorScale({ threshold, r: 0, g: 0, b: 255 })
}

// Create a map for fast id -> row lookup
Expand All @@ -241,14 +238,14 @@ class SegTrack extends TrackBase {
this.sampleHeight = this.squishedRowHeight
border = 0
break
default: // EXPANDED
default: // EXPANDED
this.sampleHeight = this.expandedRowHeight
border = 1
}
const rowHeight = this.sampleHeight

for (let segment of features) {
segment.pixelRect = undefined // !important, reset this in case segment is not drawn
segment.pixelRect = undefined // !important, reset this in case segment is not drawn
}

const pixelBottom = pixelTop + pixelHeight
Expand Down Expand Up @@ -333,7 +330,7 @@ class SegTrack extends TrackBase {
}


f.pixelRect = {x, y, w, h}
f.pixelRect = { x, y, w, h }

// Use for diagnostic rendering
// context.fillStyle = randomRGB(180, 240)
Expand All @@ -349,7 +346,6 @@ class SegTrack extends TrackBase {

}


checkForLog(features) {
if (this.isLog === undefined) {
this.isLog = false
Expand All @@ -363,8 +359,8 @@ class SegTrack extends TrackBase {
}

/**
* Optional method to compute pixel height to accomodate the list of features. The implementation below
* has side effects (modifiying the samples hash). This is unfortunate, but harmless.
* Optional method to compute pixel height to accommodate the list of features. The implementation below
* has side effects (modifying the samples hash). This is unfortunate, but harmless.
*
* Note displayMode "FILL" is handled by the viewport
*
Expand Down Expand Up @@ -393,9 +389,8 @@ class SegTrack extends TrackBase {
end = sort.end
}


if (!featureList) {
featureList = await this.featureSource.getFeatures({chr, start, end})
featureList = await this.featureSource.getFeatures({ chr, start, end })
}
if (!featureList) return

Expand Down Expand Up @@ -531,7 +526,7 @@ class SegTrack extends TrackBase {
label: sortLabel,
click: () => {
const sort = {
option: "VALUE", // Either VALUE or ATTRIBUTE
option: "VALUE", // Either VALUE or ATTRIBUTE
direction,
chr: clickState.referenceFrame.chr,
start: Math.floor(genomicLocation - bpWidth),
Expand Down Expand Up @@ -564,8 +559,8 @@ class SegTrack extends TrackBase {
}

// Default copy number scales
const POS_COLOR_SCALE = {low: 0.1, lowR: 255, lowG: 255, lowB: 255, high: 1.5, highR: 255, highG: 0, highB: 0}
const NEG_COLOR_SCALE = {low: -1.5, lowR: 0, lowG: 0, lowB: 255, high: -0.1, highR: 255, highG: 255, highB: 255}
const POS_COLOR_SCALE = { low: 0.1, lowR: 255, lowG: 255, lowB: 255, high: 1.5, highR: 255, highG: 0, highB: 0 }
const NEG_COLOR_SCALE = { low: -1.5, lowR: 0, lowG: 0, lowB: 255, high: -0.1, highR: 255, highG: 255, highB: 255 }


// Mut and MAF file default color table
Expand Down Expand Up @@ -613,5 +608,4 @@ const MUT_COLORS = {

}


export default SegTrack
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