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track hub - genome list fixes
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@jrobinso
jrobinso committed Feb 6, 2024
1 parent da0f554 commit 743baf4
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Showing 2 changed files with 55 additions and 77 deletions.
2 changes: 1 addition & 1 deletion js/app.js
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Original file line number Diff line number Diff line change
Expand Up @@ -253,7 +253,7 @@ async function initializationHelper(browser, container, options) {
genomeFileLoad: new GenomeFileLoad(genomeFileLoadConfig)
})

await initializeGenomeWidgets(browser, options.genomes, $('#igv-app-genome-dropdown-menu'))
await initializeGenomeWidgets(options.genomes)

const trackLoader = async configurations => {
try {
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130 changes: 54 additions & 76 deletions js/genomeWidgets.js
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,8 @@ import Globals from "./globals.js"

const MAX_CUSTOM_GENOMES = 5

let knownGenomeIds
let predefinedGenomeIds
let predefinedGenomes

function createGenomeWidgets({$igvMain, urlModalId, genomeFileLoad}) {

Expand Down Expand Up @@ -77,19 +78,11 @@ function createGenomeWidgets({$igvMain, urlModalId, genomeFileLoad}) {
* @param $dropdown_menu
* @returns {Promise<void>}
*/
async function initializeGenomeWidgets(browser, genomes, $dropdown_menu) {
async function initializeGenomeWidgets(genomes) {
try {

// Start with predefined genomes. This can return undefined.
knownGenomeIds = genomes ? new Set(genomes.map(g => g.id)) : new Set()
let genomeList = await getAppLaunchGenomes(genomes)

// Add user loaded genomes
genomeList = addCustomGenomes(genomeList || [])

if (genomeList.length > 0) {
updateGenomeList({browser, genomeList, $dropdown_menu})
}
predefinedGenomes = await getAppLaunchGenomes(genomes)// Default genome list
predefinedGenomeIds = new Set(predefinedGenomes.map(g => g.id))
updateGenomeList()

} catch (e) {
AlertSingleton.present(e.message)
Expand Down Expand Up @@ -119,80 +112,63 @@ async function getAppLaunchGenomes(genomes) {
}
}

function addCustomGenomes(genomeList) {
const customGenomeString = localStorage.getItem("recentGenomes")
if (customGenomeString) {
const customGenomeJson = JSON.parse(customGenomeString)
if (customGenomeJson.length > 0) {
genomeList.push('-')
for (let json of customGenomeJson.reverse()) {
genomeList.push(json)
}
}
}
return genomeList
function getCustomGenomes() {
const customGenomeString = localStorage.getItem("customGenomes")
return customGenomeString ? JSON.parse(customGenomeString) : []
}

function buildMap(arrayOrJson) {

const map = new Map()

if (true === Array.isArray(arrayOrJson)) {

for (let json of arrayOrJson.reverse()) {
map.set(json.id, json)
}

} else {
map.set(arrayOrJson.id, arrayOrJson)
}

return map
}

function updateGenomeList({browser, genomeList, $dropdown_menu}) {
function updateGenomeList() {

const $dropdown_menu = $('#igv-app-genome-dropdown-menu')
// discard all buttons preceeding the divider div
// TODO -- does this use of find assume there is 1 dropdown-divider? Searching by ID would be more robust.
let $divider = $dropdown_menu.find('.dropdown-divider')
$divider.nextAll().remove()

for (let genomeJson of genomeList) {

const addEntryFor = (genomeJson) => {
const key = genomeJson.id
const value = genomeJson

if ('-' === genomeJson) {
$('<div class="dropdown-divider"></div>').insertAfter($divider)
} else {
const $button = createButton(value.name)
$button.insertAfter($divider)
const $button = createButton(value.name)
$button.insertAfter($divider)

$button.data('id', key)
$button.data('id', key)

const str = `click.genome-dropdown.${key}`
const str = `click.genome-dropdown.${key}`

$button.on(str, async () => {
$button.on(str, async () => {
const id = $button.data('id')
if (id !== Globals.browser.genome.id) {
await loadGenome(value)
}
})
}

const id = $button.data('id')
// TODO -- why do we need to add everthing in reverse?

if (id !== browser.genome.id) {
await loadGenome(value)
}
if (predefinedGenomes && predefinedGenomes.length > 0) {
for (let genomeJson of predefinedGenomes.reverse()) {
addEntryFor(genomeJson)
}
}

})
const customGenomes = getCustomGenomes()
if (customGenomes && customGenomes.length > 0) {
$('<div class="dropdown-divider"></div>').insertAfter($divider)
for (let genomeJson of customGenomes) {
addEntryFor(genomeJson)
}

} // for (...)
}

function createButton(title) {
}

let $button = $('<button>', {class: 'dropdown-item', type: 'button'})
$button.text(title)
function createButton(title) {

return $button
}
let $button = $('<button>', {class: 'dropdown-item', type: 'button'})
$button.text(title)

return $button
}

async function loadGenome(genomeConfiguration, custom = false) {
Expand All @@ -206,20 +182,22 @@ async function loadGenome(genomeConfiguration, custom = false) {
// Last loaded genome ID, reloaded automatically on next page load
localStorage.setItem("genomeID", g.id)

// Update the recently loaded list
// Update the custom list
// hub.txt genomes are indirect, record name and id
if (!genomeConfiguration.id) genomeConfiguration.id = g.id
if (!genomeConfiguration.name) genomeConfiguration.name = g.name

const recentGenomesString = localStorage.getItem("recentGenomes")
let recentGenomes = recentGenomesString ? JSON.parse(recentGenomesString) : []
recentGenomes = recentGenomes.filter(r => r.id !== g.id) // If already present, replace
recentGenomes.unshift(genomeConfiguration)
if (recentGenomes.length > MAX_CUSTOM_GENOMES) {
recentGenomes = recentGenomes.slice(0, MAX_CUSTOM_GENOMES)
if (!predefinedGenomeIds.has(g.id)) {
if (!genomeConfiguration.id) genomeConfiguration.id = g.id
if (!genomeConfiguration.name) genomeConfiguration.name = g.name

const customGenomesString = localStorage.getItem("customGenomes")
let customGenomes = customGenomesString ? JSON.parse(customGenomesString) : []
customGenomes = customGenomes.filter(r => r.id !== g.id) // If already present, replace
customGenomes.unshift(genomeConfiguration)
if (customGenomes.length > MAX_CUSTOM_GENOMES) {
customGenomes = customGenomes.slice(0, MAX_CUSTOM_GENOMES)
}
localStorage.setItem("customGenomes", JSON.stringify(customGenomes))
updateGenomeList()
}
localStorage.setItem("recentGenomes", JSON.stringify(recentGenomes))


} catch (e) {
console.error(e)
Expand Down

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