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Split view via unified coordinates and search control (#706) - GUI, B…
…rowser tab: coordinates input enhancements
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client/client/app/shared/components/ngbGoldenLayout/ngbCoordinates/parse-coordinates.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,191 @@ | ||
| // "chr x: start - end" | ||
| const CHR_START_END_regExp = /^\s*([^:]+):\s*(\d+)\s*-\s*(\d+)\s*/; | ||
| // "chr: position" | ||
| const CHR_POSITION_regExp = /^\s*([^:]+):\s*(\d+)\s*/; | ||
| // "chr:" | ||
| const CHR_regExp = /^\s*([^:]+):\s*/; | ||
| // "start - end" | ||
| const START_END_regExp = /^\s*(\d+)\s*-\s*(\d+)\s*/; | ||
| // "position" | ||
| const POSITION_regExp = /^\s*(\d+)\s*/; | ||
| // "feature" | ||
| const FEATURE_regExp = /^\s*([^\s]+)\s*/; | ||
|
|
||
| function getChromosome(name, projectContext) { | ||
| if (!projectContext) { | ||
| return undefined; | ||
| } | ||
| return projectContext.getChromosome({name}); | ||
| } | ||
|
|
||
| function correctPosition (chromosome, position) { | ||
| if (!chromosome || Number.isNaN(Number(position))) { | ||
| return undefined; | ||
| } | ||
| return Math.max( | ||
| 1, | ||
| Math.min( | ||
| chromosome.size, | ||
| Number(position) | ||
| ) | ||
| ); | ||
| } | ||
|
|
||
| export function getCoordinatesText(navigation) { | ||
| if ( | ||
| !navigation || | ||
| !navigation.chromosome || | ||
| !navigation.chromosome.name | ||
| ) { | ||
| return undefined; | ||
| } | ||
| const { | ||
| chromosome, | ||
| position, | ||
| viewport = {} | ||
| } = navigation; | ||
| if (position) { | ||
| return `${chromosome.name}: ${position}`; | ||
| } | ||
| if (viewport && viewport.start && viewport.end) { | ||
| return `${chromosome.name}: ${viewport.start} - ${viewport.end}`; | ||
| } | ||
| return undefined; | ||
| } | ||
|
|
||
| function findBestFeatureFn (featureName) { | ||
| return function filter (o) { | ||
| return (o.featureId || '').toLowerCase() === featureName.toLowerCase() || | ||
| (o.name || '').toLowerCase() === featureName.toLowerCase() || | ||
| (o.featureName || '').toLowerCase() === featureName.toLowerCase(); | ||
| }; | ||
| } | ||
|
|
||
| async function findFeature(featureName, cache = [], projectDataService, referenceId) { | ||
| if (!featureName) { | ||
| return undefined; | ||
| } | ||
| const find = findBestFeatureFn(featureName); | ||
| const [o] = cache.filter(cacheItem => cacheItem.tag && find(cacheItem)); | ||
| let feature = o && o.tag ? o.tag : undefined; | ||
| if (!feature && projectDataService && referenceId) { | ||
| const result = await projectDataService.searchGenes(referenceId, featureName); | ||
| if (result.entries && result.entries.length > 0) { | ||
| const [best] = result.entries.filter(find); | ||
| feature = best; | ||
| } | ||
| } | ||
| if ( | ||
| feature && | ||
| feature.chromosome && | ||
| (feature.chromosome.name || feature.chromosome.id) && | ||
| feature.startIndex && | ||
| feature.endIndex | ||
| ) { | ||
| const { | ||
| chromosome, | ||
| startIndex, | ||
| endIndex | ||
| } = feature; | ||
| return { | ||
| chromosome, | ||
| viewport: { | ||
| start: startIndex, | ||
| end: endIndex | ||
| } | ||
| }; | ||
| } | ||
| return undefined; | ||
| } | ||
|
|
||
| export default async function parseCoordinates ( | ||
| string, | ||
| projectContext, | ||
| currentChromosomeName, | ||
| searchResultsCache = [], | ||
| projectDataService, | ||
| referenceId | ||
| ) { | ||
| if (!string) { | ||
| return []; | ||
| } | ||
| let rest = string.slice(); | ||
| const coordinates = []; | ||
| let currentChromosome = getChromosome(currentChromosomeName, projectContext); | ||
| do { | ||
| const chrStartEnd = CHR_START_END_regExp.exec(rest); | ||
| const chrPosition = CHR_POSITION_regExp.exec(rest); | ||
| const chr = CHR_regExp.exec(rest); | ||
| const startEnd = START_END_regExp.exec(rest); | ||
| const position = POSITION_regExp.exec(rest); | ||
| const feature = FEATURE_regExp.exec(rest); | ||
| const matchedRegExp = chrStartEnd || | ||
| chrPosition || | ||
| chr || | ||
| startEnd || | ||
| position || | ||
| feature; | ||
| if (chrStartEnd) { | ||
| const [, chrName, start, end] = chrStartEnd; | ||
| const chromosome = getChromosome(chrName, projectContext); | ||
| const viewport = { | ||
| start: correctPosition(chromosome, start), | ||
| end: correctPosition(chromosome, end) | ||
| }; | ||
| if (chromosome && viewport.start && viewport.end) { | ||
| coordinates.push({chromosome, viewport}); | ||
| currentChromosome = chromosome; | ||
| } | ||
| } else if (chrPosition) { | ||
| const [, chrName, _position] = chrPosition; | ||
| const chromosome = getChromosome(chrName, projectContext); | ||
| const positionPayload = correctPosition(chromosome, _position); | ||
| if (chromosome && positionPayload) { | ||
| coordinates.push({chromosome, position: positionPayload}); | ||
| currentChromosome = chromosome; | ||
| } | ||
| } else if (chr) { | ||
| const [, chrName] = chr; | ||
| const chromosome = getChromosome(chrName, projectContext); | ||
| if (chromosome) { | ||
| const viewport = { | ||
| start: 1, | ||
| end: currentChromosome.size | ||
| }; | ||
| coordinates.push({chromosome, viewport}); | ||
| currentChromosome = chromosome; | ||
| } | ||
| } else if (startEnd && currentChromosome) { | ||
| const [, start, end] = startEnd; | ||
| const viewport = { | ||
| start: correctPosition(currentChromosome, start), | ||
| end: correctPosition(currentChromosome, end) | ||
| }; | ||
| if (viewport.start && viewport.end) { | ||
| coordinates.push({chromosome: currentChromosome, viewport}); | ||
| } | ||
| } else if (position && currentChromosome) { | ||
| const [, _position] = position; | ||
| const positionPayload = correctPosition(currentChromosome, _position); | ||
| if (positionPayload) { | ||
| coordinates.push({chromosome: currentChromosome, position: positionPayload}); | ||
| } | ||
| } else if (feature) { | ||
| const featureNavigation = await findFeature( | ||
| feature[1], | ||
| searchResultsCache, | ||
| projectDataService, | ||
| referenceId | ||
| ); | ||
| if (featureNavigation) { | ||
| coordinates.push(featureNavigation); | ||
| } | ||
| } | ||
| if (matchedRegExp) { | ||
| rest = rest.slice(matchedRegExp.index + matchedRegExp[0].length); | ||
| } else { | ||
| rest = undefined; | ||
| } | ||
| } while (rest); | ||
| return coordinates; | ||
| } |
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