Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
generic cache implemented for features
- Loading branch information
1 parent
3f07ddd
commit 2fe8392
Showing
11 changed files
with
455 additions
and
58 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| /** | ||
| * Generic object that can be displayed. This can be a gene, feature or variant, etc. | ||
| * See ../viz/GenericFeatureCache.js | ||
| * @flow | ||
| */ | ||
| 'use strict'; | ||
|
|
||
| import ContigInterval from '../ContigInterval'; | ||
|
|
||
|
|
||
| class GenericFeature { | ||
| id: string; | ||
| position: ContigInterval<string>; | ||
| gFeature: Object; | ||
|
|
||
| constructor(id: string, position: ContigInterval<string>, genericFeature: Object) { // TODO abstract class | ||
| this.id = genericFeature.id; | ||
| this.position = genericFeature.position; | ||
| this.gFeature = genericFeature; | ||
| } | ||
| } | ||
|
|
||
| module.exports = GenericFeature; |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,116 @@ | ||
| /** | ||
| * Data management for FeatureTrack. | ||
| * | ||
| * This class groups features and piles them up. | ||
| * | ||
| * @flow | ||
| */ | ||
| 'use strict'; | ||
|
|
||
| import _ from 'underscore'; | ||
| import ContigInterval from '../ContigInterval'; | ||
| import GenericFeature from '../data/genericFeature.js'; | ||
|
|
||
| import Interval from '../Interval'; | ||
| import {addToPileup} from './pileuputils'; | ||
| import utils from '../utils'; | ||
| import type {TwoBitSource} from '../sources/TwoBitDataSource'; | ||
|
|
||
| export type VisualGroup = { | ||
| key: string; | ||
| span: ContigInterval<string>; // tip-to-tip span | ||
| row: number; // pileup row. | ||
| gFeatures: GenericFeature[]; | ||
| }; | ||
|
|
||
|
|
||
| // This class provides data management for the visualization | ||
| class GenericFeatureCache { | ||
| // maps groupKey to VisualGroup | ||
| groups: {[key: string]: VisualGroup}; | ||
| refToPileup: {[key: string]: Array<Interval[]>}; | ||
| referenceSource: TwoBitSource; | ||
|
|
||
| constructor(referenceSource: TwoBitSource) { | ||
| this.groups = {}; | ||
| this.refToPileup = {}; | ||
| this.referenceSource = referenceSource; | ||
| } | ||
|
|
||
| // name would make a good key, but features from different contigs | ||
| // shouldn't be grouped visually. Hence we use feature name + contig. | ||
| groupKey(f: GenericFeature): string { | ||
| return f.id || f.position.toString(); | ||
| } | ||
|
|
||
| // Load a new feature into the visualization cache. | ||
| // Calling this multiple times with the same feature is a no-op. | ||
| addFeature(feature: GenericFeature) { | ||
| var key = this.groupKey(feature); | ||
|
|
||
| if (!(key in this.groups)) { | ||
| this.groups[key] = { | ||
| key: key, | ||
| span: feature.position, | ||
| row: -1, // TBD | ||
| gFeatures: [] | ||
| }; | ||
| } | ||
| var group = this.groups[key]; | ||
|
|
||
| if (_.find(group.gFeatures, f => f.gFeature == feature.gFeature)) { | ||
| return; // we've already got it. | ||
| } | ||
|
|
||
| group.gFeatures.push(feature); | ||
|
|
||
| if (!(feature.position.contig in this.refToPileup)) { | ||
| this.refToPileup[feature.position.contig] = []; | ||
| } | ||
| var pileup = this.refToPileup[feature.position.contig]; | ||
| group.row = addToPileup(group.span.interval, pileup); | ||
|
|
||
| } | ||
|
|
||
| pileupForRef(ref: string): Array<Interval[]> { | ||
| if (ref in this.refToPileup) { | ||
| return this.refToPileup[ref]; | ||
| } else { | ||
| var alt = utils.altContigName(ref); | ||
| if (alt in this.refToPileup) { | ||
| return this.refToPileup[alt]; | ||
| } else { | ||
| return []; | ||
| } | ||
| } | ||
| } | ||
|
|
||
| // How many rows tall is the pileup for a given ref? This is related to the | ||
| // maximum track depth. This is 'chr'-agnostic. | ||
| pileupHeightForRef(ref: string): number { | ||
| var pileup = this.pileupForRef(ref); | ||
| return pileup ? pileup.length : 0; | ||
| } | ||
|
|
||
| // Find groups overlapping the range. This is 'chr'-agnostic. | ||
| getGroupsOverlapping(range: ContigInterval<string>): VisualGroup[] { | ||
| // TODO: speed this up using an interval tree | ||
| return _.filter(this.groups, group => group.span.intersects(range)); | ||
| } | ||
|
|
||
| // Determine the number of groups at a locus. | ||
| // Like getGroupsOverlapping(range).length > 0, but more efficient. | ||
| anyGroupsOverlapping(range: ContigInterval<string>): boolean { | ||
| for (var k in this.groups) { | ||
| var group = this.groups[k]; | ||
| if (group.span.intersects(range)) { | ||
| return true; | ||
| } | ||
| } | ||
| return false; | ||
| } | ||
| } | ||
|
|
||
| module.exports = { | ||
| GenericFeatureCache | ||
| }; |
Oops, something went wrong.