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Update entropy types #1915

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Update entropy types #1915

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864707d
Use literal string values for Strand type
victorlin Nov 20, 2024
c22d1f8
Add whitespace between types
victorlin Nov 20, 2024
4394124
Add whitespace to function signatures
victorlin Nov 20, 2024
14e93af
Move comments to JSDoc
victorlin Nov 20, 2024
7ac5a2b
Use interface for all object aliases
victorlin Nov 20, 2024
37da370
Remove unnecessary semicolons and commas
victorlin Nov 20, 2024
2d3a331
Make JsonAnnotation.strand optional
victorlin Nov 20, 2024
c2d10de
Add type for prevSegment
victorlin Nov 21, 2024
a7578d2
Update conditions for optional properties
victorlin Nov 21, 2024
ce1f446
Add type-safe function for n % 3
victorlin Nov 21, 2024
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34 changes: 27 additions & 7 deletions src/util/entropyCreateStateFromJsons.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -168,7 +168,7 @@ export const entropyCreateState = (genomeAnnotations: JsonAnnotations) => {
};


function validColor(color:(string|undefined)) {
function validColor(color: string | undefined) {
if (!color) return false;
return color; // TODO XXX
}
Expand All @@ -184,7 +184,12 @@ function* nextColorGenerator() {
/**
* Returns a CDS object parsed from the provided JsonAnnotation block
*/
function cdsFromAnnotation(cdsName: string, annotation: JsonAnnotation, rangeGenome: RangeGenome, defaultColor: (string|void)): CDS {
function cdsFromAnnotation(
cdsName: string,
annotation: JsonAnnotation,
rangeGenome: RangeGenome,
defaultColor: string | void,
): CDS {
const invalidCds: CDS = {
name: '__INVALID__',
length: 0,
Expand Down Expand Up @@ -296,7 +301,13 @@ function cdsFromAnnotation(cdsName: string, annotation: JsonAnnotation, rangeGen
* positiveStrand: boolean
* Returns a number in the set {0, 1, 2}
*/
function _frame(start:number, end:number, phase: number, genomeLength:number, positiveStrand:boolean) {
function _frame(
start: number,
end: number,
phase: number,
genomeLength: number,
positiveStrand: boolean,
) {
return positiveStrand ?
(start+phase-1)%3 :
Math.abs((end-phase-genomeLength)%3);
Expand All @@ -309,7 +320,10 @@ function _frame(start:number, end:number, phase: number, genomeLength:number, po
* refers to this being a stacking problem.) The stack position starts at 1.
* Returns the maximum position observed.
*/
function calculateStackPosition(genes: Gene[], strand: (Strand|null) = null):number {
function calculateStackPosition(
genes: Gene[],
strand: Strand | null = null,
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Related to a previous comment, null is probably not the right choice here (as it's a schema-valid strand). By the time this function is called we have already created cds objects (cdsFromAnnotation) and so restricted the strand to +/-, so in practice it doesn't mater. I'd suggest

  • (a) requiring the argument (and thus getting rid of the conditional if (strand) below)

and, potentially,

  • (b) using a more restricted type definition.

): number {
/* List of CDSs, sorted by their earliest occurrence in the genome (for any segment) */
let cdss = genes.reduce((acc: CDS[], gene) => [...acc, ...gene.cds], []);
if (strand) {
Expand Down Expand Up @@ -359,7 +373,7 @@ function calculateStackPosition(genes: Gene[], strand: (Strand|null) = null):num
* Given an array of sorted integers, if there are any spaces (starting with 1)
* then return the value which can fill that space. Returns 0 if no spaces.
*/
function _emptySlots(values: number[]):number {
function _emptySlots(values: number[]): number {
if ((values[0] || 0) > 1) return 1;
for (let i=1; i<values.length; i++) {
/* intermediate variables because of https://github.com/microsoft/TypeScript/issues/46253 */
Expand All @@ -374,7 +388,10 @@ function _emptySlots(values: number[]):number {
* between-segment space of an existing segment, then return the stackPosition
* of that existing CDS. Otherwise return 0;
*/
function _fitCdssTogether(existing: CDS[], newCds: CDS):number {
function _fitCdssTogether(
existing: CDS[],
newCds: CDS,
): number {
const a = Math.min(...newCds.segments.map((s) => s.rangeGenome[0]));
const b = Math.max(...newCds.segments.map((s) => s.rangeGenome[1]));
for (const cds of existing) {
Expand Down Expand Up @@ -409,7 +426,10 @@ function _fitCdssTogether(existing: CDS[], newCds: CDS):number {


/* Does a CDS wrap the origin? */
function _isCdsWrapping(strand: Strand, segments: CdsSegment[]): boolean {
function _isCdsWrapping(
strand: Strand,
segments: CdsSegment[],
): boolean {
const positive = strand==='+';
// segments ordered to guarantee rangeLocal will always be greater (than the previous segment)
let prevSegment;
Expand Down