react-msaview 2.0.0 → 2.1.1

package/src/model.ts

@@ -1,3 +1,4 @@
+import React from 'react'
 import { Instance, cast, types, addDisposer, SnapshotIn } from 'mobx-state-tree'
 import { hierarchy, cluster, HierarchyNode } from 'd3-hierarchy'
 import { ascending } from 'd3-array'
@@ -43,7 +44,7 @@ interface BasicTrackModel {
 }
 
 export interface TextTrackModel extends BasicTrackModel {
-  customColorScheme?: { [key: string]: string }
+  customColorScheme?: Record<string, string>
   data: string
 }
 
@@ -119,6 +120,7 @@ const MSAModel = types
     ),
   })
   .volatile(() => ({
+    rulerHeight: 20,
     error: undefined as unknown,
     margin: { left: 20, top: 20 },
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
@@ -258,7 +260,6 @@ const MSAModel = types
         self,
         autorun(async () => {
           const { msaFilehandle } = self
-
           if (msaFilehandle) {
             try {
               this.setMSA(await openLocation(msaFilehandle).readFile('utf8'))
@@ -431,13 +432,14 @@ const MSAModel = types
       return hier
     },
 
-    get structures(): {
-      [key: string]: {
+    get structures(): Record<
+      string,
+      {
         pdb: string
         startPos: number
         endPos: number
       }[]
-    } {
+    > {
       return this.MSA?.getStructures() || {}
     },
 
@@ -463,8 +465,8 @@ const MSAModel = types
 
       for (let i = 0; i < strs[0]?.length; i++) {
         let counter = 0
-        for (let j = 0; j < strs.length; j++) {
-          if (strs[j][i] === '-') {
+        for (const str of strs) {
+          if (str[i] === '-') {
             counter++
           }
         }
@@ -493,15 +495,15 @@ const MSAModel = types
     },
 
     get colStats() {
-      const r = [] as { [key: string]: number }[]
-      const m = this.columns2d
-      for (let i = 0; i < m.length; i++) {
-        for (let j = 0; j < m[i].length; j++) {
+      const r = [] as Record<string, number>[]
+      const columns = this.columns2d
+      for (const column of columns) {
+        for (let j = 0; j < column.length; j++) {
           const l = r[j] || {}
-          if (!l[m[i][j]]) {
-            l[m[i][j]] = 0
+          if (!l[column[j]]) {
+            l[column[j]] = 0
           }
-          l[m[i][j]]++
+          l[column[j]]++
           r[j] = l
         }
       }
@@ -589,13 +591,11 @@ const MSAModel = types
     },
 
     get conservation() {
-      const m = self.columns2d
-
-      if (m.length) {
-        for (let i = 0; i < m[0].length; i++) {
+      if (self.columns2d.length) {
+        for (let i = 0; i < self.columns2d[0].length; i++) {
           const col = []
-          for (let j = 0; j < m.length; j++) {
-            col.push(m[j][i])
+          for (const column of self.columns2d) {
+            col.push(column[i])
           }
         }
       }
@@ -717,17 +717,20 @@ const MSAModel = types
     relativePxToBp(rowName: string, position: number) {
       const { rowNames, rows } = self
       const index = rowNames.indexOf(rowName)
-      const row = rows[index][1]
+      if (index !== -1) {
+        const row = rows[index][1]
 
-      let k = 0
-      for (let i = 0; i < position; i++) {
-        if (row[i] !== '-') {
-          k++
-        } else if (k >= position) {
-          break
+        let k = 0
+        for (let i = 0; i < position; i++) {
+          if (row[i] !== '-') {
+            k++
+          } else if (k >= position) {
+            break
+          }
         }
+        return k
       }
-      return k
+      return 0
     },
 
     getPos(pos: number) {
@@ -745,7 +748,7 @@ const MSAModel = types
     addAnnotation(
       start: number,
       end: number,
-      attributes: { [key: string]: string[] },
+      attributes: Record<string, string[]>,
     ) {
       self.annotatedRegions.push({
         start: self.getPos(start),

package/src/parseNewick.ts

@@ -72,12 +72,11 @@ export default function parse(s: string) {
         tree = subtree
         break
       case ',': // another branch
-        ancestors[ancestors.length - 1].branchset.push(subtree)
+        ancestors.at(-1)?.branchset.push(subtree)
         tree = subtree
         break
       case ')': // optional name next
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        tree = ancestors.pop() as Record<string, any>
+        tree = ancestors.pop()!
         break
       case ':': // optional length next
         break

package/src/parsers/FastaMSA.ts

@@ -9,16 +9,16 @@ function parseSmallFasta(text: string) {
       const [id, ...description] = defLine.split(' ')
       const descriptionStr = description.join(' ')
       const seqLinesStr = seqLines.join('')
-      const sequence = seqLinesStr.replace(/\s/g, '')
+      const sequence = seqLinesStr.replaceAll(/\s/g, '')
       return { id, description: descriptionStr, sequence }
     })
 }
 export default class FastaMSA {
-  private MSA: { seqdata: { [key: string]: string } }
+  private MSA: { seqdata: Record<string, string> }
   constructor(text: string) {
     this.MSA = {
       seqdata: Object.fromEntries(
-        parseSmallFasta(text).map((m, i) => [`${m.id}-${i}`, m.sequence]),
+        parseSmallFasta(text).map(m => [`${m.id}`, m.sequence]),
       ),
     }
   }

package/src/parsers/StockholmMSA.ts

@@ -2,7 +2,7 @@ import Stockholm from 'stockholm-js'
 import parseNewick from '../parseNewick'
 
 import { NodeWithIds, generateNodeIds } from '../util'
-type StockholmEntry = {
+interface StockholmEntry {
   gf: {
     DE?: string[]
     NH?: string[]
@@ -15,7 +15,7 @@ type StockholmEntry = {
     SS_cons?: string
     seq_cons?: string
   }
-  seqdata: { [key: string]: string }
+  seqdata: Record<string, string>
 }
 
 export default class StockholmMSA {
@@ -56,8 +56,8 @@ export default class StockholmMSA {
   getRowData(rowName: string) {
     return {
       name: rowName,
-      accession: this.MSA.gs?.AC[rowName],
-      dbxref: this.MSA.gs?.DR[rowName],
+      accession: this.MSA.gs?.AC?.[rowName],
+      dbxref: this.MSA.gs?.DR?.[rowName],
     }
   }
 
@@ -81,7 +81,7 @@ export default class StockholmMSA {
         return { id, pdb, chain, startPos, endPos }
       })
 
-    const ret = {} as Record<string, Omit<typeof args[0], 'id'>[]>
+    const ret = {} as Record<string, Omit<(typeof args)[0], 'id'>[]>
     for (const entry of args) {
       const { id, ...rest } = entry
       if (!ret[id]) {

package/src/util.ts

@@ -1,7 +1,10 @@
-import Color from 'color'
 import { HierarchyNode } from 'd3-hierarchy'
 import { max } from 'd3-array'
 import { Theme } from '@mui/material'
+import { colord, extend } from 'colord'
+import namesPlugin from 'colord/plugins/names'
+
+extend([namesPlugin])
 
 export function transform<T>(
   obj: Record<string, T>,
@@ -16,7 +19,7 @@ interface Node {
   [key: string]: unknown
 }
 
-export type NodeWithIds = {
+export interface NodeWithIds {
   id: string
   name: string
   branchset: NodeWithIds[]
@@ -24,7 +27,7 @@ export type NodeWithIds = {
   noTree?: boolean
 }
 
-export type NodeWithIdsAndLength = {
+export interface NodeWithIdsAndLength {
   id: string
   name: string
   branchset: NodeWithIdsAndLength[]
@@ -51,12 +54,12 @@ export function generateNodeIds(
 }
 
 export function colorContrast(
-  colorScheme: { [key: string]: string },
+  colorScheme: Record<string, string>,
   theme: Theme,
 ) {
   return transform(colorScheme, ([letter, color]) => [
     letter,
-    theme.palette.getContrastText(Color(color).hex()),
+    theme.palette.getContrastText(colord(color).toHex()),
   ])
 }
 

package/src/version.ts

@@ -1 +1 @@
-export const version = "2.0.0";
+export const version = '2.1.1'

package/dist/components/AboutDlg.d.ts

@@ -1,4 +0,0 @@
-export default function AboutDialog({ onClose, open, }: {
-    onClose: () => void;
-    open: boolean;
-}): JSX.Element;

package/dist/components/AboutDlg.js.map

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package/dist/components/AddTrackDlg.js.map

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package/dist/components/AnnotationDlg.js.map

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package/dist/components/DetailsDlg.d.ts

@@ -1,7 +0,0 @@
-import { MsaViewModel } from '../model';
-declare const _default: ({ model, onClose, open, }: {
-    model: MsaViewModel;
-    onClose: () => void;
-    open: boolean;
-}) => JSX.Element;
-export default _default;

package/dist/components/DetailsDlg.js.map

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package/dist/components/MoreInfoDlg.js.map

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package/dist/components/SettingsDlg.d.ts

@@ -1,7 +0,0 @@
-import { MsaViewModel } from '../model';
-declare const _default: ({ model, onClose, open, }: {
-    model: MsaViewModel;
-    onClose: () => void;
-    open: boolean;
-}) => JSX.Element;
-export default _default;

package/dist/components/SettingsDlg.js.map

@@ -1 +0,0 @@
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package/dist/components/TrackInfoDlg.js.map

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package/dist/components/TracklistDlg.d.ts

@@ -1,7 +0,0 @@
-import { MsaViewModel } from '../model';
-declare const _default: ({ model, onClose, open, }: {
-    model: MsaViewModel;
-    onClose: () => void;
-    open: boolean;
-}) => JSX.Element;
-export default _default;

package/dist/components/TracklistDlg.js.map

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