react-msaview 8.3.0 → 8.4.1

package/src/types.ts

@@ -17,6 +17,13 @@ export type TrackKind = 'text' | 'bar' | 'logo' | 'arc' | 'ruler'
  */
 export type ResidueEncoding = 'fill' | 'color'
 
+/**
+ * The residue colors: a scheme name from the built-in table, or a scale's
+ * `{map}` of letter to color, which leaves every letter it does not list
+ * uncolored
+ */
+export type ColorScheme = string | Required<Pick<ScaleSpec, 'map'>>
+
 export interface BasicTrackModel {
   id: string
   name: string
@@ -324,6 +331,26 @@ export interface Highlight {
   color?: string
 }
 
+/**
+ * A feature on one row as data, the JSON form of a GFF line: `start` and `end`
+ * are residues of `row`, 1-based and inclusive. `name` is the key the legend,
+ * the palette and the filter dialog group features by, `color` overrides the
+ * palette and any scale, and a `strand` draws the span as an arrow. Every other
+ * field is a column the `featureFill` and `featureLabel` encodings can read.
+ */
+export interface Feature {
+  row: string
+  start: number
+  end: number
+  name?: string
+  description?: string
+  /** a GFF feature type; `exon`, `CDS` and the UTRs draw as numbered segments */
+  type?: string
+  strand?: '+' | '-'
+  color?: string
+  [field: string]: string | number | undefined
+}
+
 /**
  * What the viewer draws over a clade. `highlight` fills the rows behind it,
  * across the tree and the alignment. `bracket` draws a bar and the clade's
@@ -401,6 +428,27 @@ export interface Region {
   end: number
 }
 
+/**
+ * A block of the alignment the reader selected: columns `start` to `end` of the
+ * file, 1-based and inclusive like a Highlight without a row, across the rows
+ * `rows` names, or across every row where `rows` is absent.
+ */
+export interface MsaSelection {
+  start: number
+  end: number
+  rows?: string[]
+}
+
+/**
+ * An MsaSelection resolved to what is on screen: the visible columns it covers
+ * and its rows as runs of consecutive row indices, top to bottom
+ */
+export interface ResolvedSelection {
+  startCol: number
+  endCol: number
+  rowRuns: [number, number][]
+}
+
 /**
  * A cell of the alignment in the host's coordinates, 1-based like Highlight:
  * `column` counts every column of the file, hidden gappy ones included, and
@@ -421,6 +469,16 @@ export interface Viewport {
   endColumn: number
 }
 
+/**
+ * A row table as a host passes it: fields per row name. A number or a boolean
+ * reads as its string, the way a GFF value does, and the viewer leaves out any
+ * other value. See docs/layers.md
+ */
+export type RowDataInput = Record<
+  string,
+  Record<string, string | number | boolean | null>
+>
+
 /**
  * A channel of a mark the viewer always draws. `tipLabel` colors each tip label
  * in the tree, `rowTint` washes the row across the tree gutter and the

package/src/version.ts

@@ -1 +1 @@
-export const version = '8.3.0'
+export const version = '8.4.1'

package/dist/components/header/RowSearch.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-import type { MsaViewModel } from '../../model.ts';
-declare const RowSearch: ({ model }: {
-    model: MsaViewModel;
-}) => React.JSX.Element | null;
-export default RowSearch;

package/dist/components/header/RowSearch.js

@@ -1,15 +0,0 @@
-import React from 'react';
-import { Autocomplete, TextField, createFilterOptions } from '@mui/material';
-import { observer } from 'mobx-react';
-import { findableRowNames, revealRow } from './revealRow.js';
-const filterOptions = createFilterOptions({ limit: 50 });
-const RowSearch = observer(function ({ model }) {
-    const names = findableRowNames(model);
-    return names.length > 1 ? (React.createElement(Autocomplete, { size: "small", options: names, filterOptions: filterOptions, value: null, blurOnSelect: true, onChange: (_, name) => {
-            if (name) {
-                revealRow(model, name);
-            }
-        }, style: { width: 180, margin: 'auto 8px' }, renderInput: params => (React.createElement(TextField, { ...params, placeholder: "Find row", "aria-label": "Find row" })) })) : null;
-});
-export default RowSearch;
-//# sourceMappingURL=RowSearch.js.map

package/dist/components/header/RowSearch.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"RowSearch.js","sourceRoot":"","sources":["../../../src/components/header/RowSearch.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,mBAAmB,EAAE,MAAM,eAAe,CAAA;AAC5E,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAA;AAI5D,MAAM,aAAa,GAAG,mBAAmB,CAAS,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC,CAAA;AAEhE,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,KAAK,GAAG,gBAAgB,CAAC,KAAK,CAAC,CAAA;IACrC,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACxB,oBAAC,YAAY,IACX,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,KAAK,EACd,aAAa,EAAE,aAAa,EAC5B,KAAK,EAAE,IAAI,EACX,YAAY,QACZ,QAAQ,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,EAAE;YACpB,IAAI,IAAI,EAAE,CAAC;gBACT,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;YACxB,CAAC;QACH,CAAC,EACD,KAAK,EAAE,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,UAAU,EAAE,EACzC,WAAW,EAAE,MAAM,CAAC,EAAE,CAAC,CACrB,oBAAC,SAAS,OAAK,MAAM,EAAE,WAAW,EAAC,UAAU,gBAAY,UAAU,GAAG,CACvE,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

package/dist/components/header/revealRow.d.ts

@@ -1,3 +0,0 @@
-import type { MsaViewModel } from '../../model.ts';
-export declare function findableRowNames(model: MsaViewModel): string[];
-export declare function revealRow(model: MsaViewModel, name: string): void;

package/dist/components/header/revealRow.js

@@ -1,15 +0,0 @@
-export function findableRowNames(model) {
-    const collapsed = new Set(model.collapsed);
-    return model.leaves
-        .filter(({ data: { id, name } }) => !(collapsed.has(id) && name === id))
-        .map(leaf => leaf.data.name);
-}
-export function revealRow(model, name) {
-    const index = model.rowNamesSet.get(name);
-    if (index !== undefined) {
-        const { rowHeight, msaAreaHeight } = model;
-        model.setScrollY(-(index + 0.5) * rowHeight + msaAreaHeight / 2);
-        model.setMousePos(undefined, index);
-    }
-}
-//# sourceMappingURL=revealRow.js.map

package/dist/components/header/revealRow.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"revealRow.js","sourceRoot":"","sources":["../../../src/components/header/revealRow.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,gBAAgB,CAAC,KAAmB;IAClD,MAAM,SAAS,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,CAAA;IAC1C,OAAO,KAAK,CAAC,MAAM;SAChB,MAAM,CAAC,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,IAAI,KAAK,EAAE,CAAC,CAAC;SACvE,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AAChC,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,KAAmB,EAAE,IAAY;IACzD,MAAM,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IACzC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;QACxB,MAAM,EAAE,SAAS,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;QAC1C,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,GAAG,SAAS,GAAG,aAAa,GAAG,CAAC,CAAC,CAAA;QAChE,KAAK,CAAC,WAAW,CAAC,SAAS,EAAE,KAAK,CAAC,CAAA;IACrC,CAAC;AACH,CAAC"}

package/src/components/header/RowSearch.tsx

@@ -1,34 +0,0 @@
-import React from 'react'
-
-import { Autocomplete, TextField, createFilterOptions } from '@mui/material'
-import { observer } from 'mobx-react'
-
-import { findableRowNames, revealRow } from './revealRow.ts'
-
-import type { MsaViewModel } from '../../model.ts'
-
-const filterOptions = createFilterOptions<string>({ limit: 50 })
-
-const RowSearch = observer(function ({ model }: { model: MsaViewModel }) {
-  const names = findableRowNames(model)
-  return names.length > 1 ? (
-    <Autocomplete
-      size="small"
-      options={names}
-      filterOptions={filterOptions}
-      value={null}
-      blurOnSelect
-      onChange={(_, name) => {
-        if (name) {
-          revealRow(model, name)
-        }
-      }}
-      style={{ width: 180, margin: 'auto 8px' }}
-      renderInput={params => (
-        <TextField {...params} placeholder="Find row" aria-label="Find row" />
-      )}
-    />
-  ) : null
-})
-
-export default RowSearch

package/src/components/header/revealRow.ts

@@ -1,17 +0,0 @@
-import type { MsaViewModel } from '../../model.ts'
-
-export function findableRowNames(model: MsaViewModel) {
-  const collapsed = new Set(model.collapsed)
-  return model.leaves
-    .filter(({ data: { id, name } }) => !(collapsed.has(id) && name === id))
-    .map(leaf => leaf.data.name)
-}
-
-export function revealRow(model: MsaViewModel, name: string) {
-  const index = model.rowNamesSet.get(name)
-  if (index !== undefined) {
-    const { rowHeight, msaAreaHeight } = model
-    model.setScrollY(-(index + 0.5) * rowHeight + msaAreaHeight / 2)
-    model.setMousePos(undefined, index)
-  }
-}