react-msaview 7.0.0 → 8.1.0

package/src/index.ts

@@ -15,23 +15,32 @@ export {
   CHAR_WIDTH_RATIO,
   installHeadlessRenderEnv,
 } from './headlessRenderEnv.ts'
-// the row count past which calculateNeighborJoiningTreeFromMSA refuses, so a
-// host can gate its own menu item on the same number instead of offering a
-// button that throws
+// the row count above which calculateNeighborJoiningTreeFromMSA throws, for
+// hosts gating their own menu item
 export { maxNeighborJoiningRows } from './constants.ts'
 export { default as MSAView } from './components/Loading.tsx'
 export { default as MSAViewer } from './components/MSAViewer.tsx'
+export type { MSAViewerProps } from './components/MSAViewer.tsx'
+export { mount } from './mount.tsx'
+export { defineMsaElement } from './element.ts'
+export { useMsaSvgFigure } from './useMsaSvgFigure.ts'
+export type { MsaSvgFigure } from './useMsaSvgFigure.ts'
+export type { MountedViewer } from './mount.tsx'
 export { type MsaViewModel, default as MSAModelF } from './model.ts'
 export type { MSAFormat, MSAParserType } from 'msa-parsers'
 export type { HierarchyNode } from './hierarchy.ts'
 // InterProScanResults is the EBI wire format that setDomains still accepts;
 // Annotation is the source-agnostic shape everything else is written against
 export type { InterProScanResults } from 'msa-parsers'
-// ColumnCounts, DomainBand and TidyDomainAnnotation surface in the inferred type
-// of the composed state model, so a downstream plugin cannot emit declarations
-// for its own stateModelFactory without being able to name them (TS2883).
-// jbrowse-plugin-msaview already re-exports MSAFormat for exactly this reason.
+// ColumnCounts, ColumnStats, DomainBand and TidyDomainAnnotation surface in the
+// inferred type of the composed state model, so a downstream plugin cannot emit
+// declarations for its own stateModelFactory without being able to name them
+// (TS2883). jbrowse-plugin-msaview already re-exports MSAFormat for exactly this
+// reason.
 export type { ColumnCounts } from './columnCounts.ts'
+export type { ColumnStats } from './columnStats.ts'
+// the scale an encoding reads its field through, and what resolving one gives
+export type { ResolvedScale, ScaleSpec } from './scales.ts'
 export type {
   Accession,
   Annotation,
@@ -40,20 +49,35 @@ export type {
   ArcTrackModel,
   BasicTrack,
   BasicTrackModel,
+  Cell,
+  Clade,
+  CladeMark,
   ColumnTrackSpec,
   DomainBand,
+  Encoding,
+  EncodingChannel,
   Highlight,
+  Legend,
+  LegendEntry,
   Node,
   MappedStructure,
   NodeWithIds,
   NodeWithIdsAndLength,
+  Region,
+  ResidueEncoding,
   ResidueMapping,
   ResidueMappingProblem,
   ResidueSegment,
+  ResolvedClade,
+  ResolvedEncoding,
   ResolvedHighlight,
+  ResolvedRowPanel,
+  RowPanelSpec,
   RowResidue,
   StructureResidue,
   TextTrackModel,
   TidyDomainAnnotation,
+  TrackKind,
   UnshareableData,
+  Viewport,
 } from './types.ts'

package/src/model/DataModel.ts

@@ -56,11 +56,8 @@ export function DataModelF() {
       },
     }))
     .postProcessSnapshot(snap =>
-      // a large document is dropped from the snapshot rather than inlined
-      // into a session or a shared URL, and every field here holds one, so
-      // the rule is the same for all of them. The parent model's
-      // `unshareableData` reports what this drops, since dropping it silently
-      // is how a copied link comes to open an empty viewer
+      // drops any field over maxInlineSnapshotBytes; the parent model's
+      // `unshareableData` reports what was dropped
       Object.fromEntries(
         Object.entries(snap).map(([key, text]) => [
           key,

package/src/model/msaModel.ts

@@ -31,8 +31,9 @@ export function MSAModelF() {
 
       /**
        * #property
-       * show a per-column statistics tooltip (consensus, conservation, gaps,
-       * residue distribution) while hovering the alignment
+       * show a tooltip with the hovered column's value for a track while
+       * hovering that track: the conservation scores, the logo's composition,
+       * an arc's partner columns
        */
       showColumnStats: stripDefault(types.boolean, defaultShowColumnStats),
 

package/src/model/treeModel.ts

@@ -3,9 +3,12 @@ import { types } from '@jbrowse/mobx-state-tree'
 import {
   defaultDrawLabels,
   defaultDrawNodeBubbles,
+  defaultDrawNodeLabels,
   defaultDrawTree,
   defaultLabelsAlignRight,
+  defaultOverviewHeight,
   defaultShowBranchLen,
+  defaultShowTreeOverview,
   defaultTreeAreaWidth,
   defaultTreeWidth,
 } from '../constants.ts'
@@ -60,6 +63,26 @@ export function TreeModelF() {
        */
       drawNodeBubbles: stripDefault(types.boolean, defaultDrawNodeBubbles),
 
+      /**
+       * #property
+       * draw the label a newick file gives an internal node, which is where a
+       * bootstrap or posterior support value lands
+       */
+      drawNodeLabels: stripDefault(types.boolean, defaultDrawNodeLabels),
+
+      /**
+       * #property
+       * draw the whole tree small above the tree panel, with the focused
+       * subtree boxed. A click on it focuses the subtree under the pointer
+       */
+      showTreeOverview: stripDefault(types.boolean, defaultShowTreeOverview),
+
+      /**
+       * #property
+       * height of the tree overview band, px
+       */
+      overviewHeight: stripDefault(types.number, defaultOverviewHeight),
+
       /**
        * #property
        * auto-size treeAreaWidth to fit the row labels (plus the tree, if drawn)
@@ -116,6 +139,25 @@ export function TreeModelF() {
       setDrawNodeBubbles(arg: boolean) {
         self.drawNodeBubbles = arg
       },
+      /**
+       * #action
+       */
+      setDrawNodeLabels(arg: boolean) {
+        self.drawNodeLabels = arg
+      },
+      /**
+       * #action
+       */
+      setShowTreeOverview(arg: boolean) {
+        self.showTreeOverview = arg
+      },
+      /**
+       * #action
+       * set the height of the tree overview band (px)
+       */
+      setOverviewHeight(n: number) {
+        self.overviewHeight = Math.round(n)
+      },
       /**
        * #action
        */