react-msaview 9.0.0 → 9.1.0

package/dist/model/treeModel.d.ts

@@ -108,11 +108,6 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setShowTreeOverview(arg: boolean): void;
-    /**
-     * #action
-     * set the height of the tree overview band (px)
-     */
-    setOverviewHeight(n: number): void;
     /**
      * #action
      */

package/dist/model/treeModel.js

@@ -132,13 +132,6 @@ export function TreeModelF() {
         setShowTreeOverview(arg) {
             self.showTreeOverview = arg;
         },
-        /**
-         * #action
-         * set the height of the tree overview band (px)
-         */
-        setOverviewHeight(n) {
-            self.overviewHeight = Math.round(n);
-        },
         /**
          * #action
          */

package/dist/model/treeModel.js.map

@@ -1 +1 @@
-{"version":3,"file":"treeModel.js","sourceRoot":"","sources":["../../src/model/treeModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EACL,iBAAiB,EACjB,sBAAsB,EACtB,qBAAqB,EACrB,eAAe,EACf,uBAAuB,EACvB,qBAAqB,EACrB,oBAAoB,EACpB,gBAAgB,EAChB,uBAAuB,EACvB,UAAU,GACX,MAAM,iBAAiB,CAAA;AACxB,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AAIjD;;GAEG;AACH,MAAM,UAAU,UAAU;IACxB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,UAAU,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,iBAAiB,CAAC;QAC1D;;;WAGG;QACH,gBAAgB,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,uBAAuB,CAAC;QAEtE;;;;;WAKG;QACH,aAAa,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAExC;;;;;WAKG;QACH,SAAS,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAEpC;;;;;WAKG;QACH,aAAa,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,oBAAoB,CAAC;QAEhE;;;;;WAKG;QACH,SAAS,EAAE,YAAY,CACrB,KAAK,CAAC,WAAW,CAAY,WAAW,EAAE,CAAC,GAAG,UAAU,CAAC,CAAC,EAC1D,gBAAgB,CACjB;QAED;;;WAGG;QACH,QAAQ,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,eAAe,CAAC;QAEtD;;;WAGG;QACH,eAAe,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,sBAAsB,CAAC;QAEpE;;;;WAIG;QACH,cAAc,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,qBAAqB,CAAC;QAElE;;;;WAIG;QACH,gBAAgB,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,uBAAuB,CAAC;QAEtE;;;WAGG;QACH,cAAc,EAAE,YAAY,CAAC,KAAK,CAAC,MAAM,EAAE,qBAAqB,CAAC;KAClE,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;;;WAIG;QACH,gBAAgB,CAAC,CAAqB;YACpC,IAAI,CAAC,aAAa,GAAG,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChE,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;QAC5B,CAAC;QACD;;;;WAIG;QACH,YAAY,CAAC,CAAqB;YAChC,IAAI,CAAC,SAAS,GAAG,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAC9D,CAAC;QAED;;WAEG;QACH,mBAAmB,CAAC,GAAY;YAC9B,IAAI,CAAC,gBAAgB,GAAG,GAAG,CAAA;QAC7B,CAAC;QACD;;WAEG;QACH,WAAW,CAAC,GAAY;YACtB,IAAI,CAAC,QAAQ,GAAG,GAAG,CAAA;QACrB,CAAC;QAED;;WAEG;QACH,gBAAgB,CAAC,GAAY;YAC3B,IAAI,CAAC,aAAa,GAAG,GAAG,CAAA;QAC1B,CAAC;QAED;;WAEG;QACH,YAAY,CAAC,KAAgB;YAC3B,IAAI,CAAC,SAAS,GAAG,KAAK,CAAA;QACxB,CAAC;QAED;;WAEG;QACH,kBAAkB,CAAC,GAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,GAAG,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,GAAY;YAC5B,IAAI,CAAC,cAAc,GAAG,GAAG,CAAA;QAC3B,CAAC;QACD;;WAEG;QACH,mBAAmB,CAAC,GAAY;YAC9B,IAAI,CAAC,gBAAgB,GAAG,GAAG,CAAA;QAC7B,CAAC;QACD;;;WAGG;QACH,iBAAiB,CAAC,CAAS;YACzB,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QACrC,CAAC;QACD;;WAEG;QACH,aAAa,CAAC,GAAY;YACxB,IAAI,CAAC,UAAU,GAAG,GAAG,CAAA;QACvB,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
+{"version":3,"file":"treeModel.js","sourceRoot":"","sources":["../../src/model/treeModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EACL,iBAAiB,EACjB,sBAAsB,EACtB,qBAAqB,EACrB,eAAe,EACf,uBAAuB,EACvB,qBAAqB,EACrB,oBAAoB,EACpB,gBAAgB,EAChB,uBAAuB,EACvB,UAAU,GACX,MAAM,iBAAiB,CAAA;AACxB,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AAIjD;;GAEG;AACH,MAAM,UAAU,UAAU;IACxB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,UAAU,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,iBAAiB,CAAC;QAC1D;;;WAGG;QACH,gBAAgB,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,uBAAuB,CAAC;QAEtE;;;;;WAKG;QACH,aAAa,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAExC;;;;;WAKG;QACH,SAAS,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAEpC;;;;;WAKG;QACH,aAAa,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,oBAAoB,CAAC;QAEhE;;;;;WAKG;QACH,SAAS,EAAE,YAAY,CACrB,KAAK,CAAC,WAAW,CAAY,WAAW,EAAE,CAAC,GAAG,UAAU,CAAC,CAAC,EAC1D,gBAAgB,CACjB;QAED;;;WAGG;QACH,QAAQ,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,eAAe,CAAC;QAEtD;;;WAGG;QACH,eAAe,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,sBAAsB,CAAC;QAEpE;;;;WAIG;QACH,cAAc,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,qBAAqB,CAAC;QAElE;;;;WAIG;QACH,gBAAgB,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,uBAAuB,CAAC;QAEtE;;;WAGG;QACH,cAAc,EAAE,YAAY,CAAC,KAAK,CAAC,MAAM,EAAE,qBAAqB,CAAC;KAClE,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;;;WAIG;QACH,gBAAgB,CAAC,CAAqB;YACpC,IAAI,CAAC,aAAa,GAAG,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChE,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;QAC5B,CAAC;QACD;;;;WAIG;QACH,YAAY,CAAC,CAAqB;YAChC,IAAI,CAAC,SAAS,GAAG,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAC9D,CAAC;QAED;;WAEG;QACH,mBAAmB,CAAC,GAAY;YAC9B,IAAI,CAAC,gBAAgB,GAAG,GAAG,CAAA;QAC7B,CAAC;QACD;;WAEG;QACH,WAAW,CAAC,GAAY;YACtB,IAAI,CAAC,QAAQ,GAAG,GAAG,CAAA;QACrB,CAAC;QAED;;WAEG;QACH,gBAAgB,CAAC,GAAY;YAC3B,IAAI,CAAC,aAAa,GAAG,GAAG,CAAA;QAC1B,CAAC;QAED;;WAEG;QACH,YAAY,CAAC,KAAgB;YAC3B,IAAI,CAAC,SAAS,GAAG,KAAK,CAAA;QACxB,CAAC;QAED;;WAEG;QACH,kBAAkB,CAAC,GAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,GAAG,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,GAAY;YAC5B,IAAI,CAAC,cAAc,GAAG,GAAG,CAAA;QAC3B,CAAC;QACD;;WAEG;QACH,mBAAmB,CAAC,GAAY;YAC9B,IAAI,CAAC,gBAAgB,GAAG,GAAG,CAAA;QAC7B,CAAC;QACD;;WAEG;QACH,aAAa,CAAC,GAAY;YACxB,IAAI,CAAC,UAAU,GAAG,GAAG,CAAA;QACvB,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}

package/dist/model.d.ts

@@ -5,7 +5,6 @@ import type { ExportSvgOptions } from './renderToSvg.tsx';
 import type { Annotation, Arc, BasicTrack, Cell, Clade, ResidueMappingProblem, ColumnTrackSpec, DomainBand, Encoding, Feature, Highlight, Legend, MsaSelection, NodeWithIds, Region, ResidueMapping, ResolvedClade, ResolvedEncoding, ResolvedFeaturePanel, ResolvedHighlight, ResolvedSelection, TreeOrder, TreeRoot, ResolvedRowPanel, ResolvedStripPanel, RowDataInput, RowPanelSpec, RowResidue, StructureResidue, TrackKind, UnshareableData, Viewport } from './types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
-import type { InterProScanResults } from 'msa-parsers';
 export declare const defaultTrackHeights: Partial<Record<TrackKind, number>>;
 type StripPanelScale = Omit<ResolvedStripPanel, 'id' | 'width' | 'offsetX'>;
 type FeaturePanelScale = Omit<ResolvedFeaturePanel, 'id' | 'width' | 'offsetX' | 'spans'>;
@@ -602,9 +601,10 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     /**
      * #property
      * where the view opens, in `highlights` coordinates: `{row, start,
-     * end}` zooms onto residues of that row, `{start, end}` onto alignment
-     * columns. Applied once the alignment and any tree file have loaded,
-     * then cleared, so a reloaded session keeps the reader's own scroll.
+     * end}` zooms onto residues of that row and scrolls the row to the
+     * middle, `{start, end}` zooms onto alignment columns. Applied once the
+     * alignment and any tree file have loaded, then cleared, so a reloaded
+     * session keeps the reader's own scroll.
      */
     region: import("@jbrowse/mobx-state-tree").IType<Region | undefined, Region | undefined, Region | undefined>;
     /**
@@ -651,7 +651,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
-    setOverviewHeight(n: number): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -670,6 +669,12 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * of the snapshot so a link opened in the full app shows the toolbar.
      */
     hideHeader: boolean;
+    /**
+     * #volatile
+     * shows the import form while the view has no data. MSAViewer turns it
+     * off, since its host supplies the data and the form is the demo app's
+     */
+    importForm: boolean;
     /**
      * #volatile
      */
@@ -1012,13 +1017,11 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
 } & {
     /**
      * #getter
-     * hideGaps takes effect when there are collapsed rows or allowedGappyness < 100
+     * hideGaps takes effect when a collapse or a focus hides rows, whose
+     * residues leave columns all gaps among the rest, or when
+     * allowedGappyness is under 100
      */
     readonly hideGapsEffective: boolean;
-    /**
-     * #getter
-     */
-    readonly realAllowedGappyness: number;
     /**
      * #getter
      * the annotations the overlay, the legend and the encodings draw: the
@@ -1258,7 +1261,7 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * any band size.
      */
     readonly treeOverviewLayout: {
-        root: HierarchyNode<NodeWithIds>;
+        root: import("./hierarchy.ts").LaidOutNode<NodeWithIds>;
         numTips: number;
         maxDepthToLeaf: number;
         showBranchLen: boolean;
@@ -1340,11 +1343,17 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * lazily per row and cached on the parse.
      */
     seqPosIndex(rowName: string): Int32Array | undefined;
+    /**
+     * #method
+     * the row's aligned sequence by the name the tree gives it, including
+     * rows a collapsed clade hides. `MSA.getRow` resolves a FASTA name whose
+     * colon a Newick tool wrote as an underscore, which `rowMap` does not
+     */
+    rowSequence(name: string): string | undefined;
     /**
      * #getter
-     * every sequence in the alignment, keyed by row name, including rows a
-     * collapsed clade hides. `rows` holds only the rows on screen; lookups
-     * by row name use this
+     * every sequence in the alignment, keyed by the alignment's own row
+     * names, including rows a collapsed clade hides
      */
     readonly rowMap: Map<string, string>;
     /**
@@ -1437,12 +1446,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * the tree's own units
      */
     readonly rootToTipLength: number;
-    /**
-     * #getter
-     * x-position of the farthest tip in a phylogram, px: effectiveTreeWidth,
-     * or 0 for a tree with no branch lengths (drawn as a cladogram)
-     */
-    readonly maxBranchLength: number;
     /**
      * #getter
      * pixels per unit of branch length in the phylogram layout, 0 in
@@ -1831,7 +1834,9 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #action
      * swap in a different tree over the same alignment. Clears `collapsed`,
      * `rotated` and `showOnly`, since path-derived node ids (node-0-0-1) from the old
-     * tree would match unrelated nodes in the new one.
+     * tree would match unrelated nodes in the new one, and the tree's
+     * filehandle, which the snapshot would otherwise reopen in place of
+     * the new tree
      */
     replaceTree(newick: string): void;
     /**
@@ -1844,22 +1849,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * zoom by `scaleFactor` about the center of the alignment area
      */
     zoomAtCenter(scaleFactor: number, axis?: ScrollZoomAxis): void;
-    /**
-     * #action
-     */
-    zoomOutHorizontal(): void;
-    /**
-     * #action
-     */
-    zoomInHorizontal(): void;
-    /**
-     * #action
-     */
-    zoomInVertical(): void;
-    /**
-     * #action
-     */
-    zoomOutVertical(): void;
     /**
      * #action
      */
@@ -1898,13 +1887,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * GFF and must keep a hidden overlay hidden.
      */
     setAnnotations(annotations: Annotation[]): void;
-    /**
-     * #action
-     * set the overlay from raw InterProScan results keyed by row name. Kept
-     * for downstream plugins that hold the EBI wire format; new code should
-     * adapt to Annotation[] and call setAnnotations.
-     */
-    setDomains(data?: Record<string, InterProScanResults>): void;
     applyGFFText(gffText: string): void;
     /**
      * #action
@@ -2226,6 +2208,10 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #action
      */
     setHideHeader(arg: boolean): void;
+    /**
+     * #action
+     */
+    setImportForm(arg: boolean): void;
     /**
      * #action
      * focus the subtree a click `y` pixels down the tree overview lands on.
@@ -2275,6 +2261,14 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * its width, or for a span that resolves to no visible column.
      */
     zoomToRegion(region: Region): void;
+    /**
+     * #action
+     * zoomToRegion, and for a region naming a row, also scroll that row to
+     * the middle of the alignment, as Go to does. What `region` opens on; a
+     * caller following a range as it moves wants zoomToRegion alone, which
+     * leaves the reader's vertical scroll where they put it.
+     */
+    revealRegion(region: Region): void;
     /**
      * #action
      * zoom and scroll so the selected columns fill the alignment's width,