react-msaview 6.5.0 → 8.0.0

package/dist/hierarchy.js

@@ -1,14 +1,9 @@
 import { descendants, find, forEachDescendant, forEachLink, hierarchy as coreHierarchy, leaves, links, sort, sum, } from '@gmod/newick';
-// The generic traversals live in @gmod/newick now, shared with the tree sidebar
-// in jbrowse-components. They are iterative there for the reason they were here:
-// a phylogenetic tree can be a caterpillar, whose depth equals its leaf count,
-// and the recursive form overflows the stack somewhere past 5000 tips.
+// The @gmod/newick traversals are iterative: a caterpillar tree's depth equals
+// its leaf count, and recursion overflows the stack past about 5000 tips.
 export { descendants, find, forEachDescendant, forEachLink, leaves, links, sort, sum, };
-// coreHierarchy builds base nodes, and the layout fields above are written onto
-// them afterwards by this package. Every one of those fields is optional, so the
-// two node types are mutually assignable and this needs no cast -- it exists
-// only to declare the wider return type, which is what lets those later
-// assignments typecheck.
+// declares the wider return type so the layout code can assign the optional
+// fields above onto coreHierarchy's nodes
 export function hierarchy(data, childrenAccessor) {
     return coreHierarchy(data, childrenAccessor);
 }
@@ -20,16 +15,27 @@ export function clusterLayout(root, sizeX, sizeY) {
         leafNodes[i].x = (i + 0.5) * step;
     }
     // x of an internal node is the mean of its children's x, so process in
-    // post-order (children before parents)
+    // post-order (children before parents). The subtree span comes from the same
+    // pass, for the block culls in the tree renderer.
     const nodes = descendants(root);
     for (let i = nodes.length - 1; i >= 0; i--) {
         const node = nodes[i];
         if (node.children) {
             let sum = 0;
+            let min = Infinity;
+            let max = -Infinity;
             for (const child of node.children) {
                 sum += child.x;
+                min = Math.min(min, child.xMin);
+                max = Math.max(max, child.xMax);
             }
             node.x = sum / node.children.length;
+            node.xMin = min;
+            node.xMax = max;
+        }
+        else {
+            node.xMin = node.x;
+            node.xMax = node.x;
         }
     }
     const rootHeight = root.height;
@@ -111,14 +117,9 @@ export function calcDepthToLeaf(node) {
     }
     return node.depthToLeaf;
 }
-export function findMaxBranchLen(node) {
-    let maxLen = 0;
-    for (const n of descendants(node)) {
-        maxLen = Math.max(maxLen, n.len || 0);
-    }
-    return maxLen;
-}
-// Max root-to-leaf sum of branch lengths within the subtree at d
+// Max root-to-leaf sum of branch lengths within the subtree at d. Negative
+// lengths are floored at zero, the same as setBrLength does when it lays the
+// tree out, so the extent this reports is the one that gets drawn
 export function maxLength(d) {
     const nodes = descendants(d);
     const pathLen = new Map();
@@ -130,7 +131,7 @@ export function maxLength(d) {
                 childMax = Math.max(childMax, pathLen.get(child));
             }
         }
-        pathLen.set(n, (n.data.length || 0) + childMax);
+        pathLen.set(n, Math.max(n.data.length || 0, 0) + childMax);
     }
     return pathLen.get(d);
 }
@@ -147,4 +148,66 @@ export function setBrLength(d, y0, k) {
         }
     }
 }
+/**
+ * Every leaf by name, with a name two leaves share mapping to undefined: a tip
+ * set naming it cannot say which tip it means.
+ */
+export function leafIndex(root) {
+    const index = new Map();
+    for (const leaf of leaves(root)) {
+        const { name } = leaf.data;
+        index.set(name, index.has(name) ? undefined : leaf);
+    }
+    return index;
+}
+/**
+ * The most recent common ancestor of a set of tip names, or undefined when a
+ * name is not a tip of this tree or names two of them.
+ *
+ * Each name lifts through `parent` to the ancestor the names before it share,
+ * so the walk holds two nodes. Recording a root-to-tip path per name instead
+ * costs the depth in memory per name, and a caterpillar tree's depth is its tip
+ * count. `index` is `leafIndex(root)`, which a caller resolving several tip
+ * sets against one tree builds once.
+ */
+export function mrca(root, names, index = leafIndex(root)) {
+    let node;
+    for (const name of names) {
+        let other = index.get(name);
+        if (!other) {
+            return undefined;
+        }
+        if (!node) {
+            node = other;
+            continue;
+        }
+        while (node.depth > other.depth) {
+            node = node.parent;
+        }
+        while (other.depth > node.depth) {
+            other = other.parent;
+        }
+        while (node !== other) {
+            node = node.parent;
+            other = other.parent;
+        }
+    }
+    return node;
+}
+/**
+ * The deepest node whose subtree covers a run of rows, given in the row-space
+ * coordinates clusterLayout writes to xMin/xMax. A subtree's leaves are one
+ * contiguous run, so at most one child per level covers the run and the descent
+ * visits the tree's depth rather than its nodes.
+ */
+export function nodeCoveringRows(root, top, bottom) {
+    let node = root;
+    for (;;) {
+        const child = node.children?.find(c => c.xMin <= top && c.xMax >= bottom);
+        if (!child) {
+            return node;
+        }
+        node = child;
+    }
+}
 //# sourceMappingURL=hierarchy.js.map

package/dist/hierarchy.js.map

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package/dist/index.d.ts

@@ -1,11 +1,20 @@
 export { renderToSvg } from './renderToSvg.tsx';
 export type { ExportSvgOptions } from './renderToSvg.tsx';
 export { CHAR_WIDTH_RATIO, installHeadlessRenderEnv, } from './headlessRenderEnv.ts';
+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';
 export type { InterProScanResults } from 'msa-parsers';
 export type { ColumnCounts } from './columnCounts.ts';
-export type { Accession, Annotation, BasicTrack, BasicTrackModel, ColumnTrackSpec, DomainBand, Highlight, Node, NodeWithIds, NodeWithIdsAndLength, ResolvedHighlight, TextTrackModel, TidyDomainAnnotation, } from './types.ts';
+export type { ColumnStats } from './columnStats.ts';
+export type { ResolvedScale, ScaleSpec } from './scales.ts';
+export type { Accession, Annotation, Arc, ArcSpec, 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/dist/index.js

@@ -1,15 +1,23 @@
 // PUBLIC API — consumed by external JBrowse 2 plugins. Changing or removing any
 // export here is a breaking change for downstream repos:
-//   - jbrowse-plugin-msaview   (wraps MSAModelF + MSAView into a JBrowse view)
-//   - jbrowse-plugin-protein3d (drives MSA<->structure hover/highlight sync)
+//   - jbrowse-plugin-msaview (wraps MSAModelF + MSAView into a JBrowse view)
+//   - jbrowse-plugin-tview   (the same, for a tree-first view)
 // Those plugins also reach into the MsaViewModel instance at runtime; the model
 // members they rely on (e.g. mouseCol/setMousePos, setHighlightedColumns,
 // seqPosToVisibleCol/visibleColToSeqPos) are flagged inline in model.ts.
+// jbrowse-plugin-protein3d no longer depends on this package at all: it reads
+// the msaview plugin's model through a structural type of its own.
 export { renderToSvg } from './renderToSvg.js';
 // renderToSvg outside a browser needs DOM bits jsdom omits; react-msaview-cli
 // and the README figure generator both drive it that way
 export { CHAR_WIDTH_RATIO, installHeadlessRenderEnv, } from './headlessRenderEnv.js';
+// the row count above which calculateNeighborJoiningTreeFromMSA throws, for
+// hosts gating their own menu item
+export { maxNeighborJoiningRows } from './constants.js';
 export { default as MSAView } from './components/Loading.js';
 export { default as MSAViewer } from './components/MSAViewer.js';
+export { mount } from './mount.js';
+export { defineMsaElement } from './element.js';
+export { useMsaSvgFigure } from './useMsaSvgFigure.js';
 export { default as MSAModelF } from './model.js';
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,gFAAgF;AAChF,yDAAyD;AACzD,6EAA6E;AAC7E,+DAA+D;AAC/D,gFAAgF;AAChF,0EAA0E;AAC1E,yEAAyE;AACzE,8EAA8E;AAC9E,mEAAmE;AACnE,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAmB,CAAA;AAE/C,8EAA8E;AAC9E,yDAAyD;AACzD,OAAO,EACL,gBAAgB,EAChB,wBAAwB,GACzB,MAAM,wBAAwB,CAAA;AAC/B,4EAA4E;AAC5E,mCAAmC;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAA;AACvD,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,2BAA4B,CAAA;AAEjE,OAAO,EAAE,KAAK,EAAE,MAAM,YAAa,CAAA;AACnC,OAAO,EAAE,gBAAgB,EAAE,MAAM,cAAc,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AAGtD,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}

package/dist/model/DataModel.js

@@ -1,4 +1,5 @@
 import { types } from '@jbrowse/mobx-state-tree';
+import { maxInlineSnapshotBytes } from '../constants.js';
 /**
  * #stateModel DataModel
  * the data stored for the model. this is sometimes temporary in the case that
@@ -53,12 +54,11 @@ 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
+    // drops any field over maxInlineSnapshotBytes; the parent model's
+    // `unshareableData` reports what was dropped
     Object.fromEntries(Object.entries(snap).map(([key, text]) => [
         key,
-        text && text.length > 50_000 ? undefined : text,
+        text && text.length > maxInlineSnapshotBytes ? undefined : text,
     ])));
 }
 //# sourceMappingURL=DataModel.js.map

package/dist/model/DataModel.js.map

@@ -1 +1 @@
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package/dist/model/msaModel.d.ts

@@ -15,8 +15,9 @@ export declare function MSAModelF(): import("@jbrowse/mobx-state-tree").IModelTy
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     /**
      * #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: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     /**

package/dist/model/msaModel.js

@@ -20,8 +20,9 @@ export function MSAModelF() {
         colorSchemeName: stripDefault(types.string, defaultColorSchemeName),
         /**
          * #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/dist/model/msaModel.js.map

@@ -1 +1 @@
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package/dist/model/treeModel.d.ts

@@ -39,6 +39,23 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * draw node bubbles on the tree; the branches stay clickable either way
      */
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * draw the label a newick file gives an internal node, which is where a
+     * bootstrap or posterior support value lands
+     */
+    drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #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: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * height of the tree overview band, px
+     */
+    overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     /**
      * #property
      * auto-size treeAreaWidth to fit the row labels (plus the tree, if drawn)
@@ -77,6 +94,19 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setDrawNodeBubbles(arg: boolean): void;
+    /**
+     * #action
+     */
+    setDrawNodeLabels(arg: boolean): void;
+    /**
+     * #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

@@ -1,5 +1,5 @@
 import { types } from '@jbrowse/mobx-state-tree';
-import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawTree, defaultLabelsAlignRight, defaultShowBranchLen, defaultTreeAreaWidth, defaultTreeWidth, } from '../constants.js';
+import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultShowTreeOverview, defaultTreeAreaWidth, defaultTreeWidth, } from '../constants.js';
 import { stripDefault } from '../stripDefault.js';
 /**
  * #stateModel Tree
@@ -44,6 +44,23 @@ export function TreeModelF() {
          * draw node bubbles on the tree; the branches stay clickable either way
          */
         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)
@@ -97,6 +114,25 @@ export function TreeModelF() {
         setDrawNodeBubbles(arg) {
             self.drawNodeBubbles = arg;
         },
+        /**
+         * #action
+         */
+        setDrawNodeLabels(arg) {
+            self.drawNodeLabels = arg;
+        },
+        /**
+         * #action
+         */
+        setShowTreeOverview(arg) {
+            self.showTreeOverview = arg;
+        },
+        /**
+         * #action
+         * set the height of the tree overview band (px)
+         */
+        setOverviewHeight(n) {
+            self.overviewHeight = Math.round(n);
+        },
         /**
          * #action
          */

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