react-msaview 8.4.0 → 9.0.0

package/dist/components/tree/renderTreeCanvas.js.map

@@ -1 +1 @@
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package/dist/components/tree/renderTreeMouseover.js

@@ -1,6 +1,6 @@
 import { treeHoverColor } from '../overlayColors.js';
 export function renderTreeMouseover({ ctx, model, }) {
-    const { rowHeight, treeAreaWidth: width, height, scrollY, mouseRow, referenceRowIndex, hoveredRowIndices, highResScaleFactor, } = model;
+    const { rowHeight, effectiveTreeAreaWidth: width, height, scrollY, mouseRow, referenceRowIndex, hoveredRowIndices, highResScaleFactor, } = model;
     ctx.resetTransform();
     ctx.clearRect(0, 0, width * highResScaleFactor, height * highResScaleFactor);
     ctx.scale(highResScaleFactor, highResScaleFactor);

package/dist/components/tree/renderTreeMouseover.js.map

@@ -1 +1 @@
-{"version":3,"file":"renderTreeMouseover.js","sourceRoot":"","sources":["../../../src/components/tree/renderTreeMouseover.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AAIpD,MAAM,UAAU,mBAAmB,CAAC,EAClC,GAAG,EACH,KAAK,GAIN;IACC,MAAM,EACJ,SAAS,EACT,aAAa,EAAE,KAAK,EACpB,MAAM,EACN,OAAO,EACP,QAAQ,EACR,iBAAiB,EACjB,iBAAiB,EACjB,kBAAkB,GACnB,GAAG,KAAK,CAAA;IACT,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,GAAG,kBAAkB,EAAE,MAAM,GAAG,kBAAkB,CAAC,CAAA;IAC5E,GAAG,CAAC,KAAK,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAA;IAEjD,MAAM,OAAO,GAAG,CAAC,KAAa,EAAE,EAAE;QAChC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,GAAG,SAAS,GAAG,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;IAChE,CAAC,CAAA;IAED,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;IAC9B,KAAK,MAAM,KAAK,IAAI,iBAAiB,EAAE,CAAC;QACtC,OAAO,CAAC,KAAK,CAAC,CAAA;IAChB,CAAC;IACD,IACE,QAAQ,KAAK,SAAS;QACtB,QAAQ,KAAK,iBAAiB;QAC9B,CAAC,iBAAiB,CAAC,QAAQ,CAAC,QAAQ,CAAC,EACrC,CAAC;QACD,OAAO,CAAC,QAAQ,CAAC,CAAA;IACnB,CAAC;AACH,CAAC"}
+{"version":3,"file":"renderTreeMouseover.js","sourceRoot":"","sources":["../../../src/components/tree/renderTreeMouseover.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AAIpD,MAAM,UAAU,mBAAmB,CAAC,EAClC,GAAG,EACH,KAAK,GAIN;IACC,MAAM,EACJ,SAAS,EACT,sBAAsB,EAAE,KAAK,EAC7B,MAAM,EACN,OAAO,EACP,QAAQ,EACR,iBAAiB,EACjB,iBAAiB,EACjB,kBAAkB,GACnB,GAAG,KAAK,CAAA;IACT,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,GAAG,kBAAkB,EAAE,MAAM,GAAG,kBAAkB,CAAC,CAAA;IAC5E,GAAG,CAAC,KAAK,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAA;IAEjD,MAAM,OAAO,GAAG,CAAC,KAAa,EAAE,EAAE;QAChC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,GAAG,SAAS,GAAG,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;IAChE,CAAC,CAAA;IAED,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;IAC9B,KAAK,MAAM,KAAK,IAAI,iBAAiB,EAAE,CAAC;QACtC,OAAO,CAAC,KAAK,CAAC,CAAA;IAChB,CAAC;IACD,IACE,QAAQ,KAAK,SAAS;QACtB,QAAQ,KAAK,iBAAiB;QAC9B,CAAC,iBAAiB,CAAC,QAAQ,CAAC,QAAQ,CAAC,EACrC,CAAC;QACD,OAAO,CAAC,QAAQ,CAAC,CAAA;IACnB,CAAC;AACH,CAAC"}

package/dist/constants.d.ts

@@ -22,7 +22,8 @@ export declare const defaultScrollZoomAxis: ScrollZoomAxis;
 export declare const minLetterRowHeight = 8;
 export declare const minLetterColWidth = 5;
 export declare const minFeatureLabelHeight = 9;
-export declare const labelReferenceFontSize = 16;
+export declare function fontSizeFor(rowHeight: number): number;
+export declare const labelFitFontSize: number;
 export declare const minColWidth = 0.2;
 export declare const minRowHeight = 1;
 export declare const maxCellSize = 80;
@@ -31,8 +32,10 @@ export declare const defaultColorSchemeName = "maeditor";
 export declare const defaultShowColumnStats = true;
 export declare const defaultDrawLabels = true;
 export declare const defaultLabelsAlignRight = false;
-export declare const defaultTreeAreaWidth = 400;
-export declare const defaultTreeWidth = 300;
+export declare const minTreeWidth = 70;
+export declare const maxFitTreeWidth = 160;
+export declare const pxPerTreeDepth = 10;
+export declare const maxTreeAreaShare = 0.3;
 export declare const defaultShowBranchLen = true;
 export declare const treeOrders: readonly ["branchLength", "input", "ladderize", "ladderizeReverse"];
 export declare const defaultTreeOrder: TreeOrder;

package/dist/constants.js

@@ -46,9 +46,13 @@ export const minLetterColWidth = 5;
 // so a span shorter than this holds no readable text: an underline bar, a
 // sub-row band or a features panel over small rows
 export const minFeatureLabelHeight = 9;
-// Tree labels are measured once at this size and scaled to the current font
-// size, so a vertical zoom never re-measures the tree.
-export const labelReferenceFontSize = 16;
+export function fontSizeFor(rowHeight) {
+    return Math.min(Math.max(6, rowHeight - 3), 18);
+}
+// The fitted tree area measures the tip labels and the clade labels at the
+// font a default row draws, so a vertical zoom leaves the alignment in place.
+// A larger font ellipsizes the labels.
+export const labelFitFontSize = fontSizeFor(defaultRowHeight);
 // Zoom limits, px per cell. maxCellSize caps both smooth zoom and the stepwise
 // zoom-in buttons (which otherwise grow unbounded). minColWidth/minRowHeight are
 // the smooth-zoom floors.
@@ -62,8 +66,14 @@ export const defaultShowColumnStats = true;
 // Tree model defaults
 export const defaultDrawLabels = true;
 export const defaultLabelsAlignRight = false;
-export const defaultTreeAreaWidth = 400;
-export const defaultTreeWidth = 300;
+// The fitted tree area gives the tree pxPerTreeDepth per level of its depth,
+// between minTreeWidth and maxFitTreeWidth, beside the widest label, and takes
+// at most maxTreeAreaShare of a view with an alignment. Where the share binds,
+// the tree keeps minTreeWidth and the labels ellipsize.
+export const minTreeWidth = 70;
+export const maxFitTreeWidth = 160;
+export const pxPerTreeDepth = 10;
+export const maxTreeAreaShare = 0.3;
 export const defaultShowBranchLen = true;
 export const treeOrders = [
     'branchLength',
@@ -80,7 +90,7 @@ export const defaultOverviewHeight = 120;
 // Neighbor joining does not run above this many rows. The distance matrix is
 // O(n^2*L) and the join loop O(n^3), both on the main thread with no progress
 // and no cancel: 400 rows measured 1.5s, 800 rows 10s, and 1600 would be about
-// seventy. See agent-docs/ideas/neighbor-joining-scaling.md.
+// seventy. See agent-docs/reference/neighbor-joining-scaling.md.
 export const maxNeighborJoiningRows = 500;
 // The opacity a `rowTint` encoding draws its scale's color at, so the residues
 // under the wash stay readable. A color the producer already gave an alpha

package/dist/constants.js.map

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package/dist/measureTextCanvas.js

@@ -1,6 +1,6 @@
 import { setFontSize } from './setFontSize.js';
-// Cached across calls: labelWidthMap measures every leaf label on every layout,
-// and both createElement and getContext are far more expensive than measureText.
+// Cached across calls, since both createElement and getContext are far more
+// expensive than measureText.
 // `null` records that this environment has no 2d context, so the lookup is not
 // retried on every label.
 let ctxHandle;

package/dist/measureTextCanvas.js.map

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

@@ -14,15 +14,18 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     /**
      * #property
-     * width of the area the tree is drawn in, px
+     * width of the area the tree and its labels draw in, px. Undefined fits
+     * the area to the labels and the tree; `effectiveTreeAreaWidth` reads
+     * the width either way
      */
-    treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     /**
      * #property
-     * width of the tree within the treeArea, px. automatically synced to
-     * fit within treeAreaWidth
+     * width of the tree within the tree area, px. Undefined gives the tree
+     * the area less the labels; `effectiveTreeWidth` reads the width either
+     * way
      */
-    treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     /**
      * #property
      * use "branch length" e.g. evolutionary distance to draw tree branch
@@ -64,24 +67,19 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * 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)
-     * instead of using a fixed width. useful when there is no tree, so the
-     * label gutter isn't padded out to the default 400px
-     */
-    autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
     /**
      * #action
-     * set tree area width (px)
+     * set the tree area width, px, or undefined to fit it to the labels and
+     * the tree. The tree then fills the area less the labels
      */
-    setTreeAreaWidth(n: number): void;
+    setTreeAreaWidth(n: number | undefined): void;
     /**
      * #action
-     * set tree width (px)
+     * set the tree width, px, or undefined to fill the tree area less the
+     * labels
      */
-    setTreeWidth(n: number): void;
+    setTreeWidth(n: number | undefined): void;
     /**
      * #action
      */
@@ -90,10 +88,6 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setDrawTree(arg: boolean): void;
-    /**
-     * #action
-     */
-    setAutoTreeAreaWidth(arg: boolean): void;
     /**
      * #action
      */

package/dist/model/treeModel.js

@@ -1,5 +1,5 @@
 import { types } from '@jbrowse/mobx-state-tree';
-import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview, defaultTreeAreaWidth, defaultTreeWidth, treeOrders, } from '../constants.js';
+import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview, treeOrders, } from '../constants.js';
 import { stripDefault } from '../stripDefault.js';
 /**
  * #stateModel Tree
@@ -18,15 +18,18 @@ export function TreeModelF() {
         labelsAlignRight: stripDefault(types.boolean, defaultLabelsAlignRight),
         /**
          * #property
-         * width of the area the tree is drawn in, px
+         * width of the area the tree and its labels draw in, px. Undefined fits
+         * the area to the labels and the tree; `effectiveTreeAreaWidth` reads
+         * the width either way
          */
-        treeAreaWidth: stripDefault(types.number, defaultTreeAreaWidth),
+        treeAreaWidth: types.maybe(types.number),
         /**
          * #property
-         * width of the tree within the treeArea, px. automatically synced to
-         * fit within treeAreaWidth
+         * width of the tree within the tree area, px. Undefined gives the tree
+         * the area less the labels; `effectiveTreeWidth` reads the width either
+         * way
          */
-        treeWidth: stripDefault(types.number, defaultTreeWidth),
+        treeWidth: types.maybe(types.number),
         /**
          * #property
          * use "branch length" e.g. evolutionary distance to draw tree branch
@@ -68,28 +71,24 @@ export function TreeModelF() {
          * 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)
-         * instead of using a fixed width. useful when there is no tree, so the
-         * label gutter isn't padded out to the default 400px
-         */
-        autoTreeAreaWidth: stripDefault(types.boolean, false),
     })
         .actions(self => ({
         /**
          * #action
-         * set tree area width (px)
+         * set the tree area width, px, or undefined to fit it to the labels and
+         * the tree. The tree then fills the area less the labels
          */
         setTreeAreaWidth(n) {
-            self.treeAreaWidth = Math.round(n);
+            self.treeAreaWidth = n === undefined ? undefined : Math.round(n);
+            self.treeWidth = undefined;
         },
         /**
          * #action
-         * set tree width (px)
+         * set the tree width, px, or undefined to fill the tree area less the
+         * labels
          */
         setTreeWidth(n) {
-            self.treeWidth = Math.round(n);
+            self.treeWidth = n === undefined ? undefined : Math.round(n);
         },
         /**
          * #action
@@ -103,12 +102,6 @@ export function TreeModelF() {
         setDrawTree(arg) {
             self.drawTree = arg;
         },
-        /**
-         * #action
-         */
-        setAutoTreeAreaWidth(arg) {
-            self.autoTreeAreaWidth = arg;
-        },
         /**
          * #action
          */

package/dist/model/treeModel.js.map

@@ -1 +1 @@
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