react-msaview-cli 9.3.0 → 9.5.0

package/dist/index.js

@@ -45786,7 +45786,7 @@ var init_renderHighlights = __esm({
 function fontSizeFor(rowHeight) {
   return Math.min(Math.max(6, rowHeight - 3), 18);
 }
-var defaultRowHeight, defaultColWidth, defaultHeight, resizeHandleWidth, defaultScrollX, defaultScrollY, defaultCurrentAlignment, defaultShowDomains, defaultShowDomainLegend, defaultHideGaps, defaultAllowedGappyness, defaultSubFeatureRows, subFeatureRowHeight, domainUnderlineHeight, segmentFeatureTypes, segmentShades, defaultDrawMsaLetters, defaultScrollZoom, scrollZoomAxes, defaultScrollZoomAxis, minLetterRowHeight, minLetterColWidth, zoomFrameMaxLetters, minFeatureLabelHeight, labelFitFontSize, minColWidth, minRowHeight, maxCellSize, settingsPanelWidth, defaultBgColor, defaultColorSchemeName, defaultShowColumnStats, defaultDrawLabels, defaultLabelsAlignRight, minTreeWidth, maxFitTreeWidth, pxPerTreeDepth, maxTreeAreaShare, defaultShowBranchLen, treeOrders, defaultTreeOrder, defaultDrawTree, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultShowTreeOverview, defaultShowTreeScaleBar, defaultOverviewHeight, maxNeighborJoiningRows, rowTintAlpha, cladeHighlightColor, cladeHighlightAlpha, maxInlineSnapshotBytes, rowPanelHeaderHeight, treeScaleBarHeight, defaultFeaturePanelWidth, msaOverlayZIndex, legendZIndex;
+var defaultRowHeight, defaultColWidth, defaultHeight, resizeHandleWidth, defaultScrollX, defaultScrollY, defaultCurrentAlignment, defaultShowDomains, defaultShowDomainLegend, defaultHideGaps, defaultAllowedGappyness, defaultSubFeatureRows, subFeatureRowHeight, domainUnderlineHeight, segmentFeatureTypes, segmentShades, defaultDrawMsaLetters, defaultScrollZoom, scrollZoomAxes, defaultScrollZoomAxis, minLetterRowHeight, minLetterColWidth, zoomFrameMaxLetters, minFeatureLabelHeight, labelFitFontSize, minColWidth, minRowHeight, maxCellSize, settingsPanelWidth, defaultBgColor, defaultColorSchemeName, defaultShowColumnStats, defaultDrawLabels, defaultLabelsAlignRight, minTreeWidth, maxFitTreeWidth, pxPerTreeDepth, maxTreeAreaShare, defaultShowBranchLen, treeOrders, defaultTreeOrder, defaultDrawTree, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultShowTreeOverview, defaultOverviewHeight, maxNeighborJoiningRows, rowTintAlpha, cladeHighlightColor, cladeHighlightAlpha, maxInlineSnapshotBytes, rowPanelHeaderHeight, treeScaleBarHeight, defaultFeaturePanelWidth, msaOverlayZIndex, legendZIndex;
 var init_constants = __esm({
   "../lib/dist/constants.js"() {
     "use strict";
@@ -45847,7 +45847,6 @@ var init_constants = __esm({
     defaultDrawNodeBubbles = true;
     defaultDrawNodeLabels = false;
     defaultShowTreeOverview = false;
-    defaultShowTreeScaleBar = false;
     defaultOverviewHeight = 120;
     maxNeighborJoiningRows = 500;
     rowTintAlpha = 0.25;
@@ -86528,7 +86527,7 @@ var version2;
 var init_version3 = __esm({
   "../lib/dist/version.js"() {
     "use strict";
-    version2 = "9.3.0";
+    version2 = "9.5.0";
   }
 });
 
@@ -87324,7 +87323,7 @@ function outgroupLabel(outgroup) {
   return rest.length === 0 ? `Outgroup ${first}` : `Outgroup ${first} \u2026 ${rest.at(-1)}`;
 }
 function treeSubMenu(model2) {
-  const { drawTree, showBranchLen, labelsAlignRight, drawNodeLabels, drawLabels, treeAreaWidth, showTreeOverview, showTreeScaleBar, treeOrder, treeRoot, rotated } = model2;
+  const { drawTree, showBranchLen, labelsAlignRight, drawNodeLabels, drawLabels, treeAreaWidth, showTreeOverview, treeOrder, treeRoot, rotated } = model2;
   return [
     subMenu("Layout", [
       radio("Phylogram", drawTree && showBranchLen, () => {
@@ -87342,9 +87341,6 @@ function treeSubMenu(model2) {
     toggle("Tree overview", showTreeOverview, (arg2) => {
       model2.setShowTreeOverview(arg2);
     }),
-    toggle("Scale bar", showTreeScaleBar, (arg2) => {
-      model2.setShowTreeScaleBar(arg2);
-    }),
     subMenu("Order", [
       ...treeOrders.map((order2) => radio(treeOrderLabels[order2], treeOrder === order2, () => {
         model2.setTreeOrder(order2);
@@ -91669,11 +91665,6 @@ function TreeModelF() {
      * subtree boxed. A click on it focuses the subtree under the pointer
      */
     showTreeOverview: stripDefault2(types.boolean, defaultShowTreeOverview),
-    /**
-     * #property
-     * draw the branch-length scale bar above the tree of a phylogram
-     */
-    showTreeScaleBar: stripDefault2(types.boolean, defaultShowTreeScaleBar),
     /**
      * #property
      * height of the tree overview band, px
@@ -91739,12 +91730,6 @@ function TreeModelF() {
     setShowTreeOverview(arg2) {
       self.showTreeOverview = arg2;
     },
-    /**
-     * #action
-     */
-    setShowTreeScaleBar(arg2) {
-      self.showTreeScaleBar = arg2;
-    },
     /**
      * #action
      */
@@ -95145,14 +95130,11 @@ function stateModelFactory({ maxInlineSnapshotBytes: maxInlineSnapshotBytes2 = m
   })).views((self) => ({
     /**
      * #getter
-     * the branch-length scale bar over the tree, undefined while
-     * `showTreeScaleBar` is off, in cladogram mode, or when the tree area is
-     * too narrow for one
+     * the branch-length scale bar over the tree, the guide of its branch-length
+     * scale: undefined in cladogram mode, with the tree off, or when the tree
+     * area is too narrow for one
      */
     get treeScaleBar() {
-      if (!self.showTreeScaleBar) {
-        return void 0;
-      }
       return scaleBarLength(self.pxPerBranchLength, self.effectiveTreeAreaWidth - self.marginLeft * 2);
     },
     /**
@@ -95686,10 +95668,15 @@ function stateModelFactory({ maxInlineSnapshotBytes: maxInlineSnapshotBytes2 = m
     /**
      * #getter
      * categorical feature types (InterPro domains and the like) that each get
-     * their own color and a legend entry
+     * their own color and a legend entry, in palette order: grouped by
+     * feature type, types in the order they first appear. A GenPept
+     * record's CDD Sites follow every Region, so the palette spends the
+     * colors after the domains' on the sites inside them
      */
     get categoricalDomainTypes() {
-      return [...self.annotationTypes.values()].filter((d3) => !segmentFeatureTypes.has(d3.featureType ?? ""));
+      const types2 = [...self.annotationTypes.values()].filter((d3) => !segmentFeatureTypes.has(d3.featureType ?? ""));
+      const typeOrder = [...new Set(types2.map((d3) => d3.featureType))];
+      return types2.toSorted((a3, b2) => typeOrder.indexOf(a3.featureType) - typeOrder.indexOf(b2.featureType));
     },
     get fillPalette() {
       const segments = Object.fromEntries(this.segmentDomainTypes.map((d3, i2) => [
@@ -96615,7 +96602,6 @@ var init_model = __esm({
       "drawNodeBubbles",
       "drawNodeLabels",
       "showTreeOverview",
-      "showTreeScaleBar",
       "overviewHeight",
       "turnedOffTracks",
       "trackHeights",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "react-msaview-cli",
-  "version": "9.3.0",
+  "version": "9.5.0",
   "license": "MIT",
   "type": "module",
   "repository": {
@@ -20,8 +20,8 @@
     "@types/node": "^26.6.5",
     "esbuild": "^0.28.2",
     "mobx-react": "^10.0.2",
-    "msa-parsers": "9.3.0",
-    "react-msaview": "9.3.0"
+    "msa-parsers": "9.5.0",
+    "react-msaview": "9.5.0"
   },
   "dependencies": {
     "jsdom": "^30.1.3"