react-msaview 7.0.0 → 8.0.0

package/dist/components/header/getAnnotationsMenu.js

@@ -24,12 +24,9 @@ export function getAnnotationsMenu({ model }) {
                 ]);
             },
         },
-        // The viewer used to submit the whole alignment to the EBI iprscan5 queue
-        // and poll it for about fifteen minutes, capped at 140 rows and under a
-        // hardcoded email address. `react-msaview-cli interpro` answers the same
-        // question from InterPro's precomputed matches in seconds, and
-        // `interproscan` covers rows InterPro has not seen. Neither belongs in a
-        // browser tab, so this points at the page that walks through them.
+        // `react-msaview-cli interpro` reads InterPro's precomputed matches in
+        // seconds, and `interproscan` covers rows InterPro has not seen; this links
+        // the tutorial for both
         {
             label: 'How to get a domain file...',
             icon: MenuBook,

package/dist/components/header/getAnnotationsMenu.js.map

@@ -1 +1 @@
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+{"version":3,"file":"getAnnotationsMenu.js","sourceRoot":"","sources":["../../../src/components/header/getAnnotationsMenu.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,SAAS,MAAM,+BAA+B,CAAA;AACrD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,QAAQ,MAAM,8BAA8B,CAAA;AACnD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAIvD,MAAM,mBAAmB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,6BAA8B,CAAC,CAAC,CAAA;AAC9E,MAAM,oBAAoB,GAAG,IAAI,CAC/B,GAAG,EAAE,CAAC,MAAM,CAAC,oCAAqC,CAAC,CACpD,CAAA;AAED,MAAM,eAAe,GAAG,sDAAsD,CAAA;AAE9E,MAAM,UAAU,kBAAkB,CAAC,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,WAAW,EAAE,mBAAmB,EAAE,cAAc,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC7E,MAAM,UAAU,GAAG,SAAS,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,CAAA;IACpD,OAAO;QACL;YACE,KAAK,EAAE,yBAAyB;YAChC,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;oBAC/B,oBAAoB;oBACpB;wBACE,WAAW;wBACX,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;QACD,uEAAuE;QACvE,4EAA4E;QAC5E,wBAAwB;QACxB;YACE,KAAK,EAAE,6BAA6B;YACpC,IAAI,EAAE,QAAQ;YACd,OAAO,EAAE,GAAG,EAAE;gBACZ,MAAM,CAAC,IAAI,CAAC,eAAe,EAAE,QAAQ,EAAE,qBAAqB,CAAC,CAAA;YAC/D,CAAC;SACF;QACD;YACE,KAAK,EAAE,mBAAmB,UAAU,EAAE;YACtC,QAAQ,EAAE,SAAS;YACnB,IAAI,EAAE,UAAU;YAChB,OAAO,EAAE,mBAAmB;YAC5B,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;SACF;QACD;YACE,KAAK,EAAE,qBAAqB,UAAU,EAAE;YACxC,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,mBAAmB,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK;YACrD,IAAI,EAAE,IAAI;YACV,IAAI,EAAE,UAAmB;YACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;YAC1C,CAAC;SACF;QACD;YACE,KAAK,EAAE,qBAAqB,UAAU,EAAE;YACxC,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,SAAS;YACnB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,mBAAmB;oBACnB;wBACE,OAAO;wBACP,KAAK;qBACN;iBACF,CAAC,CAAA;YACJ,CAAC;SACF;KACF,CAAA;AACH,CAAC"}

package/dist/components/header/settingsMenuItems.js

@@ -8,9 +8,7 @@ function toggle(label, checked, set) {
         },
     };
 }
-// Every track the alignment can show, with its current state. Without this the
-// "Close" item on a track's own dropdown is a one-way door -- there is nowhere
-// else in the UI to turn a track back on.
+// the only place in the UI to turn a closed track back on
 function tracksSubMenu(model) {
     const shown = new Set(model.turnedOnTracks.map(t => t.model.id));
     return model.tracks.map(({ model: { id, name } }) => toggle(name, shown.has(id), () => {
@@ -26,14 +24,13 @@ export function msaSettingsMenuItems(model) {
             subMenu: tracksSubMenu(model),
         },
         { type: 'divider' },
-        toggle('Show column statistics on hover', showColumnStats, arg => {
+        toggle('Show track values on hover', showColumnStats, arg => {
             model.setShowColumnStats(arg);
         }),
         toggle('Draw letters', drawMsaLetters, arg => {
             model.setDrawMsaLetters(arg);
         }),
-        // the checkbox reads as the inverse of the property it sets: bgColor draws
-        // the tile, and turning it off is what leaves the letter itself colored
+        // inverted: bgColor colors the tile, and off colors the letter
         toggle('Color letters instead of background of tiles', !bgColor, arg => {
             model.setBgColor(!arg);
         }),
@@ -43,7 +40,7 @@ export function msaSettingsMenuItems(model) {
     ];
 }
 export function treeSettingsMenuItems(model) {
-    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawLabels, } = model;
+    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawNodeLabels, drawLabels, showTreeOverview, } = model;
     return [
         toggle('Show branch length', showBranchLen, arg => {
             model.setShowBranchLen(arg);
@@ -54,6 +51,12 @@ export function treeSettingsMenuItems(model) {
         toggle('Draw bubbles on tree branches', drawNodeBubbles, arg => {
             model.setDrawNodeBubbles(arg);
         }),
+        toggle('Draw internal node labels', drawNodeLabels, arg => {
+            model.setDrawNodeLabels(arg);
+        }),
+        toggle('Show tree overview', showTreeOverview, arg => {
+            model.setShowTreeOverview(arg);
+        }),
         toggle('Tree labels align right', labelsAlignRight, arg => {
             model.setLabelsAlignRight(arg);
         }),

package/dist/components/header/settingsMenuItems.js.map

@@ -1 +1 @@
-{"version":3,"file":"settingsMenuItems.js","sourceRoot":"","sources":["../../../src/components/header/settingsMenuItems.ts"],"names":[],"mappings":"AAGA,SAAS,MAAM,CAAC,KAAa,EAAE,OAAgB,EAAE,GAA2B;IAC1E,OAAO;QACL,KAAK;QACL,IAAI,EAAE,UAAmB;QACzB,OAAO;QACP,OAAO,EAAE,GAAG,EAAE;YACZ,GAAG,CAAC,CAAC,OAAO,CAAC,CAAA;QACf,CAAC;KACF,CAAA;AACH,CAAC;AAED,+EAA+E;AAC/E,+EAA+E;AAC/E,0CAA0C;AAC1C,SAAS,aAAa,CAAC,KAAmB;IACxC,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAA;IAChE,OAAO,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,EAAE,CAClD,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,GAAG,EAAE;QAC/B,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;IACvB,CAAC,CAAC,CACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,KAAmB;IACtD,MAAM,EAAE,cAAc,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,OAAO;QACL;YACE,KAAK,EAAE,QAAQ;YACf,IAAI,EAAE,SAAkB;YACxB,OAAO,EAAE,aAAa,CAAC,KAAK,CAAC;SAC9B;QACD,EAAE,IAAI,EAAE,SAAkB,EAAE;QAC5B,MAAM,CAAC,iCAAiC,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC/D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,cAAc,EAAE,cAAc,EAAE,GAAG,CAAC,EAAE;YAC3C,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAA;QAC9B,CAAC,CAAC;QACF,2EAA2E;QAC3E,wEAAwE;QACxE,MAAM,CAAC,8CAA8C,EAAE,CAAC,OAAO,EAAE,GAAG,CAAC,EAAE;YACrE,KAAK,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,8BAA8B,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YACrD,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,KAAmB;IACvD,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,eAAe,EACf,UAAU,GACX,GAAG,KAAK,CAAA;IACT,OAAO;QACL,MAAM,CAAC,oBAAoB,EAAE,aAAa,EAAE,GAAG,CAAC,EAAE;YAChD,KAAK,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAA;QAC7B,CAAC,CAAC;QACF,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YAClC,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,+BAA+B,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC7D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,yBAAyB,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;YACxD,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC,CAAC;QACF,MAAM,CAAC,aAAa,EAAE,UAAU,EAAE,GAAG,CAAC,EAAE;YACtC,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC1B,CAAC,CAAC;KACH,CAAA;AACH,CAAC"}
+{"version":3,"file":"settingsMenuItems.js","sourceRoot":"","sources":["../../../src/components/header/settingsMenuItems.ts"],"names":[],"mappings":"AAGA,SAAS,MAAM,CAAC,KAAa,EAAE,OAAgB,EAAE,GAA2B;IAC1E,OAAO;QACL,KAAK;QACL,IAAI,EAAE,UAAmB;QACzB,OAAO;QACP,OAAO,EAAE,GAAG,EAAE;YACZ,GAAG,CAAC,CAAC,OAAO,CAAC,CAAA;QACf,CAAC;KACF,CAAA;AACH,CAAC;AAED,0DAA0D;AAC1D,SAAS,aAAa,CAAC,KAAmB;IACxC,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAA;IAChE,OAAO,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,EAAE,CAClD,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,GAAG,EAAE;QAC/B,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;IACvB,CAAC,CAAC,CACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,KAAmB;IACtD,MAAM,EAAE,cAAc,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,OAAO;QACL;YACE,KAAK,EAAE,QAAQ;YACf,IAAI,EAAE,SAAkB;YACxB,OAAO,EAAE,aAAa,CAAC,KAAK,CAAC;SAC9B;QACD,EAAE,IAAI,EAAE,SAAkB,EAAE;QAC5B,MAAM,CAAC,4BAA4B,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC1D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,cAAc,EAAE,cAAc,EAAE,GAAG,CAAC,EAAE;YAC3C,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAA;QAC9B,CAAC,CAAC;QACF,+DAA+D;QAC/D,MAAM,CAAC,8CAA8C,EAAE,CAAC,OAAO,EAAE,GAAG,CAAC,EAAE;YACrE,KAAK,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,8BAA8B,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YACrD,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,KAAmB;IACvD,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,eAAe,EACf,cAAc,EACd,UAAU,EACV,gBAAgB,GACjB,GAAG,KAAK,CAAA;IACT,OAAO;QACL,MAAM,CAAC,oBAAoB,EAAE,aAAa,EAAE,GAAG,CAAC,EAAE;YAChD,KAAK,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAA;QAC7B,CAAC,CAAC;QACF,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YAClC,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,+BAA+B,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC7D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,2BAA2B,EAAE,cAAc,EAAE,GAAG,CAAC,EAAE;YACxD,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAA;QAC9B,CAAC,CAAC;QACF,MAAM,CAAC,oBAAoB,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;YACnD,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC,CAAC;QACF,MAAM,CAAC,yBAAyB,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;YACxD,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC,CAAC;QACF,MAAM,CAAC,aAAa,EAAE,UAAU,EAAE,GAAG,CAAC,EAAE;YACtC,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC1B,CAAC,CAAC;KACH,CAAA;AACH,CAAC"}

package/dist/components/import/util.js

@@ -8,8 +8,7 @@ export function load(model, msaFile, treeFile, gffFile) {
     }
     if (gffFile) {
         model.setGFFFilehandle(gffFile);
-        // asked for by hand, so drawn -- even if the reader hid the overlay
-        // earlier in this view
+        // a file opened by hand shows even if the overlay was hidden earlier
         model.setShowDomains(true);
     }
 }

package/dist/components/import/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/components/import/util.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,IAAI,CAClB,KAAmB,EACnB,OAAsB,EACtB,QAAuB,EACvB,OAAsB;IAEtB,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;IACzB,IAAI,OAAO,EAAE,CAAC;QACZ,KAAK,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAA;IACjC,CAAC;IACD,IAAI,QAAQ,EAAE,CAAC;QACb,KAAK,CAAC,iBAAiB,CAAC,QAAQ,CAAC,CAAA;IACnC,CAAC;IACD,IAAI,OAAO,EAAE,CAAC;QACZ,KAAK,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAA;QAC/B,oEAAoE;QACpE,uBAAuB;QACvB,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;IAC5B,CAAC;AACH,CAAC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/components/import/util.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,IAAI,CAClB,KAAmB,EACnB,OAAsB,EACtB,QAAuB,EACvB,OAAsB;IAEtB,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;IACzB,IAAI,OAAO,EAAE,CAAC;QACZ,KAAK,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAA;IACjC,CAAC;IACD,IAAI,QAAQ,EAAE,CAAC;QACb,KAAK,CAAC,iBAAiB,CAAC,QAAQ,CAAC,CAAA;IACnC,CAAC;IACD,IAAI,OAAO,EAAE,CAAC;QACZ,KAAK,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAA;QAC/B,qEAAqE;QACrE,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;IAC5B,CAAC;AACH,CAAC"}

package/dist/components/minimap/Minimap.js

@@ -9,8 +9,7 @@ const Minimap = observer(function ({ model }) {
     const { minimapHeight, msaCanvasWidth, highResScaleFactor } = model;
     const theme = useTheme();
     const { unit, s, w, polygonHeight, polygonPoints } = getMinimapLayout(model);
-    // the whole alignment, sampled down to the bar: it says where the conserved
-    // blocks and the gappy stretches are, which is what a scroll aims at
+    // the whole alignment, sampled down to the bar
     const barWidth = Math.round(msaCanvasWidth * highResScaleFactor);
     const barHeight = Math.round(MINIMAP_BAR_HEIGHT * highResScaleFactor);
     const ref = useCanvasAutorun({

package/dist/components/minimap/Minimap.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Minimap.js","sourceRoot":"","sources":["../../../src/components/minimap/Minimap.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,OAAO,CAAA;AAE1C,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,UAAU,EAAE,EAAE,kBAAkB,EAAE,MAAM,kBAAmB,CAAA;AAClE,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAClD,OAAO,EAAE,kBAAkB,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAIzE,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,aAAa,EAAE,cAAc,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,EAAE,IAAI,EAAE,CAAC,EAAE,CAAC,EAAE,aAAa,EAAE,aAAa,EAAE,GAAG,gBAAgB,CAAC,KAAK,CAAC,CAAA;IAE5E,+CAA+C;IAC/C,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,kBAAkB,CAAC,CAAA;IAChE,MAAM,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,GAAG,kBAAkB,CAAC,CAAA;IACrE,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;YACxC,MAAM,SAAS,GAAG,YAAY,CAAC;gBAC7B,KAAK;gBACL,KAAK;gBACL,MAAM,EAAE,kBAAkB;aAC3B,CAAC,CAAA;YACF,IAAI,SAAS,EAAE,CAAC;gBACd,GAAG,CAAC,qBAAqB,GAAG,IAAI,CAAA;gBAChC,GAAG,CAAC,SAAS,CACX,SAAS,EACT,CAAC,EACD,CAAC,EACD,SAAS,CAAC,KAAK,EACf,SAAS,CAAC,MAAM,EAChB,CAAC,EACD,CAAC,EACD,QAAQ,EACR,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,KAAK,EAAE,QAAQ;QACf,MAAM,EAAE,SAAS;QACjB,IAAI,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC;KACrB,CAAC,CAAA;IAEF,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,KAAK,CAAC,UAAU,CAAC,WAAW,GAAG,KAAK,GAAG,IAAI,CAAC,CAAA;IAC9C,CAAC,EACD,CAAC,KAAK,EAAE,IAAI,CAAC,CACd,CAAA;IAED,OAAO,CAIL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,aAAa;YACrB,KAAK,EAAE,cAAc;YACrB,UAAU,EAAE,CAAC;SACd;QAED,gCACE,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,QAAQ,EACf,MAAM,EAAE,SAAS,EACjB,KAAK,EAAE;gBACL,OAAO,EAAE,OAAO;gBAChB,KAAK,EAAE,cAAc;gBACrB,MAAM,EAAE,kBAAkB;gBAC1B,SAAS,EAAE,YAAY;gBACvB,MAAM,EAAE,aAAa,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,EAAE;aACpD,GACD;QACF,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,OAAO,EACf,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,OAAO,EAC7B,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;gBACL,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gBACpB,MAAM,EAAE,kBAAkB;gBAC1B,KAAK,EAAE,CAAC;aACT,GACD;QAEF,6BAAK,MAAM,EAAE,aAAa,EAAE,KAAK,EAAE,cAAc;YAC/C,iCAAS,IAAI,EAAE,kBAAkB,EAAE,MAAM,EAAE,aAAa,GAAI,CACxD,CACF,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/msa/AnnotationLegend.js

@@ -3,38 +3,46 @@ import ExpandLess from '@mui/icons-material/ExpandLess';
 import ExpandMore from '@mui/icons-material/ExpandMore';
 import { IconButton, Paper, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
+import { legendZIndex } from '../../constants.js';
+import { legendRows } from './legendRows.js';
 const AnnotationLegend = observer(function ({ model, }) {
-    const { actuallyShowDomains, visibleDomainTypes: visible, fillPalette, showDomainLegend: expanded, } = model;
+    const { legends, showDomainLegend: expanded } = model;
+    const rows = legendRows(legends);
     const ExpandIcon = expanded ? ExpandLess : ExpandMore;
-    return actuallyShowDomains && visible.length > 0 ? (React.createElement(Paper, { elevation: 3, style: {
+    return rows.length > 0 ? (React.createElement(Paper, { elevation: 3, style: {
             position: 'absolute',
             top: 4,
             right: 4,
-            zIndex: 100,
-            maxWidth: 260,
+            zIndex: legendZIndex,
+            maxWidth: 220,
             maxHeight: '60%',
             display: 'flex',
             flexDirection: 'column',
             opacity: 0.95,
         } },
-        React.createElement("div", { style: {
+        React.createElement(IconButton, { size: "small", title: expanded ? 'Collapse key' : 'Expand key', style: expanded
+                ? { position: 'absolute', top: 0, right: 0, padding: 1 }
+                : { padding: 1 }, onClick: () => {
+                model.setShowDomainLegend(!expanded);
+            } },
+            React.createElement(ExpandIcon, { style: { fontSize: 14 } })),
+        expanded ? (React.createElement("div", { style: { overflow: 'auto', padding: '2px 6px 4px' } }, rows.map((row, i) => (React.createElement("div", { key: row.key, style: {
                 display: 'flex',
                 alignItems: 'center',
-                justifyContent: 'flex-end',
-                padding: '2px 4px 2px 8px',
-            } },
-            React.createElement(IconButton, { size: "small", title: expanded ? 'Collapse key' : 'Expand key', onClick: () => {
-                    model.setShowDomainLegend(!expanded);
-                } },
-                React.createElement(ExpandIcon, { fontSize: "small" }))),
-        expanded ? (React.createElement("div", { style: { overflow: 'auto', padding: '0 8px 6px' } }, visible.map(({ accession, name }) => (React.createElement("div", { key: accession, style: { display: 'flex', alignItems: 'center', gap: 6 }, title: accession },
-            React.createElement("div", { style: {
-                    width: 12,
-                    height: 12,
+                gap: 4,
+                marginRight: i === 0 ? 18 : 0,
+            }, title: row.hint },
+            row.color ? (React.createElement("div", { style: {
+                    width: 9,
+                    height: 9,
                     flexShrink: 0,
-                    background: fillPalette[accession],
-                } }),
-            React.createElement(Typography, { variant: "caption", noWrap: true }, name)))))) : null)) : null;
+                    background: row.color,
+                } })) : null,
+            React.createElement(Typography, { variant: "caption", noWrap: true, style: {
+                    fontSize: 10,
+                    lineHeight: 1.4,
+                    fontWeight: row.color ? undefined : 'bold',
+                } }, row.label)))))) : null)) : null;
 });
 export default AnnotationLegend;
 //# sourceMappingURL=AnnotationLegend.js.map

package/dist/components/msa/AnnotationLegend.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AnnotationLegend.js","sourceRoot":"","sources":["../../../src/components/msa/AnnotationLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC7D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AACjD,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAA;AAI5C,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,EAC1C,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IACrD,MAAM,IAAI,GAAG,UAAU,CAAC,OAAO,CAAC,CAAA;IAChC,MAAM,UAAU,GAAG,QAAQ,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,UAAU,CAAA;IAErD,OAAO,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACvB,oBAAC,KAAK,IACJ,SAAS,EAAE,CAAC,EACZ,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,KAAK,EAAE,CAAC;YACR,MAAM,EAAE,YAAY;YACpB,QAAQ,EAAE,GAAG;YACb,SAAS,EAAE,KAAK;YAChB,OAAO,EAAE,MAAM;YACf,aAAa,EAAE,QAAQ;YACvB,OAAO,EAAE,IAAI;SACd;QAED,oBAAC,UAAU,IACT,IAAI,EAAC,OAAO,EACZ,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,YAAY,EAC/C,KAAK,EACH,QAAQ;gBACN,CAAC,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE;gBACxD,CAAC,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,EAEpB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,mBAAmB,CAAC,CAAC,QAAQ,CAAC,CAAA;YACtC,CAAC;YAED,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,GAAI,CAC5B;QACZ,QAAQ,CAAC,CAAC,CAAC,CACV,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,IACrD,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CACpB,6BACE,GAAG,EAAE,GAAG,CAAC,GAAG,EACZ,KAAK,EAAE;gBACL,OAAO,EAAE,MAAM;gBACf,UAAU,EAAE,QAAQ;gBACpB,GAAG,EAAE,CAAC;gBACN,WAAW,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;aAC9B,EACD,KAAK,EAAE,GAAG,CAAC,IAAI;YAEd,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CACX,6BACE,KAAK,EAAE;oBACL,KAAK,EAAE,CAAC;oBACR,MAAM,EAAE,CAAC;oBACT,UAAU,EAAE,CAAC;oBACb,UAAU,EAAE,GAAG,CAAC,KAAK;iBACtB,GACD,CACH,CAAC,CAAC,CAAC,IAAI;YACR,oBAAC,UAAU,IACT,OAAO,EAAC,SAAS,EACjB,MAAM,QACN,KAAK,EAAE;oBACL,QAAQ,EAAE,EAAE;oBACZ,UAAU,EAAE,GAAG;oBACf,UAAU,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM;iBAC3C,IAEA,GAAG,CAAC,KAAK,CACC,CACT,CACP,CAAC,CACE,CACP,CAAC,CAAC,CAAC,IAAI,CACF,CACT,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/components/msa/MSACanvas.js

@@ -13,7 +13,7 @@ const MSACanvas = observer(function ({ model }) {
         model.doScrollY(d);
     }, [model]);
     const onZoom = useCallback((scaleFactor, offsetX, offsetY) => {
-        model.zoomToPos(scaleFactor, offsetX, offsetY);
+        model.zoomToPos(scaleFactor, offsetX, offsetY, model.wheelZoomAxis);
     }, [model]);
     const { onMouseDown, onMouseUp } = useWheelScroll({
         ref,

package/dist/components/msa/MSACanvas.js.map

@@ -1 +1 @@
-{"version":3,"file":"MSACanvas.js","sourceRoot":"","sources":["../../../src/components/msa/MSACanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAA;AACxD,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,cAAc,MAAM,qBAAsB,CAAA;AAIjD,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EACJ,GAAG,EACH,aAAa,EACb,MAAM,EACN,cAAc,EACd,QAAQ,EACR,UAAU,EACV,OAAO,EACP,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,WAAmB,EAAE,OAAe,EAAE,OAAe,EAAE,EAAE;QACxD,KAAK,CAAC,SAAS,CAAC,WAAW,EAAE,OAAO,EAAE,OAAO,CAAC,CAAA;IAChD,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,GAAG,cAAc,CAAC;QAChD,GAAG;QACH,SAAS;QACT,SAAS;QACT,MAAM;QACN,UAAU;KACX,CAAC,CAAA;IAEF,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,iBAKI,YAAY,EACxB,WAAW,EAAE,WAAW,EACxB,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,KAAK,CAAC,EAAE;YACpB,KAAK,CAAC,cAAc,EAAE,CAAA;QACxB,CAAC,EACD,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM;YACN,KAAK,EAAE,cAAc;YACrB,QAAQ,EAAE,QAAQ;SACnB,IAEA,CAAC,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAGrC,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,IAAI,EAAE,CAAC;YACP,SAAS,EAAE,aAAa,OAAO,OAAO,OAAO,KAAK;YAClD,UAAU,EAAE,WAAW;SACxB,IAEA,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAC1B,oBAAC,cAAc,IACb,GAAG,EAAE,GAAG,EAAE,IAAI,EAAE,EAAE,EAClB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,EAAE,EACX,OAAO,EAAE,EAAE,GACX,CACH,CAAC,CACE,CACP,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,OAAG,CACZ,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}
+{"version":3,"file":"MSACanvas.js","sourceRoot":"","sources":["../../../src/components/msa/MSACanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAA;AACxD,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,cAAc,MAAM,qBAAsB,CAAA;AAIjD,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EACJ,GAAG,EACH,aAAa,EACb,MAAM,EACN,cAAc,EACd,QAAQ,EACR,UAAU,EACV,OAAO,EACP,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,WAAmB,EAAE,OAAe,EAAE,OAAe,EAAE,EAAE;QACxD,KAAK,CAAC,SAAS,CAAC,WAAW,EAAE,OAAO,EAAE,OAAO,EAAE,KAAK,CAAC,aAAa,CAAC,CAAA;IACrE,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,GAAG,cAAc,CAAC;QAChD,GAAG;QACH,SAAS;QACT,SAAS;QACT,MAAM;QACN,UAAU;KACX,CAAC,CAAA;IAEF,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,iBAGI,YAAY,EACxB,WAAW,EAAE,WAAW,EACxB,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,KAAK,CAAC,EAAE;YACpB,KAAK,CAAC,cAAc,EAAE,CAAA;QACxB,CAAC,EACD,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM;YACN,KAAK,EAAE,cAAc;YACrB,QAAQ,EAAE,QAAQ;SACnB,IAEA,CAAC,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAGrC,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,IAAI,EAAE,CAAC;YACP,SAAS,EAAE,aAAa,OAAO,OAAO,OAAO,KAAK;YAClD,UAAU,EAAE,WAAW;SACxB,IAEA,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAC1B,oBAAC,cAAc,IACb,GAAG,EAAE,GAAG,EAAE,IAAI,EAAE,EAAE,EAClB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,EAAE,EACX,OAAO,EAAE,EAAE,GACX,CACH,CAAC,CACE,CACP,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,OAAG,CACZ,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

package/dist/components/msa/MSACanvasBlock.js

@@ -3,7 +3,6 @@ import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
-import ColumnStats from './ColumnStats.js';
 import { drawMsaRaster, rasterSupported } from './msaRaster.js';
 import { renderBoxFeatureCanvasBlock } from './renderBoxFeatureCanvasBlock.js';
 import { renderMSABlock } from './renderMSABlock.js';
@@ -23,6 +22,7 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
             ctx.clearRect(0, 0, canvasSize, canvasSize);
             renderBoxFeatureCanvasBlock({
                 ctx,
+                theme,
                 offsetX,
                 offsetY,
                 model,
@@ -47,7 +47,7 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
         height: canvasSize,
         deps: [model, offsetX, offsetY, theme],
     });
-    const { hoveredInsertion, mouseOverDomains, showColumnStats } = model;
+    const { hoveredInsertion, mouseOverDomains } = model;
     return (React.createElement(React.Fragment, null,
         React.createElement("canvas", { ref: ref, onMouseMove: event => {
                 if (ref.current) {
@@ -74,19 +74,17 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
             ' ',
             hoveredInsertion.letters.length > 20
                 ? `${hoveredInsertion.letters.slice(0, 20)}...`
-                : hoveredInsertion.letters)) : (React.createElement(React.Fragment, null,
-            mouseOverDomains.map(d => (React.createElement("div", { key: `${d.accession}-${d.start}-${d.end}` },
-                React.createElement("b", null, d.name),
-                " (",
-                d.accession,
-                ") ",
-                d.start,
-                "-",
-                d.end,
-                d.description ? (React.createElement(React.Fragment, null,
-                    React.createElement("br", null),
-                    d.description)) : null))),
-            showColumnStats ? React.createElement(ColumnStats, { model: model }) : null)))) : null));
+                : hoveredInsertion.letters)) : (mouseOverDomains.map(d => (React.createElement("div", { key: `${d.accession}-${d.start}-${d.end}` },
+            React.createElement("b", null, d.name),
+            " (",
+            d.accession,
+            ") ",
+            d.start,
+            "-",
+            d.end,
+            d.description ? (React.createElement(React.Fragment, null,
+                React.createElement("br", null),
+                d.description)) : null)))))) : null));
 });
 export default MSACanvasBlock;
 //# sourceMappingURL=MSACanvasBlock.js.map

package/dist/components/msa/MSACanvasBlock.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MSACanvasBlock.js","sourceRoot":"","sources":["../../../src/components/msa/MSACanvasBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,EAAE,aAAa,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAA;AAC/D,OAAO,EAAE,2BAA2B,EAAE,MAAM,kCAAkC,CAAA;AAC9E,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AAIxD,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,EACP,OAAO,GAKR;IACC,MAAM,EAAE,SAAS,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAC/C,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,EAAE,YAAY,EAAE,WAAW,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,gBAAgB,CAC3E;QACE,KAAK;QACL,OAAO;QACP,OAAO;KACR,CACF,CAAA;IAED,MAAM,UAAU,GAAG,SAAS,GAAG,kBAAkB,CAAA;IACjD,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,UAAU,EAAE,UAAU,CAAC,CAAA;YAC3C,2BAA2B,CAAC;gBAC1B,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,OAAO;gBACP,KAAK;aACN,CAAC,CAAA;YACF,yEAAyE;YACzE,yEAAyE;YACzE,yBAAyB;YACzB,MAAM,WAAW,GACf,CAAC,KAAK,CAAC,mBAAmB,IAAI,KAAK,CAAC,OAAO,IAAI,eAAe,EAAE,CAAA;YAClE,IAAI,WAAW,EAAE,CAAC;gBAChB,aAAa,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,OAAO,EAAE,CAAC,CAAA;YACxD,CAAC;YACD,cAAc,CAAC;gBACb,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,OAAO;gBACP,KAAK;gBACL,WAAW;aACZ,CAAC,CAAA;QACJ,CAAC;QACD,KAAK,EAAE,UAAU;QACjB,MAAM,EAAE,UAAU;QAClB,IAAI,EAAE,CAAC,KAAK,EAAE,OAAO,EAAE,OAAO,EAAE,KAAK,CAAC;KACvC,CAAC,CAAA;IAEF,MAAM,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IAEpD,OAAO,CACL;QACE,gCACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;oBAChB,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,OAAO,CAAC,CAAA;gBACjC,CAAC;YACH,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;oBAChB,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC,OAAO,CAAC,CAAA;gBAC7B,CAAC;YACH,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,YAAY,EAAE,CAAA;YAChB,CAAC,EACD,KAAK,EAAE,UAAU,EACjB,MAAM,EAAE,UAAU,EAClB,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,OAAO;gBACZ,IAAI,EAAE,OAAO;gBACb,KAAK,EAAE,SAAS;gBAChB,MAAM,EAAE,SAAS;aAClB,GACD;QACD,YAAY,CAAC,CAAC,CAAC,CACd,oBAAC,WAAW,IACV,WAAW,EAAE,EAAE,CAAC,EAAE,YAAY,CAAC,CAAC,EAAE,CAAC,EAAE,YAAY,CAAC,CAAC,GAAG,EAAE,EAAE,IAEzD,gBAAgB,CAAC,CAAC,CAAC,CAClB;;YACc,gBAAgB,CAAC,OAAO,CAAC,MAAM;YAC1C,KAAK,CAAC,YAAY,KAAK,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI;;YAAI,GAAG;YACnD,gBAAgB,CAAC,OAAO,CAAC,MAAM,GAAG,EAAE;gBACnC,CAAC,CAAC,GAAG,gBAAgB,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK;gBAC/C,CAAC,CAAC,gBAAgB,CAAC,OAAO,CAC3B,CACJ,CAAC,CAAC,CAAC,CACF,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACxB,6BAAK,GAAG,EAAE,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,EAAE;YAC5C,+BAAI,CAAC,CAAC,IAAI,CAAK;;YAAG,CAAC,CAAC,SAAS;;YAAI,CAAC,CAAC,KAAK;;YAAG,CAAC,CAAC,GAAG;YAC/C,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CACf;gBACE,+BAAM;gBACL,CAAC,CAAC,WAAW,CACb,CACJ,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAC,CACH,CACW,CACf,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/components/msa/MSAMouseoverCanvas.js

@@ -2,6 +2,7 @@ import React from 'react';
 import { isAlive } from '@jbrowse/mobx-state-tree';
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
+import { msaOverlayZIndex } from '../../constants.js';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import { renderMouseover } from './renderMSAMouseover.js';
 const MSAMouseoverCanvas = observer(function ({ model, }) {
@@ -25,7 +26,7 @@ const MSAMouseoverCanvas = observer(function ({ model, }) {
             left: 0,
             width,
             height,
-            zIndex: 1000,
+            zIndex: msaOverlayZIndex,
             pointerEvents: 'none',
         } }));
 });

package/dist/components/msa/MSAMouseoverCanvas.js.map

@@ -1 +1 @@
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package/dist/components/msa/domainBandCursor.d.ts

@@ -1,17 +1,13 @@
 import type { DomainBand } from '../../types.ts';
 /**
- * Left-to-right cursor over one row's domain bands, answering "which band is
- * drawn on top at this column" — the fill a letter there has to contrast
- * against.
+ * Left-to-right cursor over one row's domain bands that returns the band drawn
+ * on top at a column, for a letter's contrast color.
  *
- * Not simply the first band covering the column. The overlay paints in
- * `domainBands` order, largest first, so where signatures nest — a family
- * enclosing a domain, which InterProScan emits routinely — the box a reader
- * actually sees is the last one painted over that column. `stackIndex` is that
- * paint order.
+ * The overlay paints in `domainBands` order, largest first, so where signatures
+ * nest (InterProScan often emits a family enclosing a domain) the visible band
+ * is the last one painted. `stackIndex` is that paint order.
  *
- * `bands` must be sorted by start column (`domainBandsByStart`), and columns
- * must be visited in increasing order, which is what the block renderer does.
- * Both keep this to one pass over the bands per row rather than a scan per cell.
+ * `bands` must be sorted by start column (`domainBandsByStart`) and columns
+ * visited in increasing order, which keeps this to one pass per row.
  */
 export declare function domainBandCursor(bands: DomainBand[] | undefined): (col: number) => DomainBand | undefined;

package/dist/components/msa/domainBandCursor.js

@@ -1,17 +1,13 @@
 /**
- * Left-to-right cursor over one row's domain bands, answering "which band is
- * drawn on top at this column" — the fill a letter there has to contrast
- * against.
+ * Left-to-right cursor over one row's domain bands that returns the band drawn
+ * on top at a column, for a letter's contrast color.
  *
- * Not simply the first band covering the column. The overlay paints in
- * `domainBands` order, largest first, so where signatures nest — a family
- * enclosing a domain, which InterProScan emits routinely — the box a reader
- * actually sees is the last one painted over that column. `stackIndex` is that
- * paint order.
+ * The overlay paints in `domainBands` order, largest first, so where signatures
+ * nest (InterProScan often emits a family enclosing a domain) the visible band
+ * is the last one painted. `stackIndex` is that paint order.
  *
- * `bands` must be sorted by start column (`domainBandsByStart`), and columns
- * must be visited in increasing order, which is what the block renderer does.
- * Both keep this to one pass over the bands per row rather than a scan per cell.
+ * `bands` must be sorted by start column (`domainBandsByStart`) and columns
+ * visited in increasing order, which keeps this to one pass per row.
  */
 export function domainBandCursor(bands) {
     let next = 0;

package/dist/components/msa/domainBandCursor.js.map

@@ -1 +1 @@
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package/dist/components/msa/drawFeatureSpans.d.ts

@@ -0,0 +1,53 @@
+import type { HierarchyNode } from '../../hierarchy.ts';
+import type { Annotation, NodeWithIdsAndLength } from '../../types.ts';
+import type { RenderCtx } from '../renderCtx.ts';
+/** one drawn span: a feature, the lane it sits in, and its row's depth */
+export interface SpanBand {
+    annotation: Annotation;
+    lane: number;
+    laneCount: number;
+}
+/** one row's spans, at the row baseline `y` the tree layout gives it */
+export interface SpanRow<T extends SpanBand> {
+    y: number;
+    bands: T[];
+}
+/**
+ * Where a band lands inside its row. The alignment overlay fills the row, bars
+ * it along the bottom, or stacks thin sub-rows; a `features` row panel divides
+ * the row between its lanes.
+ */
+export interface SpanLayout {
+    /** the band height in a row needing `laneCount` lanes */
+    height: (laneCount: number) => number;
+    /** the band's top edge, from its row baseline, its lane and its height */
+    top: (y: number, lane: number, height: number) => number;
+    /** how far a strand head reaches past the body */
+    headLength: (height: number) => number;
+}
+/** the rows of `bandsByRow` that `leaves` covers, in display order */
+export declare function spanRows<T extends SpanBand>(leaves: HierarchyNode<NodeWithIdsAndLength>[], bandsByRow: Map<string, T[]>): SpanRow<T>[];
+/**
+ * The span mark, in whatever x space the caller maps its bands into: alignment
+ * columns for the domain overlay, panel pixels for a `features` row panel. A
+ * feature with a strand draws as an arrow, one without as a box, and a label
+ * draws inside the span wherever the text fits.
+ *
+ * `xOf` returns the span's `[xStart, xEnd]` in the context's coordinates, and
+ * the context is translated so that `y - rowHeight` is the row's top edge.
+ */
+export declare function drawFeatureSpans<T extends SpanBand>({ ctx, rows, layout, xOf, colors, labelOf, labelDrawn, contrastText, xMin, xMax, }: {
+    ctx: RenderCtx;
+    rows: SpanRow<T>[];
+    layout: SpanLayout;
+    xOf: (band: T) => [number, number];
+    colors: Map<Annotation, {
+        fill: string;
+        stroke: string;
+    }>;
+    labelOf?: (band: T) => string | undefined;
+    labelDrawn?: (band: T) => void;
+    contrastText: (color: string) => string;
+    xMin: number;
+    xMax: number;
+}): void;

package/dist/components/msa/drawFeatureSpans.js

@@ -0,0 +1,78 @@
+/** the rows of `bandsByRow` that `leaves` covers, in display order */
+export function spanRows(leaves, bandsByRow) {
+    const rows = [];
+    for (const leaf of leaves) {
+        const bands = bandsByRow.get(leaf.data.name);
+        if (bands && bands.length > 0) {
+            rows.push({ y: leaf.x, bands });
+        }
+    }
+    return rows;
+}
+/**
+ * The span mark, in whatever x space the caller maps its bands into: alignment
+ * columns for the domain overlay, panel pixels for a `features` row panel. A
+ * feature with a strand draws as an arrow, one without as a box, and a label
+ * draws inside the span wherever the text fits.
+ *
+ * `xOf` returns the span's `[xStart, xEnd]` in the context's coordinates, and
+ * the context is translated so that `y - rowHeight` is the row's top edge.
+ */
+export function drawFeatureSpans({ ctx, rows, layout, xOf, colors, labelOf, labelDrawn, contrastText, xMin, xMax, }) {
+    for (const { y, bands } of rows) {
+        const h = layout.height(bands[0].laneCount);
+        const headLen = layout.headLength(h);
+        for (const band of bands) {
+            const [xStart, xEnd] = xOf(band);
+            const w = xEnd - xStart;
+            if (xEnd < xMin || xStart > xMax) {
+                continue;
+            }
+            const t = layout.top(y, band.lane, h);
+            const { fill, stroke } = colors.get(band.annotation);
+            ctx.fillStyle = fill;
+            ctx.strokeStyle = stroke;
+            const { strand } = band.annotation;
+            if (strand === undefined) {
+                ctx.fillRect(xStart, t, w, h);
+                ctx.strokeRect(xStart, t, w, h);
+            }
+            else {
+                drawGeneArrow({ ctx, x: xStart, t, w, h, headLen, strand });
+            }
+            const label = labelOf?.(band);
+            if (label !== undefined) {
+                const fontSize = Math.min(h - 2, 11);
+                ctx.font = `${fontSize}px sans-serif`;
+                if (ctx.measureText(label).width + 2 <= w) {
+                    labelDrawn?.(band);
+                    ctx.fillStyle = contrastText(fill);
+                    ctx.textAlign = 'center';
+                    ctx.textBaseline = 'middle';
+                    ctx.fillText(label, xStart + w / 2, t + h / 2);
+                }
+            }
+        }
+    }
+}
+// A gene arrow: a full-width rectangular body spanning the feature's
+// start..end columns, plus a triangular head that points *beyond* that end in
+// the strand direction (right for +, left for -). Keeping the body aligned to
+// the exact start/end columns means + and - strand features read as having the
+// same boundaries; the arrow lives outside them purely to show transcription
+// direction, preserving the column-by-column homology down the rows.
+function drawGeneArrow({ ctx, x, t, w, h, headLen, strand, }) {
+    const dir = strand > 0 ? 1 : -1;
+    const bodyStart = strand > 0 ? x : x + w;
+    const bodyEnd = strand > 0 ? x + w : x;
+    ctx.beginPath();
+    ctx.moveTo(bodyStart, t);
+    ctx.lineTo(bodyEnd, t);
+    ctx.lineTo(bodyEnd + dir * headLen, t + h / 2);
+    ctx.lineTo(bodyEnd, t + h);
+    ctx.lineTo(bodyStart, t + h);
+    ctx.closePath();
+    ctx.fill();
+    ctx.stroke();
+}
+//# sourceMappingURL=drawFeatureSpans.js.map

package/dist/components/msa/drawFeatureSpans.js.map

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package/dist/components/msa/legendRows.d.ts

@@ -0,0 +1,8 @@
+import type { Legend } from '../../types.ts';
+export interface LegendRow {
+    key: string;
+    label: string;
+    color?: string;
+    hint?: string;
+}
+export declare function legendRows(legends: Legend[]): LegendRow[];

package/dist/components/msa/legendRows.js

@@ -0,0 +1,16 @@
+// the legends flattened into the rows both the overlay and the export stack
+// top to bottom. A title row separates one legend from the next, and a lone
+// legend needs no title.
+export function legendRows(legends) {
+    const titled = legends.length > 1;
+    return legends.flatMap(legend => [
+        ...(titled ? [{ key: legend.id, label: legend.title }] : []),
+        ...legend.entries.map(entry => ({
+            key: `${legend.id}:${entry.id}`,
+            label: entry.label,
+            color: entry.color,
+            hint: entry.id,
+        })),
+    ]);
+}
+//# sourceMappingURL=legendRows.js.map

package/dist/components/msa/legendRows.js.map

@@ -0,0 +1 @@
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