react-msaview 5.4.1 → 5.5.0

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

@@ -1 +1 @@
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+{"version":3,"file":"renderMSABlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderMSABlock.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AACtD,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,sBAAsB,EAAE,MAAM,eAAe,CAAA;AAQtD,MAAM,UAAU,cAAc,CAAC,EAC7B,KAAK,EACL,OAAO,EACP,OAAO,EACP,cAAc,EACd,GAAG,EACH,KAAK,EACL,0BAA0B,EAC1B,kBAAkB,EAClB,kBAAkB,GAWnB;IACC,MAAM,EACJ,QAAQ,EACR,SAAS,EACT,SAAS,EACT,QAAQ,EACR,kBAAkB,EAClB,mBAAmB,EACnB,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;IAChD,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;IACxB,GAAG,CAAC,YAAY,GAAG,YAAY,CAAA;IAC/B,WAAW,CAAC,GAAG,EAAE,QAAQ,EAAE,CAAC,OAAO,CAAC,CAAA;IAEpC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,eAAe,CAAC;QACvC,OAAO;QACP,UAAU,EAAE,EAAE;QACd,QAAQ;KACT,CAAC,CAAA;IACF,MAAM,aAAa,GAAG,gBAAgB,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,UAAU,EAAE,EAAE,EAAE,CAAC,CAAA;IAC1E,MAAM,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACrC,MAAM,YAAY,GAAG,UAAU;QAC7B,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC;QAC9C,CAAC,CAAC,IAAI,CAAA;IAER,IAAI,CAAC,mBAAmB,EAAE,CAAC;QACzB,gBAAgB,CAAC;YACf,KAAK;YACL,GAAG;YACH,KAAK;YACL,cAAc;YACd,MAAM;YACN,IAAI;YACJ,aAAa;YACb,YAAY;SACb,CAAC,CAAA;IACJ,CAAC;SAAM,CAAC;QACN,QAAQ,CAAC;YACP,KAAK;YACL,GAAG;YACH,MAAM;YACN,IAAI;YACJ,aAAa;YACb,YAAY;SACb,CAAC,CAAA;IACJ,CAAC;IACD,uBAAuB,CAAC;QACtB,KAAK;QACL,GAAG;QACH,MAAM;QACN,IAAI;QACJ,aAAa;KACd,CAAC,CAAA;IACF,GAAG,CAAC,cAAc,EAAE,CAAA;AACtB,CAAC;AAED,SAAS,gBAAgB,CAAC,EACxB,KAAK,EACL,GAAG,EACH,KAAK,EACL,cAAc,EACd,aAAa,EACb,MAAM,EACN,IAAI,EACJ,YAAY,GAUb;IACC,MAAM,EACJ,OAAO,EACP,eAAe,EACf,WAAW,EACX,OAAO,EACP,QAAQ,EACR,SAAS,EACT,UAAU,EACV,cAAc,EACd,WAAW,EACX,YAAY,GACb,GAAG,KAAK,CAAA;IAET,MAAM,UAAU,GAAG,eAAe,KAAK,0BAA0B,CAAA;IACjE,MAAM,iBAAiB,GAAG,eAAe,KAAK,0BAA0B,CAAA;IACxE,IAAI,CAAC,OAAO,IAAI,CAAC,cAAc,EAAE,CAAC;QAChC,OAAM;IACR,CAAC;IACD,MAAM,cAAc,GAAG,MAAM,GAAG,QAAQ,CAAA;IACxC,MAAM,YAAY,GAAG,QAAQ,GAAG,CAAC,CAAA;IACjC,MAAM,gBAAgB,GAAG,SAAS,GAAG,CAAC,CAAA;IAEtC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,IAAI,CAAA;QAC1B,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,CAAA;QACjB,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAClD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,SAAQ;QACV,CAAC;QACD,MAAM,KAAK,GAAG,CAAC,GAAG,SAAS,CAAA;QAC3B,MAAM,KAAK,GAAG,CAAC,GAAG,gBAAgB,CAAA;QAElC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;YACtB,MAAM,CAAC,GAAG,CAAC,GAAG,QAAQ,GAAG,cAAc,CAAA;YACvC,MAAM,mBAAmB,GACvB,YAAY,IAAI,IAAI,KAAK,UAAU,IAAI,MAAM,KAAK,YAAY,CAAC,CAAC,CAAC,CAAA;YAEnE,IAAI,KAAyB,CAAA;YAC7B,IAAI,UAAU,EAAE,CAAC;gBACf,KAAK,GAAG,WAAW,CAAC,MAAM,GAAG,CAAC,CAAE,CAAC,MAAM,CAAC,CAAA;YAC1C,CAAC;iBAAM,IAAI,iBAAiB,EAAE,CAAC;gBAC7B,MAAM,SAAS,GAAG,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,CAAA;gBAC3C,KAAK,GAAG,MAAM,KAAK,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;YACnE,CAAC;iBAAM,CAAC;gBACN,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,CAAA;YAC7B,CAAC;YAED,IAAI,OAAO,EAAE,CAAC;gBACZ,GAAG,CAAC,SAAS,GAAG,mBAAmB;oBACjC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK;oBAC5B,CAAC,CAAC,KAAK,IAAI,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,CAAA;gBAC7C,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;YAC7C,CAAC;YAED,IAAI,cAAc,EAAE,CAAC;gBACnB,GAAG,CAAC,SAAS,GAAG,OAAO;oBACrB,CAAC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,IAAI,OAAO,CAAC;oBACrC,CAAC,CAAC,KAAK;wBACL,CAAC,CAAC,sBAAsB,CAAC,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,CAAC;wBACjE,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAA;gBAChC,GAAG,CAAC,QAAQ,CACV,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,EAClC,CAAC,GAAG,YAAY,EAChB,KAAK,CACN,CAAA;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,qFAAqF;AACrF,qCAAqC;AACrC,SAAS,QAAQ,CAAC,EAChB,KAAK,EACL,GAAG,EACH,aAAa,EACb,MAAM,EACN,IAAI,EACJ,YAAY,GAQb;IACC,MAAM,EAAE,cAAc,EAAE,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IAE1E,IAAI,CAAC,cAAc,EAAE,CAAC;QACpB,OAAM;IACR,CAAC;IACD,MAAM,cAAc,GAAG,MAAM,GAAG,QAAQ,CAAA;IACxC,MAAM,YAAY,GAAG,QAAQ,GAAG,CAAC,CAAA;IACjC,MAAM,gBAAgB,GAAG,SAAS,GAAG,CAAC,CAAA;IACtC,kDAAkD;IAClD,GAAG,CAAC,SAAS,GAAG,OAAO,CAAA;IAEvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,IAAI,CAAA;QAC1B,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,GAAG,gBAAgB,CAAA;QACpC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAClD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,SAAQ;QACV,CAAC;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC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package/dist/components/msa/renderMSAMouseover.js

@@ -1,7 +1,29 @@
 const hoverColor = 'rgba(0,0,0,0.15)';
 const highlightColor = 'rgba(128,128,0,0.2)';
+// the persistent highlightColumns overlay: a stronger fill plus a solid border
+// so a domain/motif band reads clearly over the colored alignment cells (the
+// faint hover-style wash alone is invisible against clustalx coloring)
+const highlightColumnsFill = 'rgba(255,140,0,0.28)';
+const highlightColumnsBorder = 'rgba(210,90,0,0.95)';
 const referenceColor = 'rgba(0,128,255,0.3)'; // Blue highlight for reference row
 const multiRowHoverColor = 'rgba(255,165,0,0.15)'; // Orange highlight for multi-row tree hover
+// Collapse sorted column indices into contiguous [start,end] runs so a run of
+// highlighted columns draws as one bordered band rather than per-column slices
+// (which would draw internal borders).
+function contiguousRuns(columns) {
+    const sorted = [...columns].sort((a, b) => a - b);
+    const runs = [];
+    for (const col of sorted) {
+        const last = runs.at(-1);
+        if (last && col === last.end + 1) {
+            last.end = col;
+        }
+        else {
+            runs.push({ start: col, end: col });
+        }
+    }
+    return runs;
+}
 export function renderMouseover({ ctx, model, }) {
     const { mouseCol, colWidth, msaAreaWidth, verticalScrollbarWidth, height, rowHeight, scrollX, scrollY, mouseRow, mouseClickRow, mouseClickCol, relativeTo, hoveredTreeNode, highlightedColumns, highResScaleFactor, } = model;
     const width = msaAreaWidth - verticalScrollbarWidth;
@@ -26,11 +48,17 @@ export function renderMouseover({ ctx, model, }) {
             }
         }
     }
-    // Highlight multiple columns
+    // Highlight multiple columns — draw each contiguous run as a filled, bordered
+    // band so a domain/motif highlight is clearly visible over the alignment
     if (highlightedColumns?.length) {
-        ctx.fillStyle = highlightColor;
-        for (const col of highlightedColumns) {
-            ctx.fillRect(col * colWidth + scrollX, 0, colWidth, height);
+        ctx.lineWidth = 2;
+        for (const { start, end } of contiguousRuns(highlightedColumns)) {
+            const x = start * colWidth + scrollX;
+            const w = (end - start + 1) * colWidth;
+            ctx.fillStyle = highlightColumnsFill;
+            ctx.fillRect(x, 0, w, height);
+            ctx.strokeStyle = highlightColumnsBorder;
+            ctx.strokeRect(x, 0, w, height);
         }
     }
     if (mouseCol !== undefined) {

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

@@ -1 +1 @@
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+{"version":3,"file":"renderMSAMouseover.js","sourceRoot":"","sources":["../../../src/components/msa/renderMSAMouseover.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,GAAG,kBAAkB,CAAA;AACrC,MAAM,cAAc,GAAG,qBAAqB,CAAA;AAC5C,+EAA+E;AAC/E,6EAA6E;AAC7E,uEAAuE;AACvE,MAAM,oBAAoB,GAAG,sBAAsB,CAAA;AACnD,MAAM,sBAAsB,GAAG,qBAAqB,CAAA;AACpD,MAAM,cAAc,GAAG,qBAAqB,CAAA,CAAC,mCAAmC;AAChF,MAAM,kBAAkB,GAAG,sBAAsB,CAAA,CAAC,4CAA4C;AAE9F,8EAA8E;AAC9E,+EAA+E;AAC/E,uCAAuC;AACvC,SAAS,cAAc,CAAC,OAAiB;IACvC,MAAM,MAAM,GAAG,CAAC,GAAG,OAAO,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IACjD,MAAM,IAAI,GAAqC,EAAE,CAAA;IACjD,KAAK,MAAM,GAAG,IAAI,MAAM,EAAE,CAAC;QACzB,MAAM,IAAI,GAAG,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;QACxB,IAAI,IAAI,IAAI,GAAG,KAAK,IAAI,CAAC,GAAG,GAAG,CAAC,EAAE,CAAC;YACjC,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,CAAC,CAAA;QACrC,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,EAC9B,GAAG,EACH,KAAK,GAIN;IACC,MAAM,EACJ,QAAQ,EACR,QAAQ,EACR,YAAY,EACZ,sBAAsB,EACtB,MAAM,EACN,SAAS,EACT,OAAO,EACP,OAAO,EACP,QAAQ,EACR,aAAa,EACb,aAAa,EACb,UAAU,EACV,eAAe,EACf,kBAAkB,EAClB,kBAAkB,GACnB,GAAG,KAAK,CAAA;IACT,MAAM,KAAK,GAAG,YAAY,GAAG,sBAAsB,CAAA;IACnD,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,oDAAoD;IACpD,IAAI,UAAU,EAAE,CAAC;QACf,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;QAC3D,IAAI,iBAAiB,KAAK,SAAS,EAAE,CAAC;YACpC,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;YAC9B,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,iBAAiB,GAAG,SAAS,GAAG,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;QAC5E,CAAC;IACH,CAAC;IAED,sEAAsE;IACtE,IAAI,eAAe,EAAE,CAAC;QACpB,GAAG,CAAC,SAAS,GAAG,kBAAkB,CAAA;QAClC,KAAK,MAAM,cAAc,IAAI,eAAe,CAAC,eAAe,EAAE,CAAC;YAC7D,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,cAAc,CAAC,CAAA;YACtD,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;gBAC3B,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,QAAQ,GAAG,SAAS,GAAG,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;YACnE,CAAC;QACH,CAAC;IACH,CAAC;IAED,8EAA8E;IAC9E,yEAAyE;IACzE,IAAI,kBAAkB,EAAE,MAAM,EAAE,CAAC;QAC/B,GAAG,CAAC,SAAS,GAAG,CAAC,CAAA;QACjB,KAAK,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,cAAc,CAAC,kBAAkB,CAAC,EAAE,CAAC;YAChE,MAAM,CAAC,GAAG,KAAK,GAAG,QAAQ,GAAG,OAAO,CAAA;YACpC,MAAM,CAAC,GAAG,CAAC,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAA;YACtC,GAAG,CAAC,SAAS,GAAG,oBAAoB,CAAA;YACpC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC,CAAA;YAC7B,GAAG,CAAC,WAAW,GAAG,sBAAsB,CAAA;YACxC,GAAG,CAAC,UAAU,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC,CAAA;QACjC,CAAC;IACH,CAAC;IAED,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;QAC3B,GAAG,CAAC,SAAS,GAAG,UAAU,CAAA;QAC1B,GAAG,CAAC,QAAQ,CAAC,QAAQ,GAAG,QAAQ,GAAG,OAAO,EAAE,CAAC,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAA;IAClE,CAAC;IACD,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;QAC3B,GAAG,CAAC,SAAS,GAAG,UAAU,CAAA;QAC1B,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,QAAQ,GAAG,SAAS,GAAG,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;IACnE,CAAC;IACD,IAAI,aAAa,KAAK,SAAS,EAAE,CAAC;QAChC,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;QAC9B,GAAG,CAAC,QAAQ,CAAC,aAAa,GAAG,QAAQ,GAAG,OAAO,EAAE,CAAC,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAA;IACvE,CAAC;IACD,IAAI,aAAa,KAAK,SAAS,EAAE,CAAC;QAChC,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;QAC9B,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,aAAa,GAAG,SAAS,GAAG,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;IACxE,CAAC;AACH,CAAC"}

package/dist/components/renderCtx.d.ts

@@ -4,4 +4,4 @@
  * SVG export) satisfy this, so renderers can be typed against it without an
  * `as any` cast at the SVG-export boundary.
  */
-export type RenderCtx = Pick<CanvasRenderingContext2D, 'arc' | 'beginPath' | 'clearRect' | 'closePath' | 'fill' | 'fillRect' | 'fillStyle' | 'fillText' | 'font' | 'lineTo' | 'lineWidth' | 'measureText' | 'moveTo' | 'resetTransform' | 'scale' | 'setLineDash' | 'stroke' | 'strokeRect' | 'strokeStyle' | 'textAlign' | 'translate'>;
+export type RenderCtx = Pick<CanvasRenderingContext2D, 'arc' | 'beginPath' | 'clearRect' | 'closePath' | 'fill' | 'fillRect' | 'fillStyle' | 'fillText' | 'font' | 'lineTo' | 'lineWidth' | 'measureText' | 'moveTo' | 'resetTransform' | 'scale' | 'setLineDash' | 'stroke' | 'strokeRect' | 'strokeStyle' | 'textAlign' | 'textBaseline' | 'translate'>;

package/dist/components/tracks/renderTracksSvg.js

@@ -23,13 +23,13 @@ export function drawTextTrackContent({ ctx, data, colorScheme, contrastScheme, b
     const str = data?.slice(xStart, xEnd);
     for (let i = 0; str && i < str.length; i++) {
         const letter = str[i];
-        const color = colorScheme[letter.toUpperCase()];
+        const upper = letter.toUpperCase();
         if (bgColor) {
             const x = (xStart + i) * colWidth;
-            ctx.fillStyle = color || 'white';
+            ctx.fillStyle = colorScheme[upper] || 'white';
             ctx.fillRect(x, 0, colWidth, rowHeight);
             if (rowHeight >= 10 && colWidth >= rowHeight / 2) {
-                ctx.fillStyle = contrastScheme[letter.toUpperCase()] || 'black';
+                ctx.fillStyle = contrastScheme[upper] || 'black';
                 ctx.fillText(letter, x + colWidth / 2, rowHeight / 2 + 1);
             }
         }

package/dist/components/tracks/renderTracksSvg.js.map

@@ -1 +1 @@
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package/dist/constants.d.ts

@@ -8,6 +8,9 @@ export declare const defaultShowDomains = false;
 export declare const defaultHideGaps = true;
 export declare const defaultAllowedGappyness = 100;
 export declare const defaultSubFeatureRows = false;
+export declare const subFeatureRowHeight = 4;
+export declare const segmentFeatureTypes: Set<string>;
+export declare const segmentShades: string[];
 export declare const defaultDrawMsaLetters = true;
 export declare const defaultScrollZoom = false;
 export declare const minColWidth = 0.2;

package/dist/constants.js

@@ -9,6 +9,22 @@ export const defaultShowDomains = false;
 export const defaultHideGaps = true;
 export const defaultAllowedGappyness = 100;
 export const defaultSubFeatureRows = false;
+// row height for each stacked feature when subFeatureRows is on
+export const subFeatureRowHeight = 4;
+// Feature types that are ordinal *segments* of a single transcript (exons and
+// the like) rather than categorical domains. Their identity is their position,
+// so the overlay alternates two shades to mark boundaries and labels them by
+// number, instead of assigning every one a distinct hue + legend row.
+export const segmentFeatureTypes = new Set([
+    'exon',
+    'CDS',
+    'five_prime_UTR',
+    'three_prime_UTR',
+    'UTR',
+    'intron',
+]);
+// the two shades alternated across adjacent segments (exons)
+export const segmentShades = ['#9fb6d4', '#d4dcea'];
 export const defaultDrawMsaLetters = true;
 export const defaultScrollZoom = false;
 // Zoom limits, px per cell. maxCellSize caps both smooth zoom and the stepwise

package/dist/constants.js.map

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package/dist/createPaletteMap.d.ts

@@ -1,6 +1,9 @@
 /**
- * Creates a map from keys to colors using ggplot-style palettes.
- * The palette is selected based on the number of keys.
+ * Creates a map from keys to colors. Up to the largest ggplot palette (8 keys)
+ * we use the hand-picked ggplot colors; beyond that — e.g. a gene-structure
+ * overlay with one feature per exon — we generate evenly spaced HSL hues so
+ * every key still gets a distinct, stable color instead of running off the end
+ * of the palette.
  */
 export declare function createPaletteMap(keys: string[]): {
     [k: string]: string;

package/dist/createPaletteMap.js

@@ -1,11 +1,21 @@
+import { colord } from 'colord';
 import palettes from "./ggplotPalettes.js";
 /**
- * Creates a map from keys to colors using ggplot-style palettes.
- * The palette is selected based on the number of keys.
+ * Creates a map from keys to colors. Up to the largest ggplot palette (8 keys)
+ * we use the hand-picked ggplot colors; beyond that — e.g. a gene-structure
+ * overlay with one feature per exon — we generate evenly spaced HSL hues so
+ * every key still gets a distinct, stable color instead of running off the end
+ * of the palette.
  */
 export function createPaletteMap(keys) {
-    const k = Math.min(keys.length - 1, palettes.length - 1);
-    const palette = palettes[k];
-    return Object.fromEntries(keys.map((key, i) => [key, palette[i]]));
+    const n = keys.length;
+    if (n <= palettes.length) {
+        const palette = palettes[n - 1];
+        return Object.fromEntries(keys.map((key, i) => [key, palette[i]]));
+    }
+    return Object.fromEntries(keys.map((key, i) => [
+        key,
+        colord({ h: (i * 360) / n, s: 60, l: 60 }).toHex(),
+    ]));
 }
 //# sourceMappingURL=createPaletteMap.js.map

package/dist/createPaletteMap.js.map

@@ -1 +1 @@
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+{"version":3,"file":"createPaletteMap.js","sourceRoot":"","sources":["../src/createPaletteMap.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAE/B,OAAO,QAAQ,MAAM,qBAAqB,CAAA;AAE1C;;;;;;GAMG;AACH,MAAM,UAAU,gBAAgB,CAAC,IAAc;IAC7C,MAAM,CAAC,GAAG,IAAI,CAAC,MAAM,CAAA;IACrB,IAAI,CAAC,IAAI,QAAQ,CAAC,MAAM,EAAE,CAAC;QACzB,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;QAChC,OAAO,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,CAAA;IACrE,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;QACnB,GAAG;QACH,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,KAAK,EAAE;KACnD,CAAC,CACH,CAAA;AACH,CAAC"}

package/dist/launchInterProScan.d.ts

@@ -6,11 +6,13 @@ export interface InterProScanResults {
                 name: string;
                 description: string;
                 accession: string;
+                featureType?: string;
             };
         };
         locations: {
             start: number;
             end: number;
+            strand?: number;
         }[];
     }[];
     xref: {

package/dist/launchInterProScan.js.map

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

@@ -6,6 +6,14 @@ import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { Theme } from '@mui/material';
 /**
  * #stateModel MsaView
+ *
+ * The main MSAView state model. Holds the loaded alignment, tree, and optional
+ * InterProScan domain annotations, plus all display state (color scheme, zoom,
+ * scroll, collapsed clades). It composes in members from `DialogQueueSessionMixin`,
+ * `Tree`, and `MSAModel` (see Inherited members below). Data is loaded reactively
+ * from the `msaFilehandle` / `treeFilehandle` / `gffFilehandle` properties, or set
+ * directly with `setData`. Most state is persisted into the shareable URL.
+ *
  * #example
  * ```js
  * import { MSAModelF } from 'react-msaview'
@@ -263,10 +271,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
 } & {
     /**
      * #action
+     * draw the alignment with positions numbered relative to the given row's
+     * sequence (its node id), instead of in raw MSA-column coordinates
      */
     drawRelativeTo(id: string | undefined): void;
     /**
      * #action
+     * hide columns that are entirely (or mostly, see allowedGappyness) gaps
      */
     setHideGaps(arg: boolean): void;
     /**
@@ -321,6 +332,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     setHighlightedColumns(columns?: number[]): void;
     /**
      * #action
+     * toggle the InterProScan protein-domain overlay on the alignment
      */
     setShowDomains(arg: boolean): void;
     /**
@@ -354,14 +366,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     setCurrentAlignment(n: number): void;
     /**
      * #action
+     * collapse or un-collapse the subtree rooted at the given tree node id
      */
     toggleCollapsed(node: string): void;
     /**
      * #action
+     * show only the subtree rooted at the given node id (pass undefined to
+     * show the whole tree again)
      */
     setShowOnly(node?: string): void;
     /**
      * #action
+     * set the alignment/tree/metadata/domain data directly from strings,
+     * bypassing the filehandle loaders
      */
     setData(data: {
         msa?: string;
@@ -675,6 +692,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     calculateNeighborJoiningTreeFromMSA(): void;
     /**
      * #action
+     * restore the default column width and row height
      */
     resetZoom(): void;
     /**
@@ -853,32 +871,40 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }>;
     readonly tidyInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[];
     readonly tidyFilteredInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[];
     readonly tidyFilteredGatheredInterProAnnotations: Record<string, {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[]>;
 } & {
     /**
@@ -890,12 +916,81 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly verticalScrollbarWidth: 0 | 20;
+    /**
+     * #getter
+     * ordinal segment types (exons etc.), ordered by sequence position so
+     * exon-1..exon-14 read left-to-right; colored by alternating shade and
+     * labeled by number rather than each getting a distinct hue + legend row
+     */
+    readonly segmentDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
+    /**
+     * #getter
+     * categorical feature types (InterPro domains and the like) that each get
+     * their own color and a legend entry
+     */
+    readonly categoricalDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
     readonly fillPalette: {
-        [k: string]: string;
+        [x: string]: string;
     };
     readonly strokePalette: {
         [k: string]: string;
     };
+    /**
+     * #getter
+     * accession -> number drawn on each segment band: the trailing number of
+     * the feature name ("exon-3" -> "3"), else its 1-based position
+     */
+    readonly segmentLabels: Map<string, string>;
+    /**
+     * #getter
+     * the domain types currently drawn on the alignment (filtered-on), shared
+     * by the on-screen legend and the SVG export legend. Ordinal segments
+     * (exons) are excluded — they read as a numbered gene model, not a color
+     * key — so this is the categorical types ordered by sequence position
+     */
+    readonly visibleDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
+    /**
+     * #getter
+     * domain annotations under the mouse, hit-tested against the exact visible
+     * column span each box is drawn at (so it matches the overlay across gaps)
+     */
+    readonly mouseOverDomains: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
     /**
      * #method
      */

package/dist/model.js

@@ -10,7 +10,7 @@ import { clustalXColumnColors } from "./clustalX.js";
 import colorSchemes from "./colorSchemes.js";
 import ConservationTrack from "./components/ConservationTrack.js";
 import TextTrack from "./components/TextTrack.js";
-import { defaultAllowedGappyness, defaultBgColor, defaultColWidth, defaultColorSchemeName, defaultCurrentAlignment, defaultDrawLabels, defaultDrawMsaLetters, defaultDrawNodeBubbles, defaultDrawTree, defaultHeight, defaultHideGaps, defaultLabelsAlignRight, defaultRowHeight, defaultScrollX, defaultScrollY, defaultScrollZoom, defaultShowBranchLen, defaultShowDomains, defaultSubFeatureRows, defaultTreeAreaWidth, defaultTreeWidth, maxCellSize, minColWidth, minRowHeight, } from "./constants.js";
+import { defaultAllowedGappyness, defaultBgColor, defaultColWidth, defaultColorSchemeName, defaultCurrentAlignment, defaultDrawLabels, defaultDrawMsaLetters, defaultDrawNodeBubbles, defaultDrawTree, defaultHeight, defaultHideGaps, defaultLabelsAlignRight, defaultRowHeight, defaultScrollX, defaultScrollY, defaultScrollZoom, defaultShowBranchLen, defaultShowDomains, defaultSubFeatureRows, defaultTreeAreaWidth, defaultTreeWidth, maxCellSize, minColWidth, minRowHeight, segmentFeatureTypes, segmentShades, } from "./constants.js";
 import { createPaletteMap } from "./createPaletteMap.js";
 import { fetchTextWithProgress, isAbortError } from "./fetchUtils.js";
 import { flatToTree } from "./flatToTree.js";
@@ -34,6 +34,14 @@ function parseTreeText(text) {
 }
 /**
  * #stateModel MsaView
+ *
+ * The main MSAView state model. Holds the loaded alignment, tree, and optional
+ * InterProScan domain annotations, plus all display state (color scheme, zoom,
+ * scroll, collapsed clades). It composes in members from `DialogQueueSessionMixin`,
+ * `Tree`, and `MSAModel` (see Inherited members below). Data is loaded reactively
+ * from the `msaFilehandle` / `treeFilehandle` / `gffFilehandle` properties, or set
+ * directly with `setData`. Most state is persisted into the shareable URL.
+ *
  * #example
  * ```js
  * import { MSAModelF } from 'react-msaview'
@@ -269,12 +277,15 @@ function stateModelFactory() {
         .actions(self => ({
         /**
          * #action
+         * draw the alignment with positions numbered relative to the given row's
+         * sequence (its node id), instead of in raw MSA-column coordinates
          */
         drawRelativeTo(id) {
             self.relativeTo = id;
         },
         /**
          * #action
+         * hide columns that are entirely (or mostly, see allowedGappyness) gaps
          */
         setHideGaps(arg) {
             self.hideGaps = arg;
@@ -350,6 +361,7 @@ function stateModelFactory() {
         },
         /**
          * #action
+         * toggle the InterProScan protein-domain overlay on the alignment
          */
         setShowDomains(arg) {
             self.showDomains = arg;
@@ -398,6 +410,7 @@ function stateModelFactory() {
         },
         /**
          * #action
+         * collapse or un-collapse the subtree rooted at the given tree node id
          */
         toggleCollapsed(node) {
             if (self.collapsed.includes(node)) {
@@ -409,12 +422,16 @@ function stateModelFactory() {
         },
         /**
          * #action
+         * show only the subtree rooted at the given node id (pass undefined to
+         * show the whole tree again)
          */
         setShowOnly(node) {
             self.showOnly = node;
         },
         /**
          * #action
+         * set the alignment/tree/metadata/domain data directly from strings,
+         * bypassing the filehandle loaders
          */
         setData(data) {
             self.data = cast(data);
@@ -1056,6 +1073,7 @@ function stateModelFactory() {
         },
         /**
          * #action
+         * restore the default column width and row height
          */
         resetZoom() {
             self.setColWidth(defaultColWidth);
@@ -1370,13 +1388,15 @@ function stateModelFactory() {
                     .flatMap(([id, val]) => val.matches.flatMap(({ signature, locations }) => {
                     const { entry } = signature;
                     return entry
-                        ? locations.map(({ start, end }) => ({
+                        ? locations.map(({ start, end, strand }) => ({
                             id,
                             name: entry.name,
                             accession: entry.accession,
                             description: entry.description,
+                            featureType: entry.featureType,
                             start,
                             end,
+                            strand,
                         }))
                         : [];
                 }))
@@ -1405,8 +1425,32 @@ function stateModelFactory() {
         get verticalScrollbarWidth() {
             return self.showVerticalScrollbar ? 20 : 0;
         },
+        /**
+         * #getter
+         * ordinal segment types (exons etc.), ordered by sequence position so
+         * exon-1..exon-14 read left-to-right; colored by alternating shade and
+         * labeled by number rather than each getting a distinct hue + legend row
+         */
+        get segmentDomainTypes() {
+            return [...self.tidyInterProAnnotationTypes.values()]
+                .filter(d => segmentFeatureTypes.has(d.featureType ?? ''))
+                .toSorted((a, b) => a.start - b.start);
+        },
+        /**
+         * #getter
+         * categorical feature types (InterPro domains and the like) that each get
+         * their own color and a legend entry
+         */
+        get categoricalDomainTypes() {
+            return [...self.tidyInterProAnnotationTypes.values()].filter(d => !segmentFeatureTypes.has(d.featureType ?? ''));
+        },
         get fillPalette() {
-            return createPaletteMap([...self.tidyInterProAnnotationTypes.keys()]);
+            const segments = Object.fromEntries(this.segmentDomainTypes.map((d, i) => [
+                d.accession,
+                segmentShades[i % segmentShades.length],
+            ]));
+            const categorical = createPaletteMap(this.categoricalDomainTypes.map(d => d.accession));
+            return { ...segments, ...categorical };
         },
         get strokePalette() {
             return transform(this.fillPalette, ([key, val]) => [
@@ -1414,6 +1458,50 @@ function stateModelFactory() {
                 colord(val).darken(0.1).toHex(),
             ]);
         },
+        /**
+         * #getter
+         * accession -> number drawn on each segment band: the trailing number of
+         * the feature name ("exon-3" -> "3"), else its 1-based position
+         */
+        get segmentLabels() {
+            return new Map(this.segmentDomainTypes.map((d, i) => {
+                const m = /(\d+)\s*$/.exec(d.name);
+                return [d.accession, m ? m[1] : `${i + 1}`];
+            }));
+        },
+        /**
+         * #getter
+         * the domain types currently drawn on the alignment (filtered-on), shared
+         * by the on-screen legend and the SVG export legend. Ordinal segments
+         * (exons) are excluded — they read as a numbered gene model, not a color
+         * key — so this is the categorical types ordered by sequence position
+         */
+        get visibleDomainTypes() {
+            return this.categoricalDomainTypes
+                .filter(d => self.featureFilters.get(d.accession))
+                .toSorted((a, b) => a.start - b.start);
+        },
+        /**
+         * #getter
+         * domain annotations under the mouse, hit-tested against the exact visible
+         * column span each box is drawn at (so it matches the overlay across gaps)
+         */
+        get mouseOverDomains() {
+            const { mouseCol } = self;
+            const name = self.mouseOverRowName;
+            if (name !== undefined && mouseCol !== undefined) {
+                const entry = self.tidyFilteredGatheredInterProAnnotations[name] ?? [];
+                return entry.filter(d => {
+                    const m1 = self.seqPosToVisibleCol(name, d.start - 1);
+                    const m2 = self.seqPosToVisibleCol(name, d.end);
+                    return (m1 !== undefined &&
+                        m2 !== undefined &&
+                        mouseCol >= m1 &&
+                        mouseCol < m2);
+                });
+            }
+            return [];
+        },
         /**
          * #method
          */