react-msaview 5.4.0 → 5.5.0

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

@@ -1 +1 @@
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+{"version":3,"file":"renderBoxFeatureCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderBoxFeatureCanvasBlock.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,mBAAmB,EAAE,MAAM,oBAAoB,CAAA;AAOxD,MAAM,UAAU,2BAA2B,CAAC,EAC1C,KAAK,EACL,OAAO,EACP,OAAO,EACP,GAAG,EACH,0BAA0B,EAC1B,kBAAkB,GAQnB;IACC,MAAM,EAAE,SAAS,EAAE,SAAS,EAAE,kBAAkB,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACvE,IAAI,WAAW,EAAE,CAAC;QAChB,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;QAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;QAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;QAEhD,MAAM,aAAa,GAAG,gBAAgB,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,UAAU,EAAE,EAAE,EAAE,CAAC,CAAA;QAE1E,SAAS,CAAC;YACR,KAAK;YACL,GAAG;YACH,aAAa;SACd,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,SAAS,SAAS,CAAC,EACjB,KAAK,EACL,GAAG,EACH,aAAa,GAKd;IACC,MAAM,EACJ,cAAc,EACd,QAAQ,EACR,SAAS,EACT,WAAW,EACX,aAAa,EACb,aAAa,EACb,cAAc,EACd,uCAAuC,GACxC,GAAG,KAAK,CAAA;IACT,MAAM,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,mBAAmB,CAAC,CAAC,CAAC,SAAS,CAAA;IAC1D,8EAA8E;IAC9E,4EAA4E;IAC5E,+CAA+C;IAC/C,MAAM,iBAAiB,GAAG,CAAC,cAAc,IAAI,CAAC,cAAc,IAAI,CAAC,IAAI,CAAC,CAAA;IAEtE,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,KAAK,GAAG,uCAAuC,CAAC,IAAI,CAAC,CAAA;QAE3D,IAAI,KAAK,EAAE,CAAC;YACV,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC/C,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;gBACnD,yDAAyD;gBACzD,6DAA6D;gBAC7D,MAAM,EAAE,GAAG,KAAK,CAAC,kBAAkB,CAAC,IAAI,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;gBACpD,MAAM,EAAE,GAAG,KAAK,CAAC,kBAAkB,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;gBAC9C,IAAI,EAAE,KAAK,SAAS,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;oBACzC,MAAM,CAAC,GAAG,EAAE,GAAG,QAAQ,CAAA;oBACvB,MAAM,CAAC,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;oBACtD,MAAM,EAAE,GAAG,QAAQ,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;oBAC/B,GAAG,CAAC,SAAS,GAAG,WAAW,CAAC,SAAS,CAAE,CAAA;oBACvC,GAAG,CAAC,WAAW,GAAG,aAAa,CAAC,SAAS,CAAE,CAAA;oBAC3C,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;wBACzB,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;wBACzB,GAAG,CAAC,UAAU,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;wBAC3B,qEAAqE;wBACrE,oDAAoD;wBACpD,MAAM,KAAK,GAAG,iBAAiB,CAAC,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;wBAC1E,IAAI,KAAK,KAAK,SAAS,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;4BACnC,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;4BACpC,GAAG,CAAC,IAAI,GAAG,GAAG,QAAQ,eAAe,CAAA;4BACrC,IAAI,GAAG,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,KAAK,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC;gCAC3C,GAAG,CAAC,SAAS,GAAG,MAAM,CAAA;gCACtB,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;gCACxB,GAAG,CAAC,YAAY,GAAG,QAAQ,CAAA;gCAC3B,GAAG,CAAC,QAAQ,CAAC,KAAK,EAAE,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;4BAC5C,CAAC;wBACH,CAAC;oBACH,CAAC;yBAAM,CAAC;wBACN,aAAa,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;oBAChD,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,qEAAqE;AACrE,8EAA8E;AAC9E,8EAA8E;AAC9E,+EAA+E;AAC/E,6EAA6E;AAC7E,qEAAqE;AACrE,SAAS,aAAa,CAAC,EACrB,GAAG,EACH,CAAC,EACD,CAAC,EACD,CAAC,EACD,CAAC,EACD,MAAM,GAQP;IACC,0EAA0E;IAC1E,kDAAkD;IAClD,MAAM,GAAG,GAAG,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC/B,MAAM,SAAS,GAAG,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IACxC,MAAM,OAAO,GAAG,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACtC,GAAG,CAAC,SAAS,EAAE,CAAA;IACf,GAAG,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;IACxB,GAAG,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,CAAC,CAAA;IACtB,GAAG,CAAC,MAAM,CAAC,OAAO,GAAG,GAAG,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;IACxC,GAAG,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;IAC1B,GAAG,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;IAC5B,GAAG,CAAC,SAAS,EAAE,CAAA;IACf,GAAG,CAAC,IAAI,EAAE,CAAA;IACV,GAAG,CAAC,MAAM,EAAE,CAAA;AACd,CAAC"}

package/dist/components/msa/renderMSABlock.js

@@ -11,6 +11,7 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
     ctx.scale(k, k);
     ctx.translate(-offsetX, rowHeight / 2 - offsetY);
     ctx.textAlign = 'center';
+    ctx.textBaseline = 'alphabetic';
     setFontSize(ctx, fontSize, !bgColor);
     const { xStart, xEnd } = visibleColRange({
         offsetX,
@@ -28,7 +29,6 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
             ctx,
             theme,
             contrastScheme,
-            offsetX,
             xStart,
             xEnd,
             visibleLeaves,
@@ -39,7 +39,6 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
         drawText({
             model,
             ctx,
-            offsetX,
             xStart,
             xEnd,
             visibleLeaves,
@@ -55,15 +54,14 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
     });
     ctx.resetTransform();
 }
-function drawTilesAndText({ model, offsetX, ctx, theme, contrastScheme, visibleLeaves, xStart, xEnd, referenceSeq, }) {
+function drawTilesAndText({ model, ctx, theme, contrastScheme, visibleLeaves, xStart, xEnd, referenceSeq, }) {
     const { bgColor, colorSchemeName, colorScheme, columns, colWidth, rowHeight, relativeTo, showMsaLetters, colClustalX, colConsensus, } = model;
     const isClustalX = colorSchemeName === 'clustalx_protein_dynamic';
     const isPercentIdentity = colorSchemeName === 'percent_identity_dynamic';
-    const drawBgTiles = bgColor || isClustalX || isPercentIdentity;
-    if (!drawBgTiles && !showMsaLetters) {
+    if (!bgColor && !showMsaLetters) {
         return;
     }
-    const offsetXAligned = offsetX - (offsetX % colWidth);
+    const offsetXAligned = xStart * colWidth;
     const halfColWidth = colWidth / 2;
     const quarterRowHeight = rowHeight / 4;
     for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {
@@ -91,7 +89,7 @@ function drawTilesAndText({ model, offsetX, ctx, theme, contrastScheme, visibleL
             else {
                 color = colorScheme[letter];
             }
-            if (drawBgTiles) {
+            if (bgColor) {
                 ctx.fillStyle = isMatchingReference
                     ? theme.palette.action.hover
                     : color || theme.palette.background.default;
@@ -110,12 +108,12 @@ function drawTilesAndText({ model, offsetX, ctx, theme, contrastScheme, visibleL
 }
 // When domains are shown the background tiles come from renderBoxFeatureCanvasBlock,
 // so we only need to draw text here.
-function drawText({ model, offsetX, ctx, visibleLeaves, xStart, xEnd, referenceSeq, }) {
+function drawText({ model, ctx, visibleLeaves, xStart, xEnd, referenceSeq, }) {
     const { showMsaLetters, columns, colWidth, rowHeight, relativeTo } = model;
     if (!showMsaLetters) {
         return;
     }
-    const offsetXAligned = offsetX - (offsetX % colWidth);
+    const offsetXAligned = xStart * colWidth;
     const halfColWidth = colWidth / 2;
     const quarterRowHeight = rowHeight / 4;
     // note: -rowHeight/4 matches +rowHeight/4 in tree

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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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 = i * colWidth + offsetX - (offsetX % colWidth);
-            ctx.fillStyle = color || 'white';
+            const x = (xStart + i) * colWidth;
+            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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+{"version":3,"file":"renderTracksSvg.js","sourceRoot":"","sources":["../../../src/components/tracks/renderTracksSvg.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAM3D,MAAM,UAAU,oBAAoB,CAAC,EACnC,GAAG,EACH,YAAY,EACZ,QAAQ,EACR,WAAW,EACX,OAAO,EACP,SAAS,GAQV;IACC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,eAAe,CAAC;QACvC,OAAO;QACP,UAAU,EAAE,SAAS;QACrB,QAAQ;KACT,CAAC,CAAA;IAEF,GAAG,CAAC,SAAS,GAAG,MAAM,CAAA;IACtB,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,IAAI,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC9D,MAAM,KAAK,GAAG,YAAY,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,SAAS,GAAG,KAAK,GAAG,WAAW,CAAA;QACrC,MAAM,CAAC,GAAG,CAAC,GAAG,QAAQ,CAAA;QACtB,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,WAAW,GAAG,SAAS,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;IAC/D,CAAC;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,EACnC,GAAG,EACH,IAAI,EACJ,WAAW,EACX,cAAc,EACd,OAAO,EACP,QAAQ,EACR,SAAS,EACT,OAAO,EACP,SAAS,GAWV;IACC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,eAAe,CAAC;QACvC,OAAO;QACP,UAAU,EAAE,SAAS;QACrB,QAAQ;KACT,CAAC,CAAA;IACF,MAAM,GAAG,GAAG,IAAI,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAErC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,IAAI,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;QACtB,MAAM,KAAK,GAAG,MAAM,CAAC,WAAW,EAAE,CAAA;QAClC,IAAI,OAAO,EAAE,CAAC;YACZ,MAAM,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAA;YACjC,GAAG,CAAC,SAAS,GAAG,WAAW,CAAC,KAAK,CAAC,IAAI,OAAO,CAAA;YAC7C,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;YACvC,IAAI,SAAS,IAAI,EAAE,IAAI,QAAQ,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;gBACjD,GAAG,CAAC,SAAS,GAAG,cAAc,CAAC,KAAK,CAAC,IAAI,OAAO,CAAA;gBAChD,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,QAAQ,GAAG,CAAC,EAAE,SAAS,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;YAC3D,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,uBAAuB,CAAC,EACtC,KAAK,EACL,GAAG,EACH,OAAO,EACP,OAAO,EACP,WAAW,EACX,kBAAkB,EAClB,0BAA0B,GAS3B;IACC,MAAM,EAAE,SAAS,EAAE,QAAQ,EAAE,kBAAkB,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IACvE,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAE1D,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;IAEhC,oBAAoB,CAAC;QACnB,GAAG;QACH,YAAY;QACZ,QAAQ;QACR,WAAW;QACX,OAAO;QACP,SAAS,EAAE,EAAE;KACd,CAAC,CAAA;IAEF,GAAG,CAAC,cAAc,EAAE,CAAA;AACtB,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,EAC9B,KAAK,EACL,GAAG,EACH,KAAK,EACL,OAAO,EACP,OAAO,EACP,cAAc,EACd,kBAAkB,EAClB,0BAA0B,GAU3B;IACC,MAAM,EACJ,SAAS,EACT,OAAO,EACP,WAAW,EAAE,gBAAgB,EAC7B,QAAQ,EACR,QAAQ,EACR,SAAS,EACT,kBAAkB,GACnB,GAAG,KAAK,CAAA;IAET,MAAM,EAAE,iBAAiB,EAAE,IAAI,EAAE,GAAG,KAAK,CAAC,KAAK,CAAA;IAC/C,MAAM,WAAW,GAAG,iBAAiB,IAAI,gBAAgB,CAAA;IACzD,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAE1D,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;IAChC,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;IACxB,WAAW,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IAE1B,oBAAoB,CAAC;QACnB,GAAG;QACH,IAAI;QACJ,WAAW;QACX,cAAc;QACd,OAAO;QACP,QAAQ;QACR,SAAS;QACT,OAAO;QACP,SAAS,EAAE,EAAE;KACd,CAAC,CAAA;IAEF,GAAG,CAAC,cAAc,EAAE,CAAA;AACtB,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,EAC9B,KAAK,EACL,GAAG,EACH,OAAO,EACP,cAAc,EACd,kBAAkB,EAClB,0BAA0B,GAQ3B;IACC,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,IAAI,QAAQ,GAAG,CAAC,CAAA;IAEhB,KAAK,MAAM,KAAK,IAAI,cAAc,EAAE,CAAC;QACnC,MAAM,WAAW,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAA;QAEtC,IAAI,KAAK,CAAC,KAAK,CAAC,EAAE,KAAK,cAAc,EAAE,CAAC;YACtC,uBAAuB,CAAC;gBACtB,KAAK;gBACL,GAAG;gBACH,OAAO;gBACP,OAAO,EAAE,QAAQ;gBACjB,WAAW;gBACX,kBAAkB;gBAClB,0BAA0B;aAC3B,CAAC,CAAA;QACJ,CAAC;aAAM,CAAC;YACN,eAAe,CAAC;gBACd,KAAK;gBACL,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,OAAO,EAAE,QAAQ;gBACjB,cAAc;gBACd,kBAAkB;gBAClB,0BAA0B;aAC3B,CAAC,CAAA;QACJ,CAAC;QAED,QAAQ,IAAI,WAAW,CAAA;IACzB,CAAC;AACH,CAAC"}

package/dist/components/tree/renderTreeCanvas.js

@@ -12,6 +12,9 @@ function getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf) {
     if (showBranchLen) {
         return node.len;
     }
+    if (maxDepthToLeaf === 0) {
+        return 0;
+    }
     const depthToLeaf = calcDepthToLeaf(node);
     return ((maxDepthToLeaf - depthToLeaf) / maxDepthToLeaf) * maxBranchLen;
 }

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

@@ -206,7 +206,10 @@ export function collapsedSubtreeLengthExtent(node) {
             const kids = n.children ?? n._children;
             if (kids?.length) {
                 for (const child of kids) {
-                    stack.push({ node: child, acc: acc + Math.max(child.data.length ?? 0, 0) });
+                    stack.push({
+                        node: child,
+                        acc: acc + Math.max(child.data.length ?? 0, 0),
+                    });
                 }
             }
             else {

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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/msaModel.js.map

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