react-msaview 3.1.7 → 3.1.8

package/dist/components/msa/renderBoxFeatureCanvasBlock.js

@@ -0,0 +1,44 @@
+export function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeYOverride, }) {
+    const { hierarchy, blockSize, rowHeight, highResScaleFactor, featureMode } = model;
+    if (featureMode) {
+        const k = highResScaleFactorOverride || highResScaleFactor;
+        const by = blockSizeYOverride || blockSize;
+        ctx.resetTransform();
+        ctx.scale(k, k);
+        ctx.translate(-offsetX, rowHeight / 2 - offsetY);
+        const leaves = hierarchy.leaves();
+        const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight));
+        const yEnd = Math.max(0, Math.ceil((offsetY + by + rowHeight) / rowHeight));
+        const visibleLeaves = leaves.slice(yStart, yEnd);
+        drawTiles({
+            model,
+            ctx,
+            visibleLeaves,
+        });
+    }
+}
+function drawTiles({ model, ctx, visibleLeaves, }) {
+    const { subFeatureRows, colWidth, rowHeight, fillPalette, strokePalette, tidyFilteredGatheredAnnotations, } = model;
+    for (const node of visibleLeaves) {
+        const { x, data: { name }, } = node;
+        const y = x;
+        const entry = tidyFilteredGatheredAnnotations?.[name];
+        let j = 0;
+        if (entry) {
+            for (const { start, end, accession } of entry) {
+                const m1 = model.seqCoordToRowSpecificGlobalCoord(name, start - 1);
+                const m2 = model.seqCoordToRowSpecificGlobalCoord(name, end);
+                const x = m1 * colWidth;
+                ctx.fillStyle = fillPalette[accession];
+                ctx.strokeStyle = strokePalette[accession];
+                const h = subFeatureRows ? 4 : rowHeight;
+                const t = y - rowHeight + (subFeatureRows ? j * h : 0);
+                const lw = colWidth * (m2 - m1);
+                ctx.fillRect(x, t, lw, h);
+                ctx.strokeRect(x, t, lw, h);
+                j++;
+            }
+        }
+    }
+}
+//# sourceMappingURL=renderBoxFeatureCanvasBlock.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"renderBoxFeatureCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderBoxFeatureCanvasBlock.ts"],"names":[],"mappings":"AAMA,MAAM,UAAU,2BAA2B,CAAC,EAC1C,KAAK,EACL,OAAO,EACP,OAAO,EACP,GAAG,EACH,0BAA0B,EAC1B,kBAAkB,GAQnB;IACC,MAAM,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,kBAAkB,EAAE,WAAW,EAAE,GACxE,KAAK,CAAA;IACP,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,MAAM,GAAG,SAAS,CAAC,MAAM,EAAE,CAAA;QACjC,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;QACzE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;QAC3E,MAAM,aAAa,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAEhD,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,+BAA+B,GAChC,GAAG,KAAK,CAAA;IAET,KAAK,MAAM,IAAI,IAAI,aAAa,EAAE,CAAC;QACjC,MAAM,EACJ,CAAC,EACD,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;QACR,MAAM,CAAC,GAAG,CAAE,CAAA;QAEZ,MAAM,KAAK,GAAG,+BAA+B,EAAE,CAAC,IAAI,CAAC,CAAA;QAErD,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,KAAK,EAAE,CAAC;YACV,KAAK,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,IAAI,KAAK,EAAE,CAAC;gBAC9C,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,IAAI,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;gBAClE,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;gBAC5D,MAAM,CAAC,GAAG,EAAE,GAAG,QAAQ,CAAA;gBACvB,GAAG,CAAC,SAAS,GAAG,WAAW,CAAC,SAAS,CAAC,CAAA;gBACtC,GAAG,CAAC,WAAW,GAAG,aAAa,CAAC,SAAS,CAAC,CAAA;gBAC1C,MAAM,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;gBACxC,MAAM,CAAC,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACtD,MAAM,EAAE,GAAG,QAAQ,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;gBAC/B,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;gBACzB,GAAG,CAAC,UAAU,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;gBAC3B,CAAC,EAAE,CAAA;YACL,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/components/{MSAPanel → msa}/renderMSABlock.js

@@ -1,12 +1,11 @@
 import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes';
 export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
-    const { hierarchy, colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, } = model;
+    const { hierarchy, colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, featureMode, } = model;
     const k = highResScaleFactorOverride || highResScaleFactor;
     const bx = blockSizeXOverride || blockSize;
     const by = blockSizeYOverride || blockSize;
     ctx.resetTransform();
     ctx.scale(k, k);
-    ctx.clearRect(0, 0, bx, by);
     ctx.translate(-offsetX, rowHeight / 2 - offsetY);
     ctx.textAlign = 'center';
     ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
@@ -16,16 +15,18 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
     const xStart = Math.max(0, Math.floor(offsetX / colWidth));
     const xEnd = Math.max(0, Math.ceil((offsetX + bx) / colWidth));
     const visibleLeaves = leaves.slice(yStart, yEnd);
-    drawTiles({
-        model,
-        ctx,
-        theme,
-        offsetX,
-        offsetY,
-        xStart,
-        xEnd,
-        visibleLeaves,
-    });
+    if (!featureMode) {
+        drawTiles({
+            model,
+            ctx,
+            theme,
+            offsetX,
+            offsetY,
+            xStart,
+            xEnd,
+            visibleLeaves,
+        });
+    }
     drawText({
         model,
         ctx,
@@ -36,13 +37,13 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
         xEnd,
         visibleLeaves,
     });
+    ctx.resetTransform();
 }
 function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, }) {
     const { bgColor, colorSchemeName, colorScheme, colStats, columns, colWidth, rowHeight, } = model;
     for (const node of visibleLeaves) {
-        const { 
-        // @ts-expect-error
-        x: y, data: { name }, } = node;
+        const { data: { name }, } = node;
+        const y = node.x;
         const str = columns[name]?.slice(xStart, xEnd);
         for (let i = 0; i < str?.length; i++) {
             const letter = str[i];
@@ -60,12 +61,11 @@ function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, })
     }
 }
 function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart, xEnd, }) {
-    const { bgColor, colorScheme, columns, colWidth, rowHeight } = model;
+    const { bgColor, featureMode, colorScheme, columns, colWidth, rowHeight } = model;
     if (rowHeight >= 5 && colWidth > rowHeight / 2) {
         for (const node of visibleLeaves) {
-            const { 
-            // @ts-expect-error
-            x: y, data: { name }, } = node;
+            const { data: { name }, } = node;
+            const y = node.x;
             const str = columns[name]?.slice(xStart, xEnd);
             for (let i = 0; i < str?.length; i++) {
                 const letter = str[i];
@@ -73,7 +73,11 @@ function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart,
                 const contrast = contrastScheme[letter.toUpperCase()] || 'black';
                 const x = i * colWidth + offsetX - (offsetX % colWidth);
                 // note: -rowHeight/4 matches +rowHeight/4 in tree
-                ctx.fillStyle = bgColor ? contrast : color || 'black';
+                ctx.fillStyle = featureMode
+                    ? 'black'
+                    : bgColor
+                        ? contrast
+                        : color || 'black';
                 ctx.fillText(letter, x + colWidth / 2, y - rowHeight / 4);
             }
         }

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

@@ -0,0 +1 @@
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package/dist/components/msa/renderMSAMouseover.js.map

@@ -0,0 +1 @@
+{"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;AAE5C,MAAM,UAAU,eAAe,CAAC,EAC9B,GAAG,EACH,KAAK,GAIN;IACC,MAAM,EACJ,QAAQ,EACR,QAAQ,EACR,KAAK,EACL,MAAM,EACN,SAAS,EACT,OAAO,EACP,OAAO,EACP,QAAQ;IACR,mBAAmB;IACnB,SAAS,EACT,aAAa,EACb,aAAa,GACd,GAAG,KAAK,CAAA;IACT,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;IAClC,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;QAC3B,GAAG,CAAC,SAAS,GAAG,UAAU,CAAA;QAC1B,GAAG,CAAC,QAAQ,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,GAAG,QAAQ,GAAG,OAAO,EAAE,CAAC,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAA;IACxE,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,CAAC,aAAa,GAAG,CAAC,CAAC,GAAG,QAAQ,GAAG,OAAO,EAAE,CAAC,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAA;IAC7E,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;IACD,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;QAC5B,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;QAC9B,GAAG,CAAC,QAAQ,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,QAAQ,GAAG,OAAO,EAAE,CAAC,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAA;IACzE,CAAC;AACH,CAAC"}

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

@@ -0,0 +1 @@
+{"version":3,"file":"TreeBranchMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeBranchMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAYrC,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,IAAI,EACJ,KAAK,EACL,OAAO,GAKR;IACC,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;YACd,IAAI,EAAE,IAAI,CAAC,CAAC;YACZ,GAAG,EAAE,IAAI,CAAC,CAAC;SACZ,EACD,kBAAkB,EAAE,CAAC,EACrB,WAAW,QACX,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,EACnB,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CAAC,IAAI,CACD;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,eAAe,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC9B,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,KAAK,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,CAAC,CAAC,kBAAkB;YACpB,CAAC,CAAC,oBAAoB,CACf;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,QAAQ,KAAK,IAAI,CAAC,EAAE;oBACxB,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,SAAS,CAAC;oBAC9B,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC9B,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,KAAK,CAAC,QAAQ,KAAK,IAAI,CAAC,EAAE;YACzB,CAAC,CAAC,6BAA6B;YAC/B,CAAC,CAAC,qBAAqB,CAChB,CACN,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/components/{TreePanel → tree}/TreeCanvas.js

@@ -27,6 +27,7 @@ const TreeCanvas = observer(function ({ model }) {
                 });
             }
             origEvent.preventDefault();
+            origEvent.stopPropagation();
         }
         curr.addEventListener('wheel', onWheel);
         return () => {
@@ -92,7 +93,6 @@ const TreeCanvas = observer(function ({ model }) {
     return (React.createElement("div", { ref: ref, onMouseDown: mouseDown, onMouseUp: mouseUp, onMouseLeave: mouseLeave, style: {
             height,
             position: 'relative',
-            overflow: 'hidden',
             width: treeWidth + padding,
         } }, blocksY.map(block => (React.createElement(TreeCanvasBlock, { key: block, model: model, offsetY: block })))));
 });

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

@@ -0,0 +1 @@
+{"version":3,"file":"TreeCanvas.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC1D,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAA;AAE5C,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC/B,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,KAAK,GAAG,MAAM,CAAS,CAAC,CAAC,CAAA;IAC/B,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEzD,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,CAAA;QACxB,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,OAAM;QACR,CAAC;QACD,SAAS,OAAO,CAAC,SAAqB;YACpC,MAAM,KAAK,GAAG,cAAc,CAAC,SAAS,CAAC,CAAA;YACvC,MAAM,CAAC,OAAO,IAAI,KAAK,CAAC,MAAM,CAAA;YAE9B,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC;gBACvB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;gBACxB,qBAAqB,CAAC,GAAG,EAAE;oBACzB,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;oBAChC,MAAM,CAAC,OAAO,GAAG,CAAC,CAAA;oBAClB,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;gBAC3B,CAAC,CAAC,CAAA;YACJ,CAAC;YACD,SAAS,CAAC,cAAc,EAAE,CAAA;YAC1B,SAAS,CAAC,eAAe,EAAE,CAAA;QAC7B,CAAC;QACD,IAAI,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QACvC,OAAO,GAAG,EAAE;YACV,IAAI,CAAC,mBAAmB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QAC5C,CAAC,CAAA;IACH,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IAEX,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,OAAO,GAAG,GAAG,EAAE,GAAE,CAAC,CAAA;QAEtB,SAAS,eAAe,CAAC,KAAiB;YACxC,KAAK,CAAC,cAAc,EAAE,CAAA;YACtB,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YAC3B,MAAM,SAAS,GAAG,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YACvC,IAAI,SAAS,EAAE,CAAC;gBACd,uEAAuE;gBACvE,8EAA8E;gBAC9E,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC;oBACvB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;oBACxB,MAAM,CAAC,qBAAqB,CAAC,GAAG,EAAE;wBAChC,KAAK,CAAC,SAAS,CAAC,SAAS,CAAC,CAAA;wBAC1B,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;wBACzB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;oBAC/B,CAAC,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QAED,SAAS,aAAa;YACpB,KAAK,CAAC,OAAO,GAAG,CAAC,CAAA;YACjB,IAAI,aAAa,EAAE,CAAC;gBAClB,gBAAgB,CAAC,KAAK,CAAC,CAAA;YACzB,CAAC;QACH,CAAC;QAED,IAAI,aAAa,EAAE,CAAC;YAClB,MAAM,CAAC,gBAAgB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;YAC3D,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YACvD,OAAO,GAAG,GAAG,EAAE;gBACb,MAAM,CAAC,mBAAmB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;gBAC9D,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YAC5D,CAAC,CAAA;QACH,CAAC;QACD,OAAO,OAAO,CAAA;IAChB,CAAC,EAAE,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC,CAAA;IAE1B,SAAS,SAAS,CAAC,KAAuB;QACxC,2DAA2D;QAC3D,MAAM,MAAM,GAAG,KAAK,CAAC,MAAqB,CAAA;QAC1C,IAAI,MAAM,CAAC,SAAS,IAAI,MAAM,CAAC,OAAO,CAAC,OAAO,EAAE,CAAC;YAC/C,OAAM;QACR,CAAC;QAED,qCAAqC;QACrC,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;YAC7B,gBAAgB,CAAC,IAAI,CAAC,CAAA;QACxB,CAAC;IACH,CAAC;IAED,yEAAyE;IACzE,wEAAwE;IACxE,SAAS,OAAO,CAAC,KAAuB;QACtC,KAAK,CAAC,cAAc,EAAE,CAAA;QACtB,gBAAgB,CAAC,KAAK,CAAC,CAAA;IACzB,CAAC;IAED,SAAS,UAAU,CAAC,KAAuB;QACzC,KAAK,CAAC,cAAc,EAAE,CAAA;IACxB,CAAC;IAED,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,SAAS,EACtB,SAAS,EAAE,OAAO,EAClB,YAAY,EAAE,UAAU,EACxB,KAAK,EAAE;YACL,MAAM;YACN,QAAQ,EAAE,UAAU;YACpB,KAAK,EAAE,SAAS,GAAG,OAAO;SAC3B,IAEA,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACpB,oBAAC,eAAe,IAAC,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,GAAI,CAC9D,CAAC,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/{TreePanel → tree}/TreeCanvasBlock.js

@@ -63,7 +63,7 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
             minY: y + offsetY,
             maxY: y + 1 + offsetY,
         });
-        return entry && entry.branch
+        return entry?.branch
             ? { ...entry, x: event.clientX, y: event.clientY }
             : undefined;
     }

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

@@ -0,0 +1 @@
+{"version":3,"file":"TreeCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvasBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvE,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,KAAK,MAAM,OAAO,CAAA;AAIzB,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,EAAE,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAmB9D,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,GAAG,GAAG,MAAM,EAAqB,CAAA;IACvC,MAAM,QAAQ,GAAG,MAAM,CAAC,IAAI,KAAK,EAAc,CAAC,CAAA;IAChD,MAAM,YAAY,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IACpD,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,EAAe,CAAA;IAC3D,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,EAAe,CAAA;IACnE,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAc,CAAA;IAEtD,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAEvE,MAAM,KAAK,GAAG,aAAa,GAAG,OAAO,CAAA;IACrC,MAAM,MAAM,GAAG,SAAS,CAAA;IACxB,MAAM,EAAE,GAAG,KAAK,GAAG,kBAAkB,CAAA;IACrC,MAAM,EAAE,GAAG,MAAM,GAAG,kBAAkB,CAAA;IAEtC,MAAM,IAAI,GAAG,WAAW,CACtB,CAAC,GAAsB,EAAE,EAAE;QACzB,KAAK,CAAC,YAAY,EAAE,CAAA;QACpB,GAAG,CAAC,OAAO,GAAG,GAAG,CAAA;IACnB,CAAC;IACD,uDAAuD;IACvD,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,CACvB,CAAA;IACD,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,EAAE,UAAU,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAM;QACR,CAAC;QAED,OAAO,OAAO,CAAC,GAAG,EAAE;YAClB,gBAAgB,CAAC;gBACf,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,QAAQ,EAAE,QAAQ,CAAC,OAAO;gBAC1B,KAAK;aACN,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;IACJ,CAAC,EAAE,CAAC,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC,CAAA;IAE3B,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,GAAG,GAAG,YAAY,CAAC,OAAO,EAAE,UAAU,CAAC,IAAI,CAAC,CAAA;QAClD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAM;QACR,CAAC;QAED,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,aAAa,GAAG,OAAO,EAAE,SAAS,CAAC,CAAA;QACvD,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,CAAA;QAE1B,IAAI,QAAQ,EAAE,CAAC;YACb,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,QAAQ,CAAA;YAE3C,GAAG,CAAC,SAAS,GAAG,iBAAiB,CAAA;YACjC,GAAG,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,GAAG,IAAI,EAAE,IAAI,GAAG,IAAI,CAAC,CAAA;QACpD,CAAC;IACH,CAAC,EAAE,CAAC,QAAQ,EAAE,OAAO,EAAE,SAAS,EAAE,aAAa,CAAC,CAAC,CAAA;IAEjD,SAAS,mBAAmB,CAAC,KAAuB;QAClD,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QACnC,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QAEnC,MAAM,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC;YACtC,IAAI,EAAE,CAAC;YACP,IAAI,EAAE,CAAC,GAAG,CAAC;YACX,IAAI,EAAE,CAAC,GAAG,OAAO;YACjB,IAAI,EAAE,CAAC,GAAG,CAAC,GAAG,OAAO;SACtB,CAAC,CAAA;QAEF,OAAO,KAAK,EAAE,MAAM;YAClB,CAAC,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE;YAClD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,SAAS,iBAAiB,CAAC,KAAuB;QAChD,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QACnC,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QACnC,MAAM,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC;YACtC,IAAI,EAAE,CAAC;YACP,IAAI,EAAE,CAAC,GAAG,CAAC;YACX,IAAI,EAAE,CAAC,GAAG,OAAO;YACjB,IAAI,EAAE,CAAC,GAAG,CAAC,GAAG,OAAO;SACtB,CAAC,CAAA;QAEF,OAAO,KAAK,IAAI,CAAC,KAAK,CAAC,MAAM;YAC3B,CAAC,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE;YAClD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IACD,MAAM,KAAK,GAAG;QACZ,KAAK;QACL,MAAM;QACN,GAAG,EAAE,OAAO,GAAG,OAAO;QACtB,IAAI,EAAE,CAAC;QACP,QAAQ,EAAE,UAAU;KACZ,CAAA;IACV,OAAO,CACL;QACG,UAAU,EAAE,EAAE,CAAC,CAAC,CAAC,CAChB,oBAAC,cAAc,IACb,IAAI,EAAE,UAAU,EAChB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,SAAS,CAAC,GACvC,CACH,CAAC,CAAC,CAAC,IAAI;QAEP,cAAc,EAAE,EAAE,CAAC,CAAC,CAAC,CACpB,oBAAC,YAAY,IACX,IAAI,EAAE,cAAc,EACpB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CAAC,iBAAiB,CAAC,SAAS,CAAC,GAC3C,CACH,CAAC,CAAC,CAAC,IAAI;QAER,gCACE,KAAK,EAAE,EAAE,EACT,MAAM,EAAE,EAAE,EACV,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC;oBACjB,OAAM;gBACR,CAAC;gBAED,MAAM,GAAG,GAAG,iBAAiB,CAAC,KAAK,CAAC,IAAI,mBAAmB,CAAC,KAAK,CAAC,CAAA;gBAClE,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;gBACtD,WAAW,CAAC,iBAAiB,CAAC,KAAK,CAAC,CAAC,CAAA;YACvC,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,MAAM,EAAE,OAAO,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,GAAG,KAAK,CAAA;gBAExC,MAAM,IAAI,GAAG,mBAAmB,CAAC,KAAK,CAAC,CAAA;gBACvC,IAAI,IAAI,EAAE,EAAE,EAAE,CAAC;oBACb,aAAa,CAAC,EAAE,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAA;gBAClC,CAAC;gBAED,MAAM,KAAK,GAAG,iBAAiB,CAAC,KAAK,CAAC,CAAA;gBACtC,IAAI,KAAK,EAAE,EAAE,EAAE,CAAC;oBACd,iBAAiB,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAA;gBACvC,CAAC;YACH,CAAC,EACD,YAAY,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,SAAS,CAAC,EAC1C,GAAG,EAAE,IAAI,GACT;QACF,gCACE,KAAK,EAAE;gBACL,GAAG,KAAK;gBACR,aAAa,EAAE,MAAM;gBACrB,MAAM,EAAE,GAAG;aACZ,EACD,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,GAAG,EAAE,YAAY,GACjB,CACD,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/{TreePanel → tree}/TreeNodeMenu.js

@@ -4,8 +4,7 @@ import { observer } from 'mobx-react';
 // lazies
 const TreeNodeInfoDialog = lazy(() => import('./dialogs/TreeNodeInfoDialog'));
 const TreeMenu = observer(function ({ node, onClose, model, }) {
-    const { selectedStructures, collapsed, collapsed2, structures } = model;
-    const nodeDetails = node ? model.getRowData(node.name) : undefined;
+    const { collapsed, collapsed2 } = model;
     return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
             top: node.y,
             left: node.x,
@@ -38,37 +37,7 @@ const TreeMenu = observer(function ({ node, onClose, model, }) {
                 onClose();
             } }, collapsed.includes(node.id) || collapsed2.includes(node.id)
             ? 'Show node'
-            : 'Hide node'),
-        structures[node.name]?.map(entry => !selectedStructures.some(n => n.id === node.name) ? (React.createElement(MenuItem, { key: JSON.stringify(entry), dense: true, onClick: () => {
-                model.addStructureToSelection({
-                    structure: entry,
-                    id: node.name,
-                });
-                onClose();
-            } },
-            "Add PDB to selection (",
-            entry.pdb,
-            ")")) : (React.createElement(MenuItem, { key: JSON.stringify(entry), dense: true, onClick: () => {
-                model.removeStructureFromSelection({
-                    structure: entry,
-                    id: node.name,
-                });
-                onClose();
-            } },
-            "Remove PDB from selection (",
-            entry.pdb,
-            ")"))), // @ts-expect-error
-        nodeDetails?.data.accession?.map(accession => (React.createElement(MenuItem, { dense: true, key: accession, onClick: () => {
-                model.addUniprotTrack({
-                    // @ts-expect-error
-                    name: nodeDetails?.data.name,
-                    accession,
-                });
-                onClose();
-            } },
-            "Open UniProt track (",
-            accession,
-            ")")))));
+            : 'Hide node')));
 });
 export default TreeMenu;
 //# sourceMappingURL=TreeNodeMenu.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"TreeNodeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeNodeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AACnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,SAAS;AACT,MAAM,kBAAkB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA8B,CAAC,CAAC,CAAA;AAE7E,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,IAAI,EACJ,OAAO,EACP,KAAK,GAKN;IACC,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IACvC,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;YACd,GAAG,EAAE,IAAI,CAAC,CAAC;YACX,IAAI,EAAE,IAAI,CAAC,CAAC;SACb,EACD,kBAAkB,EAAE,CAAC,EACrB,WAAW,QACX,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,EACnB,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CAAC,IAAI,CACD;QAEX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,kBAAkB;oBAClB;wBACE,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC;wBACjC,KAAK;wBACL,QAAQ,EAAE,IAAI,CAAC,IAAI;wBACnB,OAAO;qBACR;iBACF,CAAC,CAAA;gBACF,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC;oBAChC,KAAK,CAAC,eAAe,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAChC,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE,CAAC;wBAClC,KAAK,CAAC,gBAAgB,CAAC,GAAG,IAAI,CAAC,EAAE,EAAE,CAAC,CAAA;oBACtC,CAAC;yBAAM,CAAC;wBACN,KAAK,CAAC,gBAAgB,CAAC,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,CAAA;oBAC/C,CAAC;gBACH,CAAC;gBACD,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;YAC1D,CAAC,CAAC,WAAW;YACb,CAAC,CAAC,WAAW,CACN,CACN,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/{TreePanel/index.js → tree/TreePanel.js}

@@ -3,8 +3,8 @@ import { observer } from 'mobx-react';
 import TreeCanvas from './TreeCanvas';
 const TreePanel = observer(function ({ model }) {
     const { treeAreaWidth } = model;
-    return (React.createElement("div", { style: { flexShrink: 0, width: treeAreaWidth } },
+    return (React.createElement("div", { style: { overflow: 'hidden', flexShrink: 0, width: treeAreaWidth } },
         React.createElement(TreeCanvas, { model: model })));
 });
 export default TreePanel;
-//# sourceMappingURL=index.js.map
+//# sourceMappingURL=TreePanel.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"TreePanel.js","sourceRoot":"","sources":["../../../src/components/tree/TreePanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAGrC,OAAO,UAAU,MAAM,cAAc,CAAA;AAErC,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE;QACrE,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CACxB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

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

@@ -0,0 +1 @@
+{"version":3,"file":"TreeRuler.js","sourceRoot":"","sources":["../../../src/components/tree/TreeRuler.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,MAAM,SAAS,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IAChE,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,OAAO,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE,GAAI,CAAA;AAChE,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

package/dist/components/{TreePanel → tree}/dialogs/TreeNodeInfoDialog.js

@@ -3,13 +3,17 @@ import { Dialog } from '@jbrowse/core/ui';
 import { DialogContent } from '@mui/material';
 import { observer } from 'mobx-react';
 import { Attributes, BaseCard, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import SequenceTextArea from '../../SequenceTextArea';
 export default observer(function ({ info, model, nodeName, onClose, }) {
-    const { treeMetadata } = model;
+    const { treeMetadata, rows } = model;
     const metadata = treeMetadata[nodeName];
-    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Tree node info" },
+    const [name, sequence] = rows.find(f => f[0] === nodeName);
+    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Tree node info", maxWidth: "xl" },
         React.createElement(DialogContent, null,
             React.createElement(BaseCard, { title: "Attributes" },
                 React.createElement(Attributes, { attributes: { nodeName, ...info } })),
+            React.createElement(BaseCard, { title: "Sequence" },
+                React.createElement(SequenceTextArea, { str: [[name, sequence]] })),
             metadata ? (React.createElement(BaseCard, { title: "Extra metadata" },
                 React.createElement(Attributes, { attributes: metadata }))) : null)));
 });

package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"TreeNodeInfoDialog.js","sourceRoot":"","sources":["../../../../src/components/tree/dialogs/TreeNodeInfoDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,UAAU,EACV,QAAQ,GACT,MAAM,mDAAmD,CAAA;AAI1D,OAAO,gBAAgB,MAAM,wBAAwB,CAAA;AAErD,eAAe,QAAQ,CAAC,UAAU,EAChC,IAAI,EACJ,KAAK,EACL,QAAQ,EACR,OAAO,GAMR;IACC,MAAM,EAAE,YAAY,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,QAAQ,GAAG,YAAY,CAAC,QAAQ,CAAC,CAAA;IACvC,MAAM,CAAC,IAAI,EAAE,QAAQ,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,QAAQ,CAAE,CAAA;IAC3D,OAAO,CACL,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,EAAE,IAAI,QAAC,KAAK,EAAC,gBAAgB,EAAC,QAAQ,EAAC,IAAI;QACzE,oBAAC,aAAa;YACZ,oBAAC,QAAQ,IAAC,KAAK,EAAC,YAAY;gBAC1B,oBAAC,UAAU,IAAC,UAAU,EAAE,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAI,CACxC;YACX,oBAAC,QAAQ,IAAC,KAAK,EAAC,UAAU;gBACxB,oBAAC,gBAAgB,IAAC,GAAG,EAAE,CAAC,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC,GAAI,CACpC;YACV,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,QAAQ,IAAC,KAAK,EAAC,gBAAgB;gBAC9B,oBAAC,UAAU,IAAC,UAAU,EAAE,QAAQ,GAAI,CAC3B,CACZ,CAAC,CAAC,CAAC,IAAI,CACM,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA"}

package/dist/components/{TreePanel → tree}/renderTreeCanvas.js

@@ -6,17 +6,19 @@ export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, })
     const { hierarchy, showBranchLen, blockSize } = model;
     const by = blockSizeYOverride || blockSize;
     ctx.strokeStyle = theme.palette.text.primary;
-    for (const { source, target } of hierarchy.links()) {
-        const y = showBranchLen ? 'len' : 'y';
+    for (const link of hierarchy.links()) {
+        const { source, target } = link;
+        const sy = source.x;
+        const ty = target.x;
         // @ts-expect-error
-        const { x: sy, [y]: sx } = source;
+        const tx = showBranchLen ? target.len : target.y;
         // @ts-expect-error
-        const { x: ty, [y]: tx } = target;
+        const sx = showBranchLen ? source.len : source.y;
         const y1 = Math.min(sy, ty);
         const y2 = Math.max(sy, ty);
-        // 1d line intersection to check if line crosses block at all, this is
-        // an optimization that allows us to skip drawing most tree links
-        // outside the block
+        // 1d line intersection to check if line crosses block at all, this is an
+        // optimization that allows us to skip drawing most tree links outside the
+        // block
         if (offsetY + by >= y1 && y2 >= offsetY) {
             ctx.beginPath();
             ctx.moveTo(sx, sy);
@@ -31,11 +33,9 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
     const by = blockSizeYOverride || blockSize;
     for (const node of hierarchy.descendants()) {
         const val = showBranchLen ? 'len' : 'y';
-        const { 
         // @ts-expect-error
-        x: y, 
-        // @ts-expect-error
-        [val]: x, data, } = node;
+        const { [val]: x, data } = node;
+        const y = node.x;
         const { branchset, id = '', name = '' } = data;
         if (!id.endsWith('-leafnode') &&
             branchset.length &&
@@ -60,7 +60,7 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
     }
 }
 export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
-    const { rowHeight, showBranchLen, treeMetadata, hierarchy, blockSize, labelsAlignRight, drawTree, structures, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft: ml, noTree, } = model;
+    const { fontSize, showBranchLen, treeMetadata, hierarchy, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, noTree, } = model;
     const by = blockSizeYOverride || blockSize;
     if (labelsAlignRight) {
         ctx.textAlign = 'right';
@@ -70,34 +70,20 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
         ctx.textAlign = 'start';
     }
     for (const node of hierarchy.leaves()) {
-        const { 
-        // @ts-expect-error
-        x: y, 
-        // @ts-expect-error
-        y: x, data: { name, id }, 
+        const { data: { name, id }, 
         // @ts-expect-error
         len, } = node;
+        const y = node.x;
+        const x = node.y;
         const displayName = treeMetadata[name]?.genome || name;
         if (y > offsetY - extendBounds && y < offsetY + by + extendBounds) {
             // note: +rowHeight/4 matches with -rowHeight/4 in msa
-            const yp = y + rowHeight / 4;
-            const xp = showBranchLen ? len : x;
+            const yp = y + fontSize / 4;
+            const xp = (showBranchLen ? len : x) || 0;
             const { width } = ctx.measureText(displayName);
             const height = ctx.measureText('M').width; // use an 'em' for height
-            const hasStructure = structures[name];
-            ctx.fillStyle = hasStructure ? 'blue' : theme.palette.text.primary;
-            if (!drawTree && !labelsAlignRight) {
-                ctx.fillText(displayName, 0, yp);
-                clickMap?.insert({
-                    minX: 0 + ml,
-                    maxX: width + ml,
-                    minY: yp - height,
-                    maxY: yp,
-                    name,
-                    id,
-                });
-            }
-            else if (labelsAlignRight) {
+            ctx.fillStyle = theme.palette.text.primary;
+            if (labelsAlignRight) {
                 const smallPadding = 2;
                 const offset = treeAreaWidthMinusMargin - smallPadding;
                 if (drawTree && !noTree) {
@@ -119,8 +105,8 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
             else {
                 ctx.fillText(displayName, xp + d, yp);
                 clickMap?.insert({
-                    minX: xp + d + ml,
-                    maxX: xp + d + width + ml,
+                    minX: xp + d + marginLeft,
+                    maxX: xp + d + width + marginLeft,
                     minY: yp - height,
                     maxY: yp,
                     name,
@@ -133,7 +119,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
 }
 export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }) {
     clickMap?.clear();
-    const { noTree, drawTree, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, rowHeight, marginLeft, nref, } = model;
+    const { noTree, drawTree, drawLabels, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, rowHeight, marginLeft, nref, } = model;
     const by = blockSizeYOverride || blockSize;
     ctx.resetTransform();
     // this is a bogus use of nref, it is never less than 0. we just are using it
@@ -166,7 +152,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
             });
         }
     }
-    if (rowHeight >= 5) {
+    if (rowHeight >= 5 && drawLabels) {
         renderTreeLabels({
             ctx,
             offsetY,

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

@@ -0,0 +1 @@
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package/dist/fetchUtils.d.ts

@@ -0,0 +1,5 @@
+export declare function myfetch(url: string, args?: RequestInit): Promise<Response>;
+export declare function textfetch(url: string, args?: RequestInit): Promise<string>;
+export declare function jsonfetch(url: string, args?: RequestInit): Promise<any>;
+export declare function arraybufferfetch(url: string): Promise<ArrayBuffer>;
+export declare function timeout(time: number): Promise<unknown>;

package/dist/fetchUtils.js

@@ -0,0 +1,23 @@
+export async function myfetch(url, args) {
+    const response = await fetch(url, args);
+    if (!response.ok) {
+        throw new Error(`HTTP ${response.status} fetching ${url} ${await response.text()}`);
+    }
+    return response;
+}
+export async function textfetch(url, args) {
+    const response = await myfetch(url, args);
+    return response.text();
+}
+export async function jsonfetch(url, args) {
+    const response = await myfetch(url, args);
+    return response.json();
+}
+export async function arraybufferfetch(url) {
+    const res = await myfetch(url);
+    return res.arrayBuffer();
+}
+export function timeout(time) {
+    return new Promise(res => setTimeout(res, time));
+}
+//# sourceMappingURL=fetchUtils.js.map

package/dist/fetchUtils.js.map

@@ -0,0 +1 @@
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package/dist/ggplotPalettes.d.ts

@@ -0,0 +1,3 @@
+declare const palettes: string[][];
+export declare function getPalette(l: number): string[];
+export default palettes;

package/dist/ggplotPalettes.js

@@ -0,0 +1,24 @@
+const palettes = [
+    ['#F8766D'],
+    ['#F8766D', '#00BFC4'],
+    ['#F8766D', '#00BA38', '#619CFF'],
+    ['#F8766D', '#7CAE00', '#00BFC4', '#C77CFF'],
+    ['#F8766D', '#A3A500', '#00BF7D', '#00B0F6', '#E76BF3'],
+    ['#F8766D', '#B79F00', '#00BA38', '#00BFC4', '#619CFF', '#F564E3'],
+    ['#F8766D', '#C49A00', '#53B400', '#00C094', '#00B6EB', '#A58AFF', '#FB61D7'],
+    [
+        '#F8766D',
+        '#CD9600',
+        '#7CAE00',
+        '#00BE67',
+        '#00BFC4',
+        '#00A9FF',
+        '#C77CFF',
+        '#FF61CC',
+    ],
+];
+export function getPalette(l) {
+    return palettes[Math.min(l, palettes.length - 1)];
+}
+export default palettes;
+//# sourceMappingURL=ggplotPalettes.js.map

package/dist/ggplotPalettes.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -1,2 +1,2 @@
 export { default as MSAView } from './components/Loading';
-export { default as MSAModel, type MsaViewModel } from './model';
+export { default as MSAModelF, type MsaViewModel } from './model';

package/dist/index.js

@@ -1,3 +1,3 @@
 export { default as MSAView } from './components/Loading';
-export { default as MSAModel } from './model';
+export { default as MSAModelF } from './model';
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,sBAAsB,CAAA;AACzD,OAAO,EAAE,OAAO,IAAI,SAAS,EAAqB,MAAM,SAAS,CAAA"}

package/dist/launchInterProScan.d.ts

@@ -0,0 +1,32 @@
+export interface InterProScanResults {
+    matches: {
+        signature: {
+            entry?: {
+                name: string;
+                description: string;
+                accession: string;
+            };
+        };
+        locations: {
+            start: number;
+            end: number;
+        }[];
+    }[];
+    xref: {
+        id: string;
+    }[];
+}
+export interface InterProScanResponse {
+    results: InterProScanResults[];
+}
+export declare function loadInterProScanResults(jobId: string): Promise<InterProScanResponse>;
+export declare function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, }: {
+    algorithm: string;
+    seq: string;
+    programs: string[];
+    onProgress: (arg?: {
+        msg: string;
+        url?: string;
+    }) => void;
+    onJobId: (arg: string) => void;
+}): Promise<InterProScanResponse>;

package/dist/launchInterProScan.js

@@ -0,0 +1,47 @@
+import { jsonfetch, textfetch, timeout } from './fetchUtils';
+const base = `https://www.ebi.ac.uk/Tools/services/rest`;
+async function runInterProScan({ seq, onProgress, onJobId, programs, }) {
+    const jobId = await textfetch(`${base}/iprscan5/run`, {
+        method: 'POST',
+        body: new URLSearchParams({
+            email: 'colin.diesh@gmail.com',
+            sequence: `${seq}`,
+            programs: programs.join(','),
+        }),
+    });
+    onJobId(jobId);
+    await wait({
+        jobId,
+        onProgress,
+    });
+    return loadInterProScanResults(jobId);
+}
+export async function loadInterProScanResults(jobId) {
+    return (await jsonfetch(`${base}/iprscan5/result/${jobId}/json`));
+}
+async function wait({ onProgress, jobId, }) {
+    const url = `${base}/iprscan5/status/${jobId}`;
+    // eslint-disable-next-line no-constant-condition
+    while (true) {
+        for (let i = 0; i < 10; i++) {
+            await timeout(1000);
+            onProgress({ msg: `Checking status... ${10 - i}`, url });
+        }
+        const result = await textfetch(url);
+        if (result === 'FINISHED') {
+            break;
+        }
+    }
+}
+export async function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, }) {
+    onProgress({ msg: `Launching ${algorithm} MSA...` });
+    if (algorithm === 'interproscan') {
+        const result = await runInterProScan({ seq, onJobId, onProgress, programs });
+        onProgress();
+        return result;
+    }
+    else {
+        throw new Error('unknown algorithm');
+    }
+}
+//# sourceMappingURL=launchInterProScan.js.map

package/dist/launchInterProScan.js.map

@@ -0,0 +1 @@
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