react-msaview 4.4.6 → 4.6.0

package/dist/components/tracks/renderTracksSvg.js

@@ -0,0 +1,83 @@
+export function renderConservationTrack({ model, ctx, offsetX, offsetY, trackHeight, blockSizeXOverride, highResScaleFactorOverride, }) {
+    const { blockSize, colWidth, highResScaleFactor, conservation } = model;
+    const bx = blockSizeXOverride ?? blockSize;
+    const k = highResScaleFactorOverride ?? highResScaleFactor;
+    ctx.resetTransform();
+    ctx.scale(k, k);
+    ctx.translate(-offsetX, offsetY);
+    const xStart = Math.max(0, Math.floor(offsetX / colWidth));
+    const xEnd = Math.max(0, Math.ceil((offsetX + bx) / colWidth));
+    for (let i = xStart; i < xEnd && i < conservation.length; i++) {
+        const value = conservation[i];
+        const barHeight = value * trackHeight;
+        const x = i * colWidth;
+        const hue = value * 120;
+        ctx.fillStyle = `hsl(${hue}, 70%, 50%)`;
+        ctx.fillRect(x, trackHeight - barHeight, colWidth, barHeight);
+    }
+    ctx.resetTransform();
+}
+export function renderTextTrack({ model, ctx, track, offsetX, offsetY, contrastScheme, blockSizeXOverride, highResScaleFactorOverride, }) {
+    const { blockSize, bgColor, colorScheme: modelColorScheme, colWidth, fontSize, rowHeight, highResScaleFactor, } = model;
+    const { customColorScheme, data } = track.model;
+    const colorScheme = customColorScheme ?? modelColorScheme;
+    const bx = blockSizeXOverride ?? blockSize;
+    const k = highResScaleFactorOverride ?? highResScaleFactor;
+    ctx.resetTransform();
+    ctx.scale(k, k);
+    ctx.translate(-offsetX, offsetY);
+    ctx.textAlign = 'center';
+    ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
+    const xStart = Math.max(0, Math.floor(offsetX / colWidth));
+    const xEnd = Math.max(0, Math.ceil((offsetX + bx) / colWidth));
+    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 x = i * colWidth + offsetX - (offsetX % colWidth);
+        if (bgColor && color) {
+            ctx.fillStyle = color;
+            ctx.fillRect(x, 0, colWidth, rowHeight);
+        }
+        if (rowHeight >= 10 && colWidth >= rowHeight / 2) {
+            ctx.fillStyle =
+                bgColor && color
+                    ? (contrastScheme[letter.toUpperCase()] ?? 'black')
+                    : 'black';
+            ctx.fillText(letter, x + colWidth / 2, rowHeight / 2 + 1);
+        }
+    }
+    ctx.resetTransform();
+}
+export function renderAllTracks({ model, ctx, offsetX, contrastScheme, blockSizeXOverride, highResScaleFactorOverride, }) {
+    const { turnedOnTracks } = model;
+    let currentY = 0;
+    for (const track of turnedOnTracks) {
+        const trackHeight = track.model.height;
+        if (track.model.id === 'conservation') {
+            renderConservationTrack({
+                model,
+                ctx,
+                offsetX,
+                offsetY: currentY,
+                trackHeight,
+                blockSizeXOverride,
+                highResScaleFactorOverride,
+            });
+        }
+        else {
+            renderTextTrack({
+                model,
+                ctx,
+                track,
+                offsetX,
+                offsetY: currentY,
+                contrastScheme,
+                blockSizeXOverride,
+                highResScaleFactorOverride,
+            });
+        }
+        currentY += trackHeight;
+    }
+}
+//# sourceMappingURL=renderTracksSvg.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"renderTracksSvg.js","sourceRoot":"","sources":["../../../src/components/tracks/renderTracksSvg.ts"],"names":[],"mappings":"AAGA,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,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC1D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAA;IAE9D,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;QAEtB,MAAM,GAAG,GAAG,KAAK,GAAG,GAAG,CAAA;QACvB,GAAG,CAAC,SAAS,GAAG,OAAO,GAAG,aAAa,CAAA;QACvC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,WAAW,GAAG,SAAS,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;IAC/D,CAAC;IAED,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,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG,QAAQ,IAAI,CAAC,CAAA;IAErD,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC1D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC9D,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,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;QAC/C,MAAM,CAAC,GAAG,CAAC,GAAG,QAAQ,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAA;QAEvD,IAAI,OAAO,IAAI,KAAK,EAAE,CAAC;YACrB,GAAG,CAAC,SAAS,GAAG,KAAK,CAAA;YACrB,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;QACzC,CAAC;QAED,IAAI,SAAS,IAAI,EAAE,IAAI,QAAQ,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;YACjD,GAAG,CAAC,SAAS;gBACX,OAAO,IAAI,KAAK;oBACd,CAAC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IAAI,OAAO,CAAC;oBACnD,CAAC,CAAC,OAAO,CAAA;YACb,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,QAAQ,GAAG,CAAC,EAAE,SAAS,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;QAC3D,CAAC;IACH,CAAC;IAED,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/TreeNodeMenu.js

@@ -29,10 +29,10 @@ const TreeMenu = observer(function ({ node, onClose, model, }) {
                 }
                 else {
                     if (node.id.endsWith('-leafnode')) {
-                        model.toggleCollapsed2(node.id);
+                        model.toggleCollapsedLeaf(node.id);
                     }
                     else {
-                        model.toggleCollapsed2(`${node.id}-leafnode`);
+                        model.toggleCollapsedLeaf(`${node.id}-leafnode`);
                     }
                 }
                 onClose();

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

@@ -1 +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;AAEnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,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,GAUN;IACC,MAAM,EAAE,SAAS,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IACrB,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,CACI;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;wBAC5B,KAAK;wBACL,QAAQ,EAAE,IAAI;wBACd,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,IAAI,CAAC,EAAE,CAAC,CAAA;oBACjC,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,eAAe,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/D,CAAC,CAAC,WAAW;YACb,CAAC,CAAC,WAAW,CACN;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,yCAGQ;QACV,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAClB,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,0BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI,CACH,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}
+{"version":3,"file":"TreeNodeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeNodeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,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,GAUN;IACC,MAAM,EAAE,SAAS,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IACrB,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,CACI;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;wBAC5B,KAAK;wBACL,QAAQ,EAAE,IAAI;wBACd,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,mBAAmB,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;oBACpC,CAAC;yBAAM,CAAC;wBACN,KAAK,CAAC,mBAAmB,CAAC,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,CAAA;oBAClD,CAAC;gBACH,CAAC;gBACD,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,eAAe,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/D,CAAC,CAAC,WAAW;YACb,CAAC,CAAC,WAAW,CACN;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,yCAGQ;QACV,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAClB,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,0BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI,CACH,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/tree/renderTreeCanvas.d.ts

@@ -33,7 +33,6 @@ export declare function renderNodeBubbles({ ctx, clickMap, offsetY, model, block
     clickMap?: ClickMapIndex;
     offsetY: number;
     model: MsaViewModel;
-    theme: Theme;
     blockSizeYOverride?: number;
 }): void;
 export declare function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }: {

package/dist/components/tree/renderTreeCanvas.js

@@ -3,10 +3,9 @@ const extendBounds = 5;
 const radius = 2.5;
 const d = radius * 2;
 export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, }) {
-    const { hierarchy, allBranchesLength0, showBranchLen: showBranchLenPre, blockSize, } = model;
+    const { hierarchy, showBranchLenEffective: showBranchLen, blockSize } = model;
     const by = blockSizeYOverride || blockSize;
     ctx.strokeStyle = theme.palette.text.primary;
-    const showBranchLen = allBranchesLength0 ? false : showBranchLenPre;
     for (const link of hierarchy.links()) {
         const { source, target } = link;
         if (target.height === 0 && !showBranchLen) {
@@ -33,15 +32,14 @@ export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, })
     }
 }
 export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOverride, }) {
-    const { hierarchy, showBranchLen: showBranchLenPre, allBranchesLength0, collapsed, blockSize, marginLeft: ml, } = model;
+    const { hierarchy, showBranchLenEffective: showBranchLen, collapsed, blockSize, marginLeft: ml, } = model;
     const by = blockSizeYOverride || blockSize;
-    const showBranchLen = allBranchesLength0 ? false : showBranchLenPre;
     for (const node of hierarchy.descendants()) {
         const val = showBranchLen ? 'len' : 'y';
         // @ts-expect-error
         const { [val]: x, data } = node;
         const y = node.x;
-        const { id = '', name = '' } = data;
+        const { id, name } = data;
         if (node.height > 1 &&
             y > offsetY - extendBounds &&
             y < offsetY + by + extendBounds) {
@@ -64,8 +62,9 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
     }
 }
 export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
-    const { fontSize, showBranchLen: showBranchLenPre, allBranchesLength0, treeMetadata, hierarchy, collapsed, collapsedLeaves, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, } = model;
+    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, hierarchy, collapsed, collapsedLeaves, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, } = model;
     const by = blockSizeYOverride || blockSize;
+    const emHeight = ctx.measureText('M').width;
     if (labelsAlignRight) {
         ctx.textAlign = 'right';
         ctx.setLineDash([1, 3]);
@@ -73,7 +72,6 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
     else {
         ctx.textAlign = 'start';
     }
-    const showBranchLen = allBranchesLength0 ? false : showBranchLenPre;
     for (const node of leaves) {
         const { data: { name, id }, 
         // @ts-expect-error
@@ -84,24 +82,25 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
         if (y > offsetY - extendBounds && y < offsetY + by + extendBounds) {
             // note: +rowHeight/4 matches with -rowHeight/4 in msa
             const yp = y + fontSize / 4;
-            let xp = (showBranchLen ? len : x) || 0;
-            if (!showBranchLen &&
-                !collapsed.includes(id) &&
-                !collapsedLeaves.includes(id)) {
-                // this subtraction is a hack to compensate for the leafnode rendering
-                // glitch (issue #71). the context is that an extra leaf node is added
-                // so that 'collapsing/hiding leaf nodes is possible' but this causes
-                // weird workarounds
-                xp -= treeWidth / hierarchy.height;
+            let xp = 0;
+            if (!noTree) {
+                xp = (showBranchLen ? len : x) || 0;
+                if (!showBranchLen &&
+                    !collapsed.includes(id) &&
+                    !collapsedLeaves.includes(id)) {
+                    // this subtraction is a hack to compensate for the leafnode rendering
+                    // glitch (issue #71). the context is that an extra leaf node is added
+                    // so that 'collapsing/hiding leaf nodes is possible' but this causes
+                    // weird workarounds
+                    xp -= treeWidth / hierarchy.height;
+                }
             }
             const { width } = ctx.measureText(displayName);
-            const height = ctx.measureText('M').width; // use an 'em' for height
             ctx.fillStyle = theme.palette.text.primary;
             if (labelsAlignRight) {
                 const smallPadding = 2;
                 const offset = treeAreaWidthMinusMargin - smallPadding;
                 if (drawTree && !noTree) {
-                    const { width } = ctx.measureText(displayName);
                     ctx.moveTo(xp + radius + 2, y);
                     ctx.lineTo(offset - smallPadding - width, y);
                     ctx.stroke();
@@ -110,18 +109,19 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
                 clickMap?.insert({
                     minX: treeAreaWidth - width,
                     maxX: treeAreaWidth,
-                    minY: yp - height,
+                    minY: yp - emHeight,
                     maxY: yp,
                     name,
                     id,
                 });
             }
             else {
-                ctx.fillText(displayName, xp + d, yp);
+                const labelX = noTree ? 2 : xp + d;
+                ctx.fillText(displayName, labelX, yp);
                 clickMap?.insert({
-                    minX: xp + d + marginLeft,
-                    maxX: xp + d + width + marginLeft,
-                    minY: yp - height,
+                    minX: labelX + marginLeft,
+                    maxX: labelX + width + marginLeft,
+                    minY: yp - emHeight,
                     maxY: yp,
                     name,
                     id,
@@ -165,7 +165,6 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
                 offsetY,
                 clickMap,
                 model,
-                theme,
                 blockSizeYOverride,
             });
         }

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

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

@@ -0,0 +1,22 @@
+export declare const defaultRowHeight = 16;
+export declare const defaultColWidth = 12;
+export declare const defaultHeight = 550;
+export declare const defaultScrollX = 0;
+export declare const defaultScrollY = 0;
+export declare const defaultCurrentAlignment = 0;
+export declare const defaultShowDomains = false;
+export declare const defaultHideGaps = true;
+export declare const defaultAllowedGappyness = 100;
+export declare const defaultContrastLettering = true;
+export declare const defaultSubFeatureRows = false;
+export declare const defaultDrawMsaLetters = true;
+export declare const defaultBgColor = true;
+export declare const defaultColorSchemeName = "maeditor";
+export declare const defaultDrawLabels = true;
+export declare const defaultLabelsAlignRight = false;
+export declare const defaultTreeAreaWidth = 400;
+export declare const defaultTreeWidth = 300;
+export declare const defaultTreeWidthMatchesArea = true;
+export declare const defaultShowBranchLen = true;
+export declare const defaultDrawTree = true;
+export declare const defaultDrawNodeBubbles = true;

package/dist/constants.js

@@ -0,0 +1,26 @@
+// Main model defaults
+export const defaultRowHeight = 16;
+export const defaultColWidth = 12;
+export const defaultHeight = 550;
+export const defaultScrollX = 0;
+export const defaultScrollY = 0;
+export const defaultCurrentAlignment = 0;
+export const defaultShowDomains = false;
+export const defaultHideGaps = true;
+export const defaultAllowedGappyness = 100;
+export const defaultContrastLettering = true;
+export const defaultSubFeatureRows = false;
+export const defaultDrawMsaLetters = true;
+// MSA model defaults
+export const defaultBgColor = true;
+export const defaultColorSchemeName = 'maeditor';
+// Tree model defaults
+export const defaultDrawLabels = true;
+export const defaultLabelsAlignRight = false;
+export const defaultTreeAreaWidth = 400;
+export const defaultTreeWidth = 300;
+export const defaultTreeWidthMatchesArea = true;
+export const defaultShowBranchLen = true;
+export const defaultDrawTree = true;
+export const defaultDrawNodeBubbles = true;
+//# sourceMappingURL=constants.js.map

package/dist/constants.js.map

@@ -0,0 +1 @@
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package/dist/layout.js.map

@@ -1 +1 @@
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package/dist/model/msaModel.js

@@ -1,4 +1,5 @@
 import { types } from 'mobx-state-tree';
+import { defaultBgColor, defaultColorSchemeName } from '../constants';
 /**
  * #stateModel MSAModel
  */
@@ -10,12 +11,12 @@ export function MSAModelF() {
          * #property
          * draw MSA tiles with a background color
          */
-        bgColor: true,
+        bgColor: defaultBgColor,
         /**
          * #property
          * default color scheme name
          */
-        colorSchemeName: 'maeditor',
+        colorSchemeName: defaultColorSchemeName,
     })
         .actions(self => ({
         /**

package/dist/model/msaModel.js.map

@@ -1 +1 @@
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package/dist/model/treeModel.js

@@ -1,4 +1,5 @@
 import { types } from 'mobx-state-tree';
+import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawTree, defaultLabelsAlignRight, defaultShowBranchLen, defaultTreeAreaWidth, defaultTreeWidth, defaultTreeWidthMatchesArea, } from '../constants';
 /**
  * #stateModel Tree
  */
@@ -9,44 +10,44 @@ export function TreeModelF() {
         /**
          * #property
          */
-        drawLabels: true,
+        drawLabels: defaultDrawLabels,
         /**
          * #property
          * right-align the labels
          */
-        labelsAlignRight: false,
+        labelsAlignRight: defaultLabelsAlignRight,
         /**
          * #property
          * width of the area the tree is drawn in, px
          */
-        treeAreaWidth: types.optional(types.number, 400),
+        treeAreaWidth: types.optional(types.number, defaultTreeAreaWidth),
         /**
          * #property
          * width of the tree within the treeArea, px
          */
-        treeWidth: types.optional(types.number, 300),
+        treeWidth: types.optional(types.number, defaultTreeWidth),
         /**
          * #getter
          * synchronization that matches treeWidth to treeAreaWidth
          */
-        treeWidthMatchesArea: true,
+        treeWidthMatchesArea: defaultTreeWidthMatchesArea,
         /**
          * #property
          * use "branch length" e.g. evolutionary distance to draw tree branch
          * lengths. if false, the layout is a "cladogram" that does not take into
          * account evolutionary distances
          */
-        showBranchLen: true,
+        showBranchLen: defaultShowBranchLen,
         /**
          * #property
          * draw tree, boolean
          */
-        drawTree: true,
+        drawTree: defaultDrawTree,
         /**
          * #property
          * draw clickable node bubbles on the tree
          */
-        drawNodeBubbles: true,
+        drawNodeBubbles: defaultDrawNodeBubbles,
     })
         .actions(self => ({
         /**

package/dist/model/treeModel.js.map

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