react-msaview 6.0.0 → 6.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/bundle/index.js +98 -98
- package/bundle/index.js.map +4 -4
- package/dist/columnCounts.d.ts +7 -0
- package/dist/columnCounts.js +18 -0
- package/dist/columnCounts.js.map +1 -1
- package/dist/components/DragHandle.d.ts +25 -0
- package/dist/components/DragHandle.js +49 -0
- package/dist/components/DragHandle.js.map +1 -0
- package/dist/components/ResizeHandles.d.ts +4 -2
- package/dist/components/ResizeHandles.js +29 -32
- package/dist/components/ResizeHandles.js.map +1 -1
- package/dist/components/VerticalScrollbar.js +2 -2
- package/dist/components/VerticalScrollbar.js.map +1 -1
- package/dist/components/dialogs/InterProScanDialog.js +52 -129
- package/dist/components/dialogs/InterProScanDialog.js.map +1 -1
- package/dist/components/header/settingsMenuItems.js +15 -0
- package/dist/components/header/settingsMenuItems.js.map +1 -1
- package/dist/components/minimap/Minimap.js +32 -4
- package/dist/components/minimap/Minimap.js.map +1 -1
- package/dist/components/msa/MSACanvas.js +8 -2
- package/dist/components/msa/MSACanvas.js.map +1 -1
- package/dist/components/msa/MSACanvasBlock.js +12 -3
- package/dist/components/msa/MSACanvasBlock.js.map +1 -1
- package/dist/components/msa/msaRaster.d.ts +63 -0
- package/dist/components/msa/msaRaster.js +252 -0
- package/dist/components/msa/msaRaster.js.map +1 -0
- package/dist/components/msa/renderMSABlock.d.ts +2 -1
- package/dist/components/msa/renderMSABlock.js +13 -21
- package/dist/components/msa/renderMSABlock.js.map +1 -1
- package/dist/components/msa/tileColor.d.ts +6 -0
- package/dist/components/msa/tileColor.js +35 -0
- package/dist/components/msa/tileColor.js.map +1 -0
- package/dist/components/renderCtx.d.ts +1 -1
- package/dist/components/tracks/TrackBlocks.d.ts +14 -0
- package/dist/components/tracks/TrackBlocks.js +65 -0
- package/dist/components/tracks/TrackBlocks.js.map +1 -0
- package/dist/components/tracks/{renderTracksSvg.d.ts → drawTracks.d.ts} +22 -10
- package/dist/components/tracks/drawTracks.js +193 -0
- package/dist/components/tracks/drawTracks.js.map +1 -0
- package/dist/components/tree/TreeCanvas.js +8 -2
- package/dist/components/tree/TreeCanvas.js.map +1 -1
- package/dist/components/tree/TreeCanvasBlock.js +7 -4
- package/dist/components/tree/TreeCanvasBlock.js.map +1 -1
- package/dist/components/tree/renderTreeCanvas.js +5 -2
- package/dist/components/tree/renderTreeCanvas.js.map +1 -1
- package/dist/constants.d.ts +3 -0
- package/dist/constants.js +8 -0
- package/dist/constants.js.map +1 -1
- package/dist/model/DataModel.d.ts +1 -4
- package/dist/model/DataModel.js +8 -10
- package/dist/model/DataModel.js.map +1 -1
- package/dist/model.d.ts +36 -7
- package/dist/model.js +113 -58
- package/dist/model.js.map +1 -1
- package/dist/neighborJoining.js +34 -18
- package/dist/neighborJoining.js.map +1 -1
- package/dist/renderTestEnv.d.ts +43 -0
- package/dist/renderTestEnv.js +88 -0
- package/dist/renderTestEnv.js.map +1 -0
- package/dist/renderToSvg.js +1 -1
- package/dist/renderToSvg.js.map +1 -1
- package/dist/sequenceLogo.d.ts +28 -0
- package/dist/sequenceLogo.js +47 -0
- package/dist/sequenceLogo.js.map +1 -0
- package/dist/types.d.ts +2 -0
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +3 -3
- package/src/columnCounts.test.ts +15 -0
- package/src/columnCounts.ts +19 -0
- package/src/components/DragHandle.tsx +81 -0
- package/src/components/ResizeHandles.tsx +46 -54
- package/src/components/VerticalScrollbar.tsx +3 -2
- package/src/components/dialogs/InterProScanDialog.tsx +54 -131
- package/src/components/header/settingsMenuItems.ts +18 -0
- package/src/components/minimap/Minimap.tsx +47 -4
- package/src/components/msa/MSACanvas.tsx +30 -10
- package/src/components/msa/MSACanvasBlock.tsx +13 -3
- package/src/components/msa/msaRaster.test.ts +145 -0
- package/src/components/msa/msaRaster.ts +350 -0
- package/src/components/msa/renderMSABlock.ts +15 -20
- package/src/components/msa/tileColor.ts +37 -0
- package/src/components/renderCtx.ts +2 -0
- package/src/components/tracks/TrackBlocks.tsx +111 -0
- package/src/components/tracks/drawTracks.ts +323 -0
- package/src/components/tree/TreeCanvas.tsx +16 -4
- package/src/components/tree/TreeCanvasBlock.tsx +18 -11
- package/src/components/tree/renderTreeCanvas.ts +5 -1
- package/src/constants.ts +10 -0
- package/src/impgRender.test.tsx +2 -57
- package/src/largeTree.test.ts +16 -2
- package/src/model/DataModel.ts +11 -11
- package/src/model.ts +128 -60
- package/src/neighborJoining.ts +36 -18
- package/src/renderDomainsSvg.test.tsx +2 -57
- package/src/renderMinimapSvg.test.tsx +2 -56
- package/src/renderSequenceLogoSvg.test.tsx +176 -0
- package/src/renderTestEnv.ts +96 -0
- package/src/renderToSvg.tsx +1 -1
- package/src/sequenceLogo.test.ts +88 -0
- package/src/sequenceLogo.ts +63 -0
- package/src/types.ts +7 -1
- package/src/version.ts +1 -1
- package/dist/components/ConservationTrack.d.ts +0 -8
- package/dist/components/ConservationTrack.js +0 -49
- package/dist/components/ConservationTrack.js.map +0 -1
- package/dist/components/ScrollbarThumb.d.ts +0 -14
- package/dist/components/ScrollbarThumb.js +0 -28
- package/dist/components/ScrollbarThumb.js.map +0 -1
- package/dist/components/TextTrack.d.ts +0 -8
- package/dist/components/TextTrack.js +0 -58
- package/dist/components/TextTrack.js.map +0 -1
- package/dist/components/tracks/renderTracksSvg.js +0 -126
- package/dist/components/tracks/renderTracksSvg.js.map +0 -1
- package/src/components/ConservationTrack.tsx +0 -99
- package/src/components/ScrollbarThumb.tsx +0 -48
- package/src/components/TextTrack.tsx +0 -103
- package/src/components/tracks/renderTracksSvg.ts +0 -247
package/dist/neighborJoining.js
CHANGED
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@@ -29,23 +29,39 @@ const BLOSUM62_DATA = [
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[0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4],
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[-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1],
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];
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const
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-
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const NUM_SYMBOLS = BLOSUM62_KEYS.length;
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const BLOSUM62 = Int8Array.from(BLOSUM62_DATA.flat());
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// charCode -> row/column in BLOSUM62, -1 for anything the matrix does not name.
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// A flat table rather than a Map of Maps keyed by an upper-cased character, for
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// the reason columnCounts.ts gives: the distance matrix is O(rows^2 * columns)
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// lookups, and on a 120x800 alignment the Map form spent nearly all of its time
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// allocating one-character strings in toUpperCase: 2.6s to build a tree, versus
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// 0.34s here for a byte-identical newick.
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const symbolOfCode = new Int8Array(128).fill(-1);
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for (let i = 0; i < NUM_SYMBOLS; i++) {
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const key = BLOSUM62_KEYS[i];
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symbolOfCode[key.charCodeAt(0)] = i;
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symbolOfCode[key.toLowerCase().charCodeAt(0)] = i;
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}
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// gap, or past the end of a row shorter than the alignment
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const GAP = -2;
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// stockholm and a3m write gaps as '.', not just '-'. Scoring a '.' as a residue
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// charges the pair the unknown-symbol penalty on every padded column, so two
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// sequences that differ only in where an unrelated row forced padding come out
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// as divergent.
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function
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function symbolAt(seq, i) {
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if (i >= seq.length) {
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return GAP;
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}
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const code = seq.charCodeAt(i);
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// bit trick: (code - 45) >>> 0 <= 1 checks for '-' (45) or '.' (46)
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if ((code - 45) >>> 0 <= 1) {
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return GAP;
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}
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return code < 128 ? symbolOfCode[code] : -1;
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}
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function blosumScore(a, b) {
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return a < 0 || b < 0 ? -4 : BLOSUM62[a * NUM_SYMBOLS + b];
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}
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function computePairwiseDistance(seq1, seq2) {
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// ragged input is real -- a3m and hand-edited fasta both produce rows shorter
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let totalScore = 0;
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let maxPossibleScore = 0;
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for (let i = 0; i < len; i++) {
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const a = seq1
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const b = seq2
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const aGap =
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const bGap =
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const a = symbolAt(seq1, i);
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const b = symbolAt(seq2, i);
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const aGap = a === GAP;
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const bGap = b === GAP;
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if (aGap && bGap) {
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continue;
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}
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if (aGap || bGap) {
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continue;
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}
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totalScore +=
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maxPossibleScore += Math.max(
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totalScore += blosumScore(a, b);
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maxPossibleScore += Math.max(blosumScore(a, a), blosumScore(b, b));
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}
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if (compared === 0) {
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return 1;
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@@ -1 +1 @@
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1
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-
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1
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@@ -0,0 +1,43 @@
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1
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/**
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2
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* jsdom shims for the SVG-export tests. Test-only -- nothing in the viewer
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3
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* imports this.
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4
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*
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5
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* jsdom implements neither DOMMatrix nor a canvas 2D context, and
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6
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* `@jbrowse/svgcanvas` needs both: it tracks the current transform as a real
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7
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* matrix, and the renderers ask a throwaway canvas to measure text.
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8
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*
|
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9
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* The matrix stub has to accept the ARRAY constructor. svgcanvas normalizes
|
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10
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* every transform through `new DOMMatrix([a, b, c, d, e, f])`, so a stub that
|
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11
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* only takes six positional arguments silently binds the whole array to `a` and
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12
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* leaves the rest undefined -- every emitted transform then carries `NaN` in its
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13
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+
* x components, which no assertion on a drawn x-position can survive.
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14
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+
*/
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15
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+
export declare class TestDOMMatrix {
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16
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a: number;
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b: number;
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18
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c: number;
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d: number;
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20
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e: number;
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21
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f: number;
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22
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+
constructor(init?: number[]);
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23
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multiply(o: TestDOMMatrix): TestDOMMatrix;
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24
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+
translate(x: number, y?: number): TestDOMMatrix;
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25
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+
scale(x: number, y?: number): TestDOMMatrix;
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}
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27
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+
export declare class TestDOMPoint {
|
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28
|
+
x: number;
|
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29
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+
y: number;
|
|
30
|
+
constructor(x?: number, y?: number);
|
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31
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+
matrixTransform(m: TestDOMMatrix): TestDOMPoint;
|
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32
|
+
}
|
|
33
|
+
/**
|
|
34
|
+
* Install the shims. Call from `beforeAll` in any test that exports SVG.
|
|
35
|
+
*
|
|
36
|
+
* `measureText` reports 0.6em per character, close enough to a real sans-serif
|
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37
|
+
* average for layout assertions and, more usefully, exactly predictable: a test
|
|
38
|
+
* can compute the width a renderer will see rather than hardcoding a number
|
|
39
|
+
* measured from one machine's fonts.
|
|
40
|
+
*/
|
|
41
|
+
export declare function installRenderTestEnv(): void;
|
|
42
|
+
/** the per-character width factor `measureText` above reports */
|
|
43
|
+
export declare const TEST_CHAR_WIDTH_RATIO = 0.6;
|
|
@@ -0,0 +1,88 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* jsdom shims for the SVG-export tests. Test-only -- nothing in the viewer
|
|
3
|
+
* imports this.
|
|
4
|
+
*
|
|
5
|
+
* jsdom implements neither DOMMatrix nor a canvas 2D context, and
|
|
6
|
+
* `@jbrowse/svgcanvas` needs both: it tracks the current transform as a real
|
|
7
|
+
* matrix, and the renderers ask a throwaway canvas to measure text.
|
|
8
|
+
*
|
|
9
|
+
* The matrix stub has to accept the ARRAY constructor. svgcanvas normalizes
|
|
10
|
+
* every transform through `new DOMMatrix([a, b, c, d, e, f])`, so a stub that
|
|
11
|
+
* only takes six positional arguments silently binds the whole array to `a` and
|
|
12
|
+
* leaves the rest undefined -- every emitted transform then carries `NaN` in its
|
|
13
|
+
* x components, which no assertion on a drawn x-position can survive.
|
|
14
|
+
*/
|
|
15
|
+
export class TestDOMMatrix {
|
|
16
|
+
a;
|
|
17
|
+
b;
|
|
18
|
+
c;
|
|
19
|
+
d;
|
|
20
|
+
e;
|
|
21
|
+
f;
|
|
22
|
+
constructor(init) {
|
|
23
|
+
const [a = 1, b = 0, c = 0, d = 1, e = 0, f = 0] = init ?? [];
|
|
24
|
+
this.a = a;
|
|
25
|
+
this.b = b;
|
|
26
|
+
this.c = c;
|
|
27
|
+
this.d = d;
|
|
28
|
+
this.e = e;
|
|
29
|
+
this.f = f;
|
|
30
|
+
}
|
|
31
|
+
multiply(o) {
|
|
32
|
+
return new TestDOMMatrix([
|
|
33
|
+
this.a * o.a + this.c * o.b,
|
|
34
|
+
this.b * o.a + this.d * o.b,
|
|
35
|
+
this.a * o.c + this.c * o.d,
|
|
36
|
+
this.b * o.c + this.d * o.d,
|
|
37
|
+
this.a * o.e + this.c * o.f + this.e,
|
|
38
|
+
this.b * o.e + this.d * o.f + this.f,
|
|
39
|
+
]);
|
|
40
|
+
}
|
|
41
|
+
translate(x, y = 0) {
|
|
42
|
+
return this.multiply(new TestDOMMatrix([1, 0, 0, 1, x, y]));
|
|
43
|
+
}
|
|
44
|
+
scale(x, y = x) {
|
|
45
|
+
return this.multiply(new TestDOMMatrix([x, 0, 0, y, 0, 0]));
|
|
46
|
+
}
|
|
47
|
+
}
|
|
48
|
+
export class TestDOMPoint {
|
|
49
|
+
x;
|
|
50
|
+
y;
|
|
51
|
+
constructor(x = 0, y = 0) {
|
|
52
|
+
this.x = x;
|
|
53
|
+
this.y = y;
|
|
54
|
+
}
|
|
55
|
+
matrixTransform(m) {
|
|
56
|
+
return new TestDOMPoint(m.a * this.x + m.c * this.y + m.e, m.b * this.x + m.d * this.y + m.f);
|
|
57
|
+
}
|
|
58
|
+
}
|
|
59
|
+
/**
|
|
60
|
+
* Install the shims. Call from `beforeAll` in any test that exports SVG.
|
|
61
|
+
*
|
|
62
|
+
* `measureText` reports 0.6em per character, close enough to a real sans-serif
|
|
63
|
+
* average for layout assertions and, more usefully, exactly predictable: a test
|
|
64
|
+
* can compute the width a renderer will see rather than hardcoding a number
|
|
65
|
+
* measured from one machine's fonts.
|
|
66
|
+
*/
|
|
67
|
+
export function installRenderTestEnv() {
|
|
68
|
+
const g = globalThis;
|
|
69
|
+
g.DOMMatrix = TestDOMMatrix;
|
|
70
|
+
g.DOMPoint = TestDOMPoint;
|
|
71
|
+
HTMLCanvasElement.prototype.getContext = function () {
|
|
72
|
+
let font = '10px sans-serif';
|
|
73
|
+
return {
|
|
74
|
+
get font() {
|
|
75
|
+
return font;
|
|
76
|
+
},
|
|
77
|
+
set font(v) {
|
|
78
|
+
font = v;
|
|
79
|
+
},
|
|
80
|
+
measureText: (t) => ({
|
|
81
|
+
width: t.length * (Number.parseFloat(font) || 10) * 0.6,
|
|
82
|
+
}),
|
|
83
|
+
};
|
|
84
|
+
};
|
|
85
|
+
}
|
|
86
|
+
/** the per-character width factor `measureText` above reports */
|
|
87
|
+
export const TEST_CHAR_WIDTH_RATIO = 0.6;
|
|
88
|
+
//# sourceMappingURL=renderTestEnv.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"renderTestEnv.js","sourceRoot":"","sources":["../src/renderTestEnv.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AACH,MAAM,OAAO,aAAa;IACxB,CAAC,CAAQ;IACT,CAAC,CAAQ;IACT,CAAC,CAAQ;IACT,CAAC,CAAQ;IACT,CAAC,CAAQ;IACT,CAAC,CAAQ;IAET,YAAY,IAAe;QACzB,MAAM,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,IAAI,EAAE,CAAA;QAC7D,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;QACV,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;QACV,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;QACV,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;QACV,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;QACV,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACZ,CAAC;IAED,QAAQ,CAAC,CAAgB;QACvB,OAAO,IAAI,aAAa,CAAC;YACvB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;YAC3B,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;YAC3B,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;YAC3B,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;YAC3B,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;YACpC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;SACrC,CAAC,CAAA;IACJ,CAAC;IAED,SAAS,CAAC,CAAS,EAAE,CAAC,GAAG,CAAC;QACxB,OAAO,IAAI,CAAC,QAAQ,CAAC,IAAI,aAAa,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7D,CAAC;IAED,KAAK,CAAC,CAAS,EAAE,CAAC,GAAG,CAAC;QACpB,OAAO,IAAI,CAAC,QAAQ,CAAC,IAAI,aAAa,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7D,CAAC;CACF;AAED,MAAM,OAAO,YAAY;IAEd,CAAC;IACD,CAAC;IAFV,YACS,CAAC,GAAG,CAAC,EACL,CAAC,GAAG,CAAC;iBADL,CAAC;iBACD,CAAC;IACP,CAAC;IAEJ,eAAe,CAAC,CAAgB;QAC9B,OAAO,IAAI,YAAY,CACrB,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EACjC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAClC,CAAA;IACH,CAAC;CACF;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,oBAAoB;IAClC,MAAM,CAAC,GAAG,UAAqC,CAAA;IAC/C,CAAC,CAAC,SAAS,GAAG,aAAa,CAAA;IAC3B,CAAC,CAAC,QAAQ,GAAG,YAAY,CAAA;IACzB,iBAAiB,CAAC,SAAS,CAAC,UAAU,GAAG;QACvC,IAAI,IAAI,GAAG,iBAAiB,CAAA;QAC5B,OAAO;YACL,IAAI,IAAI;gBACN,OAAO,IAAI,CAAA;YACb,CAAC;YACD,IAAI,IAAI,CAAC,CAAS;gBAChB,IAAI,GAAG,CAAC,CAAA;YACV,CAAC;YACD,WAAW,EAAE,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC;gBAC3B,KAAK,EAAE,CAAC,CAAC,MAAM,GAAG,CAAC,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,GAAG,GAAG;aACxD,CAAC;SACoC,CAAA;IAC1C,CAA6D,CAAA;AAC/D,CAAC;AAED,iEAAiE;AACjE,MAAM,CAAC,MAAM,qBAAqB,GAAG,GAAG,CAAA"}
|
package/dist/renderToSvg.js
CHANGED
|
@@ -5,7 +5,7 @@ import { when } from 'mobx';
|
|
|
5
5
|
import MinimapSVG from './components/minimap/MinimapSVG.js';
|
|
6
6
|
import { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock.js';
|
|
7
7
|
import { renderMSABlock } from './components/msa/renderMSABlock.js';
|
|
8
|
-
import { renderAllTracks } from './components/tracks/
|
|
8
|
+
import { renderAllTracks } from './components/tracks/drawTracks.js';
|
|
9
9
|
import { renderTreeCanvas } from './components/tree/renderTreeCanvas.js';
|
|
10
10
|
import { colorContrast } from './util.js';
|
|
11
11
|
// domain-legend geometry, shared by the width calculation and the renderer so
|
package/dist/renderToSvg.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"renderToSvg.js","sourceRoot":"","sources":["../src/renderToSvg.tsx"],"names":[],"mappings":"AAAA,yDAAyD;AACzD,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AACzD,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAE3B,OAAO,UAAU,MAAM,oCAAqC,CAAA;AAC5D,OAAO,EAAE,2BAA2B,EAAE,MAAM,iDAAiD,CAAA;AAC7F,OAAO,EAAE,cAAc,EAAE,MAAM,oCAAoC,CAAA;AACnE,OAAO,EAAE,eAAe,EAAE,MAAM,
|
|
1
|
+
{"version":3,"file":"renderToSvg.js","sourceRoot":"","sources":["../src/renderToSvg.tsx"],"names":[],"mappings":"AAAA,yDAAyD;AACzD,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AACzD,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAE3B,OAAO,UAAU,MAAM,oCAAqC,CAAA;AAC5D,OAAO,EAAE,2BAA2B,EAAE,MAAM,iDAAiD,CAAA;AAC7F,OAAO,EAAE,cAAc,EAAE,MAAM,oCAAoC,CAAA;AACnE,OAAO,EAAE,eAAe,EAAE,MAAM,mCAAmC,CAAA;AACnE,OAAO,EAAE,gBAAgB,EAAE,MAAM,uCAAuC,CAAA;AACxE,OAAO,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AAazC,8EAA8E;AAC9E,iEAAiE;AACjE,MAAM,UAAU,GAAG,CAAC,CAAA;AACpB,MAAM,YAAY,GAAG,EAAE,CAAA;AACvB,MAAM,aAAa,GAAG,EAAE,CAAA;AACxB,MAAM,WAAW,GAAG,EAAE,CAAA;AACtB,MAAM,aAAa,GAAG,CAAC,CAAA;AAEvB,SAAS,cAAc,CAAC,KAAmB;IACzC,MAAM,KAAK,GAAG,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IACvD,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;IACvD,MAAM,CAAC,GAAG,UAAU,GAAG,CAAC,GAAG,aAAa,GAAG,CAAC,GAAG,MAAM,GAAG,aAAa,CAAA;IACrE,OAAO,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAA;AACxC,CAAC;AAgBD,SAAS,SAAS,CAAC,KAAmB,EAAE,IAAsB;IAC5D,MAAM,EACJ,KAAK,EACL,MAAM,EACN,OAAO,EACP,OAAO,EACP,UAAU,EACV,WAAW,EACX,aAAa,EACb,oBAAoB,EACpB,aAAa,GACd,GAAG,KAAK,CAAA;IACT,MAAM,WAAW,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,oBAAoB,CAAC,CAAC,CAAC,CAAC,CAAA;IACjE,uEAAuE;IACvE,mEAAmE;IACnE,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,KAAK,UAAU,IAAI,CAAC,CAAC,IAAI,CAAC,cAAc,CAAA;IAC9E,MAAM,WAAW,GACf,KAAK,CAAC,mBAAmB,IAAI,KAAK,CAAC,kBAAkB,CAAC,MAAM,GAAG,CAAC;QAC9D,CAAC,CAAC,cAAc,CAAC,KAAK,CAAC;QACvB,CAAC,CAAC,CAAC,CAAA;IAEP,4EAA4E;IAC5E,kEAAkE;IAClE,OAAO,IAAI,CAAC,UAAU,KAAK,QAAQ;QACjC,CAAC,CAAC;YACE,KAAK,EAAE,UAAU,GAAG,aAAa;YACjC,MAAM,EAAE,WAAW,GAAG,WAAW;YACjC,aAAa,EAAE,WAAW;YAC1B,WAAW;YACX,OAAO,EAAE,CAAC;YACV,OAAO,EAAE,CAAC;YACV,cAAc;YACd,WAAW;SACZ;QACH,CAAC,CAAC;YACE,KAAK;YACL,MAAM,EAAE,MAAM,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,WAAW;YACnE,aAAa,EAAE,MAAM;YACrB,WAAW;YACX,OAAO,EAAE,CAAC,OAAO;YACjB,OAAO,EAAE,CAAC,OAAO;YACjB,cAAc;YACd,WAAW;SACZ,CAAA;AACP,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,WAAW,CAAC,KAAmB,EAAE,IAAsB;IAC3E,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,eAAe,CAAC,CAAA;IACvC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,CAAA;IACtD,OAAO,oBAAoB,CACzB,oBAAC,MAAM,IACL,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,IAAI,CAAC,KAAK,EACjB,OAAO,EAAE,OAAO,EAChB,MAAM,EAAE,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,GAC9B,CACH,CAAA;AACH,CAAC;AAED,SAAS,MAAM,CAAC,EACd,KAAK,EACL,KAAK,EACL,OAAO,EACP,MAAM,GAMP;IACC,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,cAAc,EAAE,WAAW,EAAE,GAAG,MAAM,CAAA;IAC1E,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC9C,MAAM,UAAU,GAAG,KAAK,GAAG,WAAW,CAAA;IACtC,MAAM,SAAS,GAAG,cAAc,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAA;IAEpD,MAAM,IAAI,GAAG,CACX;QACG,WAAW,GAAG,CAAC,CAAC,CAAC,CAAC,CACjB,oBAAC,cAAc,IACb,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,GACd,CACH,CAAC,CAAC,CAAC,IAAI;QACR,2BACE,SAAS,EAAE,WAAW,GAAG,CAAC,CAAC,CAAC,CAAC,eAAe,WAAW,GAAG,CAAC,CAAC,CAAC,SAAS;YAEtE,oBAAC,aAAa,IACZ,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,GACd,CACA,CACH,CACJ,CAAA;IAED,OAAO,CACL,6BACE,KAAK,EAAE,UAAU,EACjB,MAAM,EAAE,MAAM,EACd,KAAK,EAAC,4BAA4B,EAClC,UAAU,EAAC,8BAA8B,EACzC,OAAO,EAAE,OAAO,UAAU,IAAI,MAAM,EAAE;QAEtC,8BAAM,KAAK,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,IAAI,EAAC,OAAO,GAAG;QAC/C,cAAc,CAAC,CAAC,CAAC,CAChB;YACE,2BAAG,SAAS,EAAE,aAAa,aAAa,KAAK;gBAC3C,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAG,aAAa,GAAI,CACxD;YACJ,2BAAG,SAAS,EAAE,eAAe,aAAa,GAAG,IAAG,IAAI,CAAK,CACxD,CACJ,CAAC,CAAC,CAAC,CACF,IAAI,CACL;QACA,WAAW,GAAG,CAAC,CAAC,CAAC,CAAC,CACjB,2BAAG,SAAS,EAAE,aAAa,KAAK,IAAI,SAAS,GAAG;YAC9C,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,WAAW,GAAI,CAC7C,CACL,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC;AAED,sEAAsE;AACtE,8DAA8D;AAC9D,SAAS,SAAS,CAAC,EAAE,KAAK,EAAE,KAAK,EAA0C;IACzE,MAAM,EAAE,kBAAkB,EAAE,WAAW,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAChE,MAAM,SAAS,GAAG,UAAU,GAAG,CAAC,GAAG,kBAAkB,CAAC,MAAM,GAAG,YAAY,CAAA;IAC3E,OAAO,CACL;QACE,8BACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,KAAK,GAAG,CAAC,EAChB,MAAM,EAAE,SAAS,EACjB,IAAI,EAAC,OAAO,EACZ,MAAM,EAAC,MAAM,EACb,EAAE,EAAE,CAAC,GACL;QACD,kBAAkB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YAC/B,MAAM,CAAC,GAAG,UAAU,GAAG,CAAC,GAAG,YAAY,CAAA;YACvC,OAAO,CACL,2BAAG,GAAG,EAAE,CAAC,CAAC,SAAS;gBACjB,8BACE,CAAC,EAAE,UAAU,EACb,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,aAAa,EACpB,MAAM,EAAE,aAAa,EACrB,IAAI,EAAE,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,EAC9B,MAAM,EAAE,aAAa,CAAC,CAAC,CAAC,SAAS,CAAC,GAClC;gBACF,8BACE,CAAC,EAAE,UAAU,GAAG,aAAa,GAAG,CAAC,EACjC,CAAC,EAAE,CAAC,GAAG,aAAa,GAAG,CAAC,EACxB,QAAQ,EAAE,WAAW,IAEpB,CAAC,CAAC,IAAI,CACF,CACL,CACL,CAAA;QACH,CAAC,CAAC,CACA,CACL,CAAA;AACH,CAAC;AAED,SAAS,aAAa,CAAC,EACrB,KAAK,EACL,KAAK,EACL,MAAM,EACN,OAAO,GAMR;IACC,MAAM,EAAE,aAAa,EAAE,OAAO,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;IACzD,MAAM,EAAE,aAAa,EAAE,WAAW,EAAE,EAAE,EAAE,GAAG,KAAK,CAAA;IAChD,MAAM,YAAY,GAAG,KAAK,GAAG,aAAa,CAAA;IAC1C,MAAM,cAAc,GAAG,aAAa,CAAC,WAAW,EAAE,KAAK,CAAC,CAAA;IAExD,MAAM,OAAO,GAAG,IAAI,OAAO,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA;IACzD,gBAAgB,CAAC;QACf,KAAK;QACL,KAAK;QACL,GAAG,EAAE,OAAO;QACZ,OAAO;QACP,kBAAkB,EAAE,aAAa;QACjC,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IAEF,MAAM,MAAM,GAAG,IAAI,OAAO,CAAC,YAAY,EAAE,aAAa,CAAC,CAAA;IACvD,2BAA2B,CAAC;QAC1B,KAAK;QACL,GAAG,EAAE,MAAM;QACX,OAAO;QACP,OAAO;QACP,0EAA0E;QAC1E,iEAAiE;QACjE,kBAAkB,EAAE,YAAY;QAChC,kBAAkB,EAAE,aAAa;QACjC,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,cAAc,CAAC;QACb,KAAK;QACL,KAAK;QACL,GAAG,EAAE,MAAM;QACX,cAAc;QACd,OAAO;QACP,OAAO;QACP,kBAAkB,EAAE,YAAY;QAChC,kBAAkB,EAAE,aAAa;QACjC,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IAEF,OAAO,CACL;QACE,oBAAC,SAAS,IACR,MAAM,EAAE,QAAQ,EAAE,EAAE,EACpB,KAAK,EAAE,aAAa,EACpB,MAAM,EAAE,aAAa,EACrB,GAAG,EAAE,OAAO,GACZ;QACF,oBAAC,SAAS,IACR,MAAM,EAAE,OAAO,EAAE,EAAE,EACnB,KAAK,EAAE,YAAY,EACnB,MAAM,EAAE,aAAa,EACrB,SAAS,EAAE,aAAa,aAAa,KAAK,EAC1C,GAAG,EAAE,MAAM,GACX,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAS,cAAc,CAAC,EACtB,KAAK,EACL,KAAK,EACL,MAAM,EACN,OAAO,GAMR;IACC,MAAM,EAAE,WAAW,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;IAC9C,MAAM,EAAE,aAAa,EAAE,WAAW,EAAE,EAAE,EAAE,GAAG,KAAK,CAAA;IAChD,MAAM,YAAY,GAAG,KAAK,GAAG,aAAa,CAAA;IAC1C,MAAM,cAAc,GAAG,aAAa,CAAC,WAAW,EAAE,KAAK,CAAC,CAAA;IAExD,MAAM,GAAG,GAAG,IAAI,OAAO,CAAC,YAAY,EAAE,WAAW,CAAC,CAAA;IAClD,eAAe,CAAC;QACd,KAAK;QACL,GAAG;QACH,cAAc;QACd,KAAK;QACL,OAAO;QACP,kBAAkB,EAAE,YAAY;QAChC,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IAEF,OAAO,CACL,2BAAG,SAAS,EAAE,aAAa,aAAa,KAAK;QAC3C,oBAAC,SAAS,IACR,MAAM,EAAE,UAAU,EAAE,EAAE,EACtB,KAAK,EAAE,YAAY,EACnB,MAAM,EAAE,WAAW,EACnB,GAAG,EAAE,GAAG,GACR,CACA,CACL,CAAA;AACH,CAAC;AAED,8EAA8E;AAC9E,sCAAsC;AACtC,SAAS,SAAS,CAAC,EACjB,MAAM,EACN,KAAK,EACL,MAAM,EACN,SAAS,EACT,GAAG,GAOJ;IACC,OAAO,CACL;QACE;YACE,kCAAU,EAAE,EAAE,MAAM;gBAClB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAI,CACzC,CACN;QACP,2BACE,QAAQ,EAAE,QAAQ,MAAM,GAAG,EAC3B,SAAS,EAAE,SAAS,EACpB,uBAAuB,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,GAC3D,CACD,CACJ,CAAA;AACH,CAAC"}
|
|
@@ -0,0 +1,28 @@
|
|
|
1
|
+
import type { ColumnCounts } from './columnCounts.ts';
|
|
2
|
+
export interface LogoLetter {
|
|
3
|
+
letter: string;
|
|
4
|
+
/** height of this letter's slice of the stack, in bits */
|
|
5
|
+
bits: number;
|
|
6
|
+
}
|
|
7
|
+
/** the y-axis ceiling of a logo: the information content of a fully conserved
|
|
8
|
+
* column, log2 of the alphabet size */
|
|
9
|
+
export declare function maxBitsFor(sequenceType: 'dna' | 'rna' | 'amino'): number;
|
|
10
|
+
/**
|
|
11
|
+
* One column of a sequence logo, tallest letter last so a caller can draw the
|
|
12
|
+
* stack bottom-up in array order.
|
|
13
|
+
*
|
|
14
|
+
* Heights follow Schneider & Stephens: the column's information content is
|
|
15
|
+
* `log2(alphabet) - H` bits, and each residue takes the share of that its own
|
|
16
|
+
* frequency earns. Frequencies come from the non-gap residues only, so a column
|
|
17
|
+
* of two residues and eight gaps is read as a two-way choice rather than a
|
|
18
|
+
* ten-way one -- otherwise every gappy column would look uninformative for the
|
|
19
|
+
* wrong reason.
|
|
20
|
+
*
|
|
21
|
+
* The whole stack is then scaled by the non-gap fraction, which plain WebLogo
|
|
22
|
+
* does not do. Here it earns its place: the track sits directly under an
|
|
23
|
+
* alignment where the gaps are visible, and a column that is 90% gap drawing a
|
|
24
|
+
* full-height stack off its one remaining pair of residues reads as a conserved
|
|
25
|
+
* site. Scaling makes stack height mean "how much this column tells you about
|
|
26
|
+
* the family", matching what the conservation track above it already plots.
|
|
27
|
+
*/
|
|
28
|
+
export declare function columnLogoStack(colStats: ColumnCounts, col: number, maxBits: number): LogoLetter[];
|
|
@@ -0,0 +1,47 @@
|
|
|
1
|
+
import { letterOfResidueSlot } from './columnCounts.js';
|
|
2
|
+
/** the y-axis ceiling of a logo: the information content of a fully conserved
|
|
3
|
+
* column, log2 of the alphabet size */
|
|
4
|
+
export function maxBitsFor(sequenceType) {
|
|
5
|
+
return Math.log2(sequenceType === 'amino' ? 20 : 4);
|
|
6
|
+
}
|
|
7
|
+
/**
|
|
8
|
+
* One column of a sequence logo, tallest letter last so a caller can draw the
|
|
9
|
+
* stack bottom-up in array order.
|
|
10
|
+
*
|
|
11
|
+
* Heights follow Schneider & Stephens: the column's information content is
|
|
12
|
+
* `log2(alphabet) - H` bits, and each residue takes the share of that its own
|
|
13
|
+
* frequency earns. Frequencies come from the non-gap residues only, so a column
|
|
14
|
+
* of two residues and eight gaps is read as a two-way choice rather than a
|
|
15
|
+
* ten-way one -- otherwise every gappy column would look uninformative for the
|
|
16
|
+
* wrong reason.
|
|
17
|
+
*
|
|
18
|
+
* The whole stack is then scaled by the non-gap fraction, which plain WebLogo
|
|
19
|
+
* does not do. Here it earns its place: the track sits directly under an
|
|
20
|
+
* alignment where the gaps are visible, and a column that is 90% gap drawing a
|
|
21
|
+
* full-height stack off its one remaining pair of residues reads as a conserved
|
|
22
|
+
* site. Scaling makes stack height mean "how much this column tells you about
|
|
23
|
+
* the family", matching what the conservation track above it already plots.
|
|
24
|
+
*/
|
|
25
|
+
export function columnLogoStack(colStats, col, maxBits) {
|
|
26
|
+
const total = colStats.total(col);
|
|
27
|
+
const nonGapTotal = total - colStats.gapCount(col);
|
|
28
|
+
if (nonGapTotal === 0) {
|
|
29
|
+
return [];
|
|
30
|
+
}
|
|
31
|
+
const informationContent = Math.max(0, maxBits - colStats.entropy(col)) * (nonGapTotal / total);
|
|
32
|
+
if (informationContent === 0) {
|
|
33
|
+
return [];
|
|
34
|
+
}
|
|
35
|
+
const stack = [];
|
|
36
|
+
colStats.forEachResidue(col, (slot, count) => {
|
|
37
|
+
stack.push({
|
|
38
|
+
letter: letterOfResidueSlot(slot),
|
|
39
|
+
bits: (count / nonGapTotal) * informationContent,
|
|
40
|
+
});
|
|
41
|
+
});
|
|
42
|
+
// ascending, so drawing in order stacks the tallest letter on top. Ties break
|
|
43
|
+
// on letter to keep the stack order stable between redraws.
|
|
44
|
+
stack.sort((a, b) => a.bits - b.bits || a.letter.localeCompare(b.letter));
|
|
45
|
+
return stack;
|
|
46
|
+
}
|
|
47
|
+
//# sourceMappingURL=sequenceLogo.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"sequenceLogo.js","sourceRoot":"","sources":["../src/sequenceLogo.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAA;AAUvD;uCACuC;AACvC,MAAM,UAAU,UAAU,CAAC,YAAqC;IAC9D,OAAO,IAAI,CAAC,IAAI,CAAC,YAAY,KAAK,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrD,CAAC;AAED;;;;;;;;;;;;;;;;;GAiBG;AACH,MAAM,UAAU,eAAe,CAC7B,QAAsB,EACtB,GAAW,EACX,OAAe;IAEf,MAAM,KAAK,GAAG,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACjC,MAAM,WAAW,GAAG,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;IAClD,IAAI,WAAW,KAAK,CAAC,EAAE,CAAC;QACtB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,MAAM,kBAAkB,GACtB,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,OAAO,GAAG,QAAQ,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,WAAW,GAAG,KAAK,CAAC,CAAA;IACtE,IAAI,kBAAkB,KAAK,CAAC,EAAE,CAAC;QAC7B,OAAO,EAAE,CAAA;IACX,CAAC;IAED,MAAM,KAAK,GAAiB,EAAE,CAAA;IAC9B,QAAQ,CAAC,cAAc,CAAC,GAAG,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE;QAC3C,KAAK,CAAC,IAAI,CAAC;YACT,MAAM,EAAE,mBAAmB,CAAC,IAAI,CAAC;YACjC,IAAI,EAAE,CAAC,KAAK,GAAG,WAAW,CAAC,GAAG,kBAAkB;SACjD,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IACF,8EAA8E;IAC9E,4DAA4D;IAC5D,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,MAAM,CAAC,aAAa,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;IACzE,OAAO,KAAK,CAAA;AACd,CAAC"}
|
package/dist/types.d.ts
CHANGED
|
@@ -4,11 +4,13 @@ export interface Accession {
|
|
|
4
4
|
name: string;
|
|
5
5
|
description: string;
|
|
6
6
|
}
|
|
7
|
+
export type TrackKind = 'text' | 'bar' | 'logo';
|
|
7
8
|
export interface BasicTrackModel {
|
|
8
9
|
id: string;
|
|
9
10
|
name: string;
|
|
10
11
|
associatedRowName?: string;
|
|
11
12
|
height: number;
|
|
13
|
+
kind: TrackKind;
|
|
12
14
|
}
|
|
13
15
|
export interface TextTrackModel extends BasicTrackModel {
|
|
14
16
|
customColorScheme?: Record<string, string>;
|
package/dist/version.d.ts
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
export declare const version = "6.
|
|
1
|
+
export declare const version = "6.1.0";
|
package/dist/version.js
CHANGED
|
@@ -1,2 +1,2 @@
|
|
|
1
|
-
export const version = '6.
|
|
1
|
+
export const version = '6.1.0';
|
|
2
2
|
//# sourceMappingURL=version.js.map
|
package/package.json
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "react-msaview",
|
|
3
3
|
"author": "Colin",
|
|
4
|
-
"version": "6.
|
|
4
|
+
"version": "6.1.0",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"type": "module",
|
|
7
7
|
"repository": {
|
|
@@ -43,8 +43,8 @@
|
|
|
43
43
|
"@gmod/newick": "^1.0.0",
|
|
44
44
|
"colord": "^2.9.3",
|
|
45
45
|
"flatbush": "^4.6.2",
|
|
46
|
-
"@jbrowse/svgcanvas": "6.
|
|
47
|
-
"msa-parsers": "6.
|
|
46
|
+
"@jbrowse/svgcanvas": "6.1.0",
|
|
47
|
+
"msa-parsers": "6.1.0"
|
|
48
48
|
},
|
|
49
49
|
"scripts": {
|
|
50
50
|
"clean": "rimraf dist bundle",
|
package/src/columnCounts.test.ts
CHANGED
|
@@ -47,6 +47,21 @@ describe('columnCounts', () => {
|
|
|
47
47
|
expect(counts.total(3)).toBe(1)
|
|
48
48
|
})
|
|
49
49
|
|
|
50
|
+
test('entropy is taken over the non-gap residues only', () => {
|
|
51
|
+
const counts = columnCountsFromColumns(['AAAA', 'AACC', 'ACGT', 'AC--'])
|
|
52
|
+
// fully conserved: no choice left to make
|
|
53
|
+
expect(counts.entropy(0)).toBeCloseTo(0, 10)
|
|
54
|
+
// even two-way and four-way splits
|
|
55
|
+
expect(counts.entropy(1)).toBeCloseTo(1, 10)
|
|
56
|
+
expect(counts.entropy(2)).toBeCloseTo(2, 10)
|
|
57
|
+
// the two gaps do not turn a 1-bit choice into a 2-bit one
|
|
58
|
+
expect(counts.entropy(3)).toBeCloseTo(1, 10)
|
|
59
|
+
})
|
|
60
|
+
|
|
61
|
+
test('an all-gap column has no entropy rather than NaN', () => {
|
|
62
|
+
expect(columnCountsFromColumns(['----']).entropy(0)).toBe(0)
|
|
63
|
+
})
|
|
64
|
+
|
|
50
65
|
test('residue slots round-trip to their letters', () => {
|
|
51
66
|
const counts = columnCountsFromColumns(['WY'])
|
|
52
67
|
const slots: number[] = []
|
package/src/columnCounts.ts
CHANGED
|
@@ -109,6 +109,25 @@ export class ColumnCounts {
|
|
|
109
109
|
}
|
|
110
110
|
}
|
|
111
111
|
|
|
112
|
+
/**
|
|
113
|
+
* Shannon entropy of a column in bits, taken over its non-gap residues only:
|
|
114
|
+
* a column of two residues and eight gaps is a two-way choice, not a ten-way
|
|
115
|
+
* one, and gap occupancy is accounted for separately by every caller. 0 for
|
|
116
|
+
* an all-gap column.
|
|
117
|
+
*/
|
|
118
|
+
entropy(col: number) {
|
|
119
|
+
const nonGapTotal = this.total(col) - this.gapCount(col)
|
|
120
|
+
if (nonGapTotal === 0) {
|
|
121
|
+
return 0
|
|
122
|
+
}
|
|
123
|
+
let entropy = 0
|
|
124
|
+
this.forEachResidue(col, (_slot, count) => {
|
|
125
|
+
const freq = count / nonGapTotal
|
|
126
|
+
entropy -= freq * Math.log2(freq)
|
|
127
|
+
})
|
|
128
|
+
return entropy
|
|
129
|
+
}
|
|
130
|
+
|
|
112
131
|
/** non-gap [letter, count] pairs for one column, for display */
|
|
113
132
|
residueEntries(col: number) {
|
|
114
133
|
const entries: [string, number][] = []
|
|
@@ -0,0 +1,81 @@
|
|
|
1
|
+
import React, { useState } from 'react'
|
|
2
|
+
|
|
3
|
+
import { useDragScroll } from '../useDragScroll.ts'
|
|
4
|
+
|
|
5
|
+
export const scrollbarThumbFill = 'rgba(66,119,127,0.3)'
|
|
6
|
+
|
|
7
|
+
// The scroll thumbs (minimap, vertical scrollbar) and the resize dividers are
|
|
8
|
+
// one widget -- press, drag along an axis, report the pixel delta -- differing
|
|
9
|
+
// only in the affordance they present, so the variant carries the whole
|
|
10
|
+
// difference rather than a second copy of the drag wiring.
|
|
11
|
+
const variants: Record<
|
|
12
|
+
'thumb' | 'resizer',
|
|
13
|
+
{
|
|
14
|
+
fill: string
|
|
15
|
+
fillHovered: string
|
|
16
|
+
cursor: (axis: 'x' | 'y') => string
|
|
17
|
+
position: React.CSSProperties['position']
|
|
18
|
+
zIndex?: number
|
|
19
|
+
}
|
|
20
|
+
> = {
|
|
21
|
+
thumb: {
|
|
22
|
+
fill: scrollbarThumbFill,
|
|
23
|
+
fillHovered: 'rgba(66,119,127,0.6)',
|
|
24
|
+
cursor: () => 'pointer',
|
|
25
|
+
position: 'absolute',
|
|
26
|
+
zIndex: 100,
|
|
27
|
+
},
|
|
28
|
+
resizer: {
|
|
29
|
+
fill: 'rgba(200,200,200)',
|
|
30
|
+
fillHovered: 'rgba(150,150,150)',
|
|
31
|
+
cursor: axis => (axis === 'x' ? 'ew-resize' : 'ns-resize'),
|
|
32
|
+
position: 'relative',
|
|
33
|
+
},
|
|
34
|
+
}
|
|
35
|
+
|
|
36
|
+
/**
|
|
37
|
+
* A handle dragged along a single axis. `getStart` is read at mousedown and
|
|
38
|
+
* handed back to `onDrag` alongside the pixel delta since, so a caller only
|
|
39
|
+
* supplies the dimension it drives and where the handle sits.
|
|
40
|
+
*
|
|
41
|
+
* Memoize `onDrag` (useCallback) so the document listeners are not re-attached
|
|
42
|
+
* on every render.
|
|
43
|
+
*/
|
|
44
|
+
export default function DragHandle({
|
|
45
|
+
axis,
|
|
46
|
+
variant,
|
|
47
|
+
getStart,
|
|
48
|
+
onDrag,
|
|
49
|
+
style,
|
|
50
|
+
}: {
|
|
51
|
+
axis: 'x' | 'y'
|
|
52
|
+
variant: keyof typeof variants
|
|
53
|
+
getStart: () => number
|
|
54
|
+
onDrag: (delta: number, startValue: number) => void
|
|
55
|
+
style: React.CSSProperties
|
|
56
|
+
}) {
|
|
57
|
+
const [hovered, setHovered] = useState(false)
|
|
58
|
+
const { startDrag } = useDragScroll(axis, onDrag)
|
|
59
|
+
const { fill, fillHovered, cursor, position, zIndex } = variants[variant]
|
|
60
|
+
|
|
61
|
+
return (
|
|
62
|
+
<div
|
|
63
|
+
onMouseEnter={() => {
|
|
64
|
+
setHovered(true)
|
|
65
|
+
}}
|
|
66
|
+
onMouseLeave={() => {
|
|
67
|
+
setHovered(false)
|
|
68
|
+
}}
|
|
69
|
+
onMouseDown={event => {
|
|
70
|
+
startDrag(event, getStart())
|
|
71
|
+
}}
|
|
72
|
+
style={{
|
|
73
|
+
position,
|
|
74
|
+
zIndex,
|
|
75
|
+
cursor: cursor(axis),
|
|
76
|
+
background: hovered ? fillHovered : fill,
|
|
77
|
+
...style,
|
|
78
|
+
}}
|
|
79
|
+
/>
|
|
80
|
+
)
|
|
81
|
+
}
|