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| 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 | 16x 8x 8x 4x 4x 4x 4x 4x 4x 340x 8x 3x 8x 8x 8x 8x 8x 2x 2x 1x 8x 5x 8x 8x 4x 4x 1x 6x 6x | import {
useState,
type ReactNode,
useMemo,
useCallback,
memo,
useEffect,
useRef,
type CSSProperties,
} from 'react';
import cn from 'classnames';
import Button from './button';
import { Dropdown } from './dropdown-button';
import CopyToClipboard from './copy-to-clipboard';
import InfoList, { type InfoListItem } from './info-list';
import SequenceTools, { type SequenceToolName } from './sequence-tools';
import DownloadIcon from '../svg/download.svg';
import SpinnerIcon from '../svg/spinner.svg';
import aminoAcidsProps from './data/amino-acid-properties.json' with { type: 'json' };
import '../styles/components/sequence.scss';
type AminoAcidProperty = {
name: string;
aminoAcids: Set<string>;
colour: string;
};
const aaProps: AminoAcidProperty[] = aminoAcidsProps.map((aaProp) => ({
...aaProp,
// Optimise for later lookup
aminoAcids: new Set(aaProp.aminoAcids),
}));
const chunksOfTen = /(.{1,10})/g;
const SequenceChunks = memo(
({
sequence,
computeHighlights,
}: {
sequence: string;
computeHighlights: boolean;
}) => {
const ref = useRef<HTMLDivElement>(null);
const chunks = useMemo(() => sequence.match(chunksOfTen) || [], [sequence]);
useEffect(() => {
// Don't run until needed the first time
Eif (!computeHighlights) {
return;
}
// OK, we requested a highlight, compute them all at once
for (const [index, chunk] of chunks.entries()) {
const boxShadow: string[] = [];
let xOffset = 0;
// start at negative values to get closer to the letters
let yOffset = -3;
for (const { name, aminoAcids } of aaProps) {
for (const letter of chunk) {
if (aminoAcids.has(letter)) {
boxShadow.push(
`${xOffset}ch ${yOffset}px 0 1px var(--color-${name}, transparent)`
);
}
xOffset += 10;
}
yOffset += 2;
xOffset = 0;
}
const node = ref.current?.children[index] as HTMLElement | undefined;
if (node) {
// Avoid React by setting directly on the nodes
node?.style.setProperty('--box-shadow', boxShadow.join(', '));
}
}
}, [chunks, computeHighlights]);
return (
<div className="sequence" ref={ref}>
{chunks.map((chunk, index) => (
<span
key={index}
className={cn('sequence__chunk', {
'sequence__chunk--display-last':
index + 1 === chunks.length && chunk.length === 10,
})}
>
{chunk}
</span>
))}
</div>
);
}
);
const visibleElement = (onClick: () => unknown) => (
<Button variant="tertiary" onClick={onClick}>
Highlight
</Button>
);
type SequenceProps = {
/**
* The sequence
*/
sequence?: string;
/**
* The accession corresponding to the sequence
*/
accession?: string;
/**
* Action triggered when the "Show sequence" button is clicked.
* This button will be displayed by default if no sequence is passed
* down to the component.
*/
onShowSequence?: () => void;
/**
* Display option to show/hide the sequence. If no sequence is
* provided and `onShowSequence` is defined, this defaults to "true"
*/
isCollapsible?: boolean;
/**
* If the sequence is loading, display a spinner in the button
*/
isLoading?: boolean;
/**
* Data to be displayed in an InfoData component above the sequence
*/
infoData?: InfoListItem[];
/**
* The URL to download the isoform sequence
*/
downloadUrl?: string;
/**
* Callback which is fired when the BLAST button is clicked. If no callback
* is provided then no BLAST button will be displayed.
*/
onBlastClick?: () => void;
/** Callback which is fired when the Add button is clicked. If no callback
* is provided then no Add button will be displayed.
*/
addToBasketButton?: ReactNode;
showActionBar?: boolean;
onCopy?: (copied: string) => void;
sequenceTools?: SequenceToolName[];
};
const Sequence = ({
sequence,
accession,
onShowSequence,
onCopy,
isCollapsible = false,
isLoading = false,
infoData,
onBlastClick,
addToBasketButton,
downloadUrl,
showActionBar = true,
sequenceTools,
}: SequenceProps) => {
const [highlights, setHighlights] = useState<AminoAcidProperty[]>([]);
const [computeHighlights, setComputeHighlights] = useState(false);
const [isCollapsed, setIsCollapsed] = useState(
isCollapsible || (onShowSequence && !sequence)
);
const handleShowSequenceClick = useCallback(() => {
setIsCollapsed(false);
// Request call of sequence
if (!sequence && onShowSequence) {
onShowSequence();
}
}, [onShowSequence, sequence]);
const sequenceStyle = useMemo(
() =>
Object.fromEntries(
highlights.map((highlight) => [
`--color-${highlight.name}`,
highlight.colour,
])
),
[highlights]
);
const handleToggleHighlight = useCallback((aaProp: AminoAcidProperty) => {
setComputeHighlights(true);
setHighlights((highlights) => {
const highlightsSet = new Set(highlights);
if (highlightsSet.has(aaProp)) {
highlightsSet.delete(aaProp);
} else {
highlightsSet.add(aaProp);
}
return Array.from(highlightsSet);
});
}, []);
if (isCollapsed || !sequence) {
return (
<div>
<Button variant="secondary" onClick={handleShowSequenceClick}>
Show sequence {isLoading && <SpinnerIcon />}
</Button>
</div>
);
}
return (
<div>
{isCollapsible && (
<Button variant="secondary" onClick={() => setIsCollapsed(true)}>
Hide sequence
</Button>
)}
<section className="sequence-container" style={sequenceStyle}>
{showActionBar && accession && (
<div className="action-bar button-group">
{/* Not sure why keys are needed, but otherwise gets the React key
warnings messages and children are rendered as array... */}
<SequenceTools
accession={accession}
onBlastClick={onBlastClick}
tools={sequenceTools}
key="tools"
/>
{downloadUrl && (
<a
className="button tertiary"
href={downloadUrl}
download
key="link"
>
<DownloadIcon />
Download
</a>
)}
{addToBasketButton}
<Dropdown visibleElement={visibleElement} key="highlight">
{aaProps.map((aaProp) => {
const inputId = `${accession}-${aaProp.name}`;
return (
<label key={aaProp.name} htmlFor={inputId}>
<input
type="checkbox"
id={inputId}
onChange={() => handleToggleHighlight(aaProp)}
checked={highlights.includes(aaProp)}
style={{ accentColor: aaProp.colour } as CSSProperties}
/>
{aaProp.name}
</label>
);
})}
</Dropdown>
<CopyToClipboard
textToCopy={sequence}
beforeCopy="Copy sequence"
afterCopy="Copied"
className="tertiary"
onCopy={onCopy}
key="copy"
/>
</div>
)}
<InfoList infoData={infoData} isCompact columns />
<SequenceChunks
sequence={sequence}
computeHighlights={computeHighlights}
/>
</section>
</div>
);
};
export default Sequence;
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