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import { useMemo } from 'react';
import { DownloadSimple as Download, ChartScatter as Scatter } from '@phosphor-icons/react';
import type { PairwiseAlignResult } from '@/types/pipeline';
import { downloadText, downloadTsv } from '@/lib/export-utils';
import { computeAlignmentStats } from '@/lib/alignment-stats';
import { AlignmentStatsBar } from '@/components/alignment/AlignmentStatsBar';
const DOTPLOT_MATRICES = ['blosum62', 'blosum50', 'blosum45', 'pam30', 'pam70', 'pam250'];
function dotplotScoringFor(matrix: string): string {
const m = matrix.toLowerCase();
return DOTPLOT_MATRICES.includes(m) ? m : 'identity';
}
const BLOCK_SIZE = 60;
interface Column {
q: string;
h: string;
qPos: number;
hPos: number;
match: boolean;
gap: boolean;
}
function buildColumns(result: PairwiseAlignResult): Column[] {
const a = result.aligned_query;
const b = result.aligned_hit;
const cols: Column[] = [];
let qPos = result.query_start;
let hPos = result.hit_start;
for (let i = 0; i < a.length; i++) {
const q = a[i];
const h = b[i];
cols.push({
q,
h,
qPos,
hPos,
match: q !== '-' && h !== '-' && q === h,
gap: q === '-' || h === '-',
});
if (q !== '-') qPos++;
if (h !== '-') hPos++;
}
return cols;
}
function charClass(c: string, match: boolean): string {
if (c === '-') return 'text-text-muted/25';
return match ? 'text-accent-cyan' : 'text-text-primary';
}
function CoverageStrip({
label,
start,
end,
length,
}: {
label: string;
start: number;
end: number;
length: number;
}) {
const covered = length > 0 ? ((end - start + 1) / length) * 100 : 0;
const left = length > 0 ? ((start - 1) / length) * 100 : 0;
return (
<div className="flex items-center gap-2">
<span className="w-10 shrink-0 text-[10px] uppercase tracking-wider text-text-muted">{label}</span>
<div className="h-1.5 flex-1 rounded-full bg-surface-1 overflow-hidden relative">
<div
className="absolute inset-y-0 rounded-full bg-gradient-to-r from-accent-cyan/40 to-accent-cyan/80"
style={{ left: `${left}%`, width: `${covered}%` }}
/>
</div>
<span className="w-8 shrink-0 text-right text-[10px] font-mono text-text-muted">{Math.round(covered)}%</span>
</div>
);
}
function CoverageNote({ result }: { result: PairwiseAlignResult }) {
if (result.alignment_length === 0) {
return (
<p className="mt-3 text-sm text-accent-amber">
No significant {result.mode} alignment detected — the two sequences show no local similarity.
</p>
);
}
const queryOnlyCoversPart =
result.query_start > 1 || result.query_end < result.query_length;
const hitOnlyCoversPart = result.hit_start > 1 || result.hit_end < result.hit_length;
if (!queryOnlyCoversPart && !hitOnlyCoversPart) return null;
return (
<p className="text-xs text-text-muted">
{queryOnlyCoversPart && (
<>
Alignment covers residues <strong className="text-accent-cyan">{result.query_start}–{result.query_end}</strong> of a {result.query_length}-residue query.
</>
)}
{queryOnlyCoversPart && hitOnlyCoversPart && <span className="mx-1.5">·</span>}
{hitOnlyCoversPart && (
<>
Residues <strong className="text-accent-cyan">{result.hit_start}–{result.hit_end}</strong> of a {result.hit_length}-residue subject.
</>
)}
</p>
);
}
function AlignmentBlocks({ result }: { result: PairwiseAlignResult }) {
const cols = useMemo(() => buildColumns(result), [result]);
const blocks = useMemo(() => {
const out: Column[][] = [];
for (let i = 0; i < cols.length; i += BLOCK_SIZE) out.push(cols.slice(i, i + BLOCK_SIZE));
return out;
}, [cols]);
if (cols.length === 0) return null;
return (
<div className="rounded-xl bg-surface-0 border border-glass-border overflow-x-auto">
<div className="min-w-max font-mono text-[13px] leading-[1.55] p-4 space-y-3">
{blocks.map((block, bi) => (
<div key={bi} className="space-y-0.5">
<div className="flex">
<span className="w-14 shrink-0 pr-3 text-right text-[10px] text-text-muted/70 pt-[3px]">
Q{block[0].qPos}
</span>
<span className="whitespace-pre">
{block.map((c, i) => (
<span key={i} className={charClass(c.q, c.match)}>{c.q}</span>
))}
</span>
</div>
<div className="flex">
<span className="w-14 shrink-0 pr-3" />
<span className="whitespace-pre">
{block.map((c, i) => (
<span key={i} className={c.match ? 'text-accent-cyan/50' : 'text-text-muted/10'}>
{c.match ? '|' : ' '}
</span>
))}
</span>
</div>
<div className="flex">
<span className="w-14 shrink-0 pr-3 text-right text-[10px] text-text-muted/70 pt-[3px]">
S{block[0].hPos}
</span>
<span className="whitespace-pre">
{block.map((c, i) => (
<span key={i} className={charClass(c.h, c.match)}>{c.h}</span>
))}
</span>
</div>
</div>
))}
</div>
</div>
);
}
function Legend() {
return (
<div className="flex items-center gap-4 text-[10px] text-text-muted flex-wrap">
<span className="flex items-center gap-1.5">
<span className="w-2 h-2 rounded-[2px] bg-accent-cyan" /> Match
</span>
<span className="flex items-center gap-1.5">
<span className="w-2 h-2 rounded-[2px] bg-text-primary" /> Mismatch
</span>
<span className="flex items-center gap-1.5">
<span className="w-2 h-2 rounded-[2px] bg-text-muted/25" /> Gap
</span>
<span className="flex items-center gap-1.5">
<span className="font-mono text-accent-cyan/50">|</span> Identical position
</span>
</div>
);
}
export function PairwiseResultDisplay({
result,
queryLabel = 'Query',
subjectLabel = 'Subject',
}: {
result: PairwiseAlignResult;
queryLabel?: string;
subjectLabel?: string;
}) {
const stats = useMemo(
() => computeAlignmentStats([result.aligned_query, result.aligned_hit]),
[result],
);
if (result.alignment_length === 0) {
return <CoverageNote result={result} />;
}
const exportFasta = () => {
const fasta = `>${queryLabel}\n${result.aligned_query.replace(/-/g, '')}\n>${subjectLabel}\n${result.aligned_hit.replace(/-/g, '')}`;
downloadText(fasta, `${result.mode}_alignment.fasta`);
};
const exportTsv = () => {
downloadTsv(
['Field', 'Value'],
[
['Mode', result.mode],
['Matrix', result.matrix],
['Score', String(result.score)],
['Matched', String(stats.matched)],
['Mismatched', String(stats.mismatched)],
['Gapped columns', String(stats.gapped)],
['Gap characters', String(result.gaps_total)],
['Alignment length', String(stats.length)],
['Identity (%)', String(result.pct_identity)],
['Identical residues', String(result.identity)],
['Query start', String(result.query_start)],
['Query end', String(result.query_end)],
['Query length', String(result.query_length)],
['Subject start', String(result.hit_start)],
['Subject end', String(result.hit_end)],
['Subject length', String(result.hit_length)],
],
`${result.mode}_alignment_stats.tsv`,
);
};
return (
<div>
<div className="flex items-center gap-x-4 gap-y-1 text-xs text-text-muted mb-3 flex-wrap">
<span>
Score: <strong className="text-text-primary">{result.score}</strong>
</span>
<span>
Identity: <strong className="text-accent-cyan">{result.pct_identity}%</strong> ({result.identity}/{result.alignment_length})
</span>
<span>
Matrix: <strong className="text-text-primary">{result.matrix.toUpperCase()}</strong>
</span>
<span>
Mode: <strong className="text-text-primary capitalize">{result.mode} {result.mode === 'global' ? 'Needleman-Wunsch' : 'Smith-Waterman'}</strong>
</span>
<span className="ml-auto flex items-center gap-2">
<a
href={`/analyze/dotplot?seq_a=${encodeURIComponent(result.aligned_query.replace(/-/g, ''))}&seq_b=${encodeURIComponent(result.aligned_hit.replace(/-/g, ''))}&scoring=${dotplotScoringFor(result.matrix)}`}
className="text-xs px-2.5 py-1 rounded bg-surface-1 border border-glass-border text-text-secondary hover:text-accent-cyan transition-colors flex items-center gap-1.5"
>
<Scatter className="w-3.5 h-3.5" /> Dot plot
</a>
<button onClick={exportFasta}
className="text-xs px-2.5 py-1 rounded bg-surface-1 border border-glass-border text-text-secondary hover:text-accent-cyan transition-colors flex items-center gap-1.5">
<Download className="w-3.5 h-3.5" /> FASTA
</button>
<button onClick={exportTsv}
className="text-xs px-2.5 py-1 rounded bg-surface-1 border border-glass-border text-text-secondary hover:text-accent-cyan transition-colors flex items-center gap-1.5">
<Download className="w-3.5 h-3.5" /> TSV
</button>
</span>
</div>
<AlignmentStatsBar
stats={stats}
gapDetail={`${result.gaps_total} gap chars`}
className="mb-3"
/>
<div className="mb-3 space-y-1.5">
<CoverageStrip label="Query" start={result.query_start} end={result.query_end} length={result.query_length} />
<CoverageStrip label="Subject" start={result.hit_start} end={result.hit_end} length={result.hit_length} />
</div>
<div className="rounded-xl border border-glass-border overflow-hidden">
<div className="flex items-center justify-between px-4 py-2 border-b border-glass-border bg-surface-1/80 backdrop-blur text-[10px] font-mono text-text-muted">
<span>{queryLabel}</span>
<span className="hidden sm:inline">{result.query_start}–{result.query_end} · {result.query_length} aa</span>
</div>
<AlignmentBlocks result={result} />
<div className="flex items-center justify-between px-4 py-2 border-t border-glass-border bg-surface-1/80 backdrop-blur text-[10px] font-mono text-text-muted">
<span>{subjectLabel}</span>
<span className="hidden sm:inline">{result.hit_start}–{result.hit_end} · {result.hit_length} aa</span>
</div>
</div>
<div className="mt-3 flex flex-col gap-2 sm:flex-row sm:items-center sm:justify-between">
<Legend />
<CoverageNote result={result} />
</div>
</div>
);
}
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