1 选择任务类型Choose the task type

在左栏顶部「任务」下拉里挑一个：Open the "Task" dropdown at the top of the left panel and pick one:

• 单品系维护或纯合 → 建系 (stock)Single-stock maintenance or homozygotes → Stock
• 两元件放同一染色体 → 重组 (recombine)Two elements on the same chromosome → Recombine
• 两染色体元件合并 → 多基因组装 (assemble)Elements from different chromosomes combined → Assemble
• 背景纯化 / 染色体替换 → 染色体替换 (replace)Background cleanup / chromosome replacement → Replace
• 只导入目标位点 → 位点导入 (introgression)Import only the target locus → Introgression

2 选择染色体 / 组装类型 / 回交代数Choose chromosome / assembly type / backcross generation

任务确定后，下方联动控件会切换：Once the task is chosen, the linked controls below update:

• 单染色体任务：选「染色体」1 (X) / 2 / 3Single-chromosome tasks: pick the "Chromosome" 1 (X) / 2 / 3
• 多基因组装任务：选「组装类型」X+2 / X+3 / 2+3Assemble tasks: pick the "Assembly type" X+2 / X+3 / 2+3
• 染色体替换 / 位点导入任务：还要选「回交代数」（默认 5，最高 10）Replace / introgression tasks: also pick "Backcross generation" (default 5, max 10)
• X 染色体 + 建系任务：多一个「致死假设」下拉（纯合可育 / 雌性致死 / 雄性致死 / 雌雄致死）X-chromosome + Stock tasks: an extra "Lethality assumption" dropdown appears (viable / female-lethal / male-lethal / lethal in both sexes)

3 输入品系 1 基因型Enter stock 1 genotype

每张「基因型输入卡」支持 3 种输入方式：Each "Genotype input card" supports three input methods:

• 方式 A — 品系编号：选 BDSC / FlyBase / VDRC 来源，输入 6 或 FBst0000006 或 v10004，按 Enter 或点「解析」自动载入完整基因型。Method A — Stock number: pick a source (BDSC / FlyBase / VDRC), enter 6 or FBst0000006 or v10004, then press Enter or click "Resolve" to auto-load the full genotype.
• 方式 B — 直接写基因型字符串：在「基因型字符串」框粘贴 FlyBase compact 串，例如 w[1118]; Tg1/CyO; +/+，实时显示预览与置信度。Method B — Type a genotype string: paste a FlyBase compact string into the "Genotype string" box, for example w[1118]; Tg1/CyO; +/+. A live preview and confidence score update in real time.
• 方式 C — 逐条染色体手填：在 X / 2 / 3 各两行 homolog A / homolog B 手填元件符号。Method C — Manual per chromosome: under X / 2 / 3, fill in the two rows (homolog A / homolog B) with element symbols by hand.

4 输入品系 2 基因型（双品系任务）Enter stock 2 genotype (two-stock tasks)

重组 / 组装任务需要填两张卡。品系 1 作 ♀ 亲本，品系 2 作 ♂ 亲本。Recombine / assemble tasks need both cards. Stock 1 acts as the ♀-parent, stock 2 as the ♂-parent.

• 双品系任务在参数面板选完后，页面会自动展开「品系 2」输入卡。After the task is set to a two-stock task in the parameters panel, the "Stock 2" input card expands automatically.
• 若只需要单亲本（如建系 / 染色体替换任务的母本侧），「品系 2」保持空白即可。If only one parental stock is needed (for example, the ♀-parent side of a Stock or Replace task), leave "Stock 2" blank.

5 设置致死 / 不育Set lethality / sterility

recombine / assemble / replace / introgression 任务会在模式行露出「致死 / 不育」下拉，按元件所在染色体自动切换 4 态（X）或 2 态（常染色体）。For recombine / assemble / replace / introgression tasks, a "Lethality / Sterility" dropdown appears on the mode row. It offers four states for X-linked elements and two states for autosomes.

6 生成杂交方案Generate the crossing scheme

点左栏底部「生成杂交方案」按钮：Click the "Generate Cross Plan" button at the bottom of the left panel:

• 按钮颜色由橙变绿表示参数变更。The button turns from gray to orange (is-dirty) whenever parameters change.
• 中栏立即渲染分代杂交图（节点 + × 连线 + tooltip）。The center column immediately renders the per-generation cross diagram (nodes + × connectors + tooltips).
• 右栏出现预计世代数、**预计周期（周）**、警告框（如有）和分步 Protocol。The right column shows estimated generations, **estimated duration (weeks)**, the warning panel (if any), and the step-by-step Protocol.

7 检查警告与调整Review warnings and adjust

右栏警告框里有红线提示时（例如「回交对象必须是受体背景平衡系」「平衡子断点覆盖不足」），优先采纳。When the warning panel on the right shows red messages (for example, "Backcross partner must be a recipient-background balanced stock" or "Balancer breakpoints do not cover the region"), treat them as authoritative.

• 拖动画布平移、用 − / ⤾ / ＋ 缩放看清结构。Drag the canvas to pan; use − / ⤾ / ＋ to zoom in or out.
• 修改任何输入后按钮变橙，再次点「生成杂交方案」刷新。Any input change turns the button orange — click "Generate Cross Plan" again to refresh.

8 复制 ProtocolCopy the Protocol

点右栏「复制 Protocol」按钮：Click the "Copy Protocol" button on the right:

• 分步操作被复制成纯文本（步骤1: …）到剪贴板。The step-by-step actions are copied to the clipboard as plain text (Step 1: …).
• 粘贴到实验记录本（电子或纸质）即可执行。Paste them into a lab notebook (digital or paper) to run the experiment.

9 导出 / 切换语言 / 清空重来Export / switch language / start over

• 保存 PDF：点右栏「保存 PDF」调用浏览器打印对话框，选「另存为 PDF」（@media print 已隐藏按钮与滚动条）。Save PDF: click "Save PDF" on the right to open the browser print dialog, then choose "Save as PDF" (@media print hides buttons and scrollbars).
• 切换语言：顶部「中 / EN」切换 i18n；nav 文案切换，已有 canvas 不被覆盖。Switch language: use the "中 / EN" toggle at the top to switch i18n. Nav labels translate, but the rendered canvas is preserved.
• 清空重来：「清除品系 1 / 清除品系 2 / 全部清除」一键清空该侧的基因型与致死/不育下拉（回到「可育」默认），并清空画布、协议、警告与统计；保留模式、性别与来源选择。画布被清空后，需再次点击「生成杂交方案」才会重画。Clear and restart: "Clear Stock 1 / Clear Stock 2 / Clear All" wipes the genotype and lethality/sterility dropdowns on that side (defaulting back to "viable"), and clears the canvas, protocol, warnings, and stats. Mode, sex, and source are preserved. After clearing the canvas, click "Generate Cross Plan" again to redraw.

大小写规范与自动补全Case sensitivity & autocomplete

FlyCross 默认按 FlyBase / BDSC 规范大小写解析基因型（TM6B、CyO、GAL4）。小写或混写也能识别——解析层会自动归一化，无需用户死记硬背。FlyCross parses genotypes using FlyBase / BDSC canonical case (TM6B, CyO, GAL4). Lowercase or mixed-case also works — the parser layer normalises automatically; you don't have to memorise case.

• 实时提示：输入 tm6b、cyo、gal4 时，下方会弹出候选（如 TM6B、CyO、GAL4），按 ↑/↓ 选中、Enter/Tab 确认。直接忽略候选也无所谓，解析层会兜底。Live suggestions: when you type tm6b, cyo, gal4, a dropdown shows canonical candidates (e.g. TM6B, CyO, GAL4). Use ↑/↓ to navigate, Enter/Tab to confirm. You can ignore the dropdown entirely — the parser still resolves it.

Q1 输入裸编号「6」是哪个库的品系？Which stock library does the bare number "6" come from?

默认走 BDSC。前缀 v 或 VDRC_ 走 VDRC；FBst… 或 FlyBase_ 走 FlyBase。例如 v10004 自动识别为 VDRC v10004。By default, BDSC is used. A v or VDRC_ prefix routes to VDRC; FBst… or FlyBase_ routes to FlyBase. For example, v10004 is auto-recognized as VDRC v10004.

Q2 在「品系编号」输入框按 Enter 会发生什么？What happens when I press Enter in the "Stock number" input?

等价于点「解析」按钮，立即调 /api/stock-lookup 拉取完整基因型并写回。Equivalent to clicking the "Resolve" button — it calls /api/stock-lookup immediately, fetches the full genotype, and writes it back.

Q3 雄性 X 的第二同源会自动锁 Y 吗？Does the second X homolog auto-lock to Y for males?

是。选个体模式 + 雄性时，X 第二同源框变灰自动写 Y；切回雌性自动重置 +，避免无效基因型。Yes. In individual mode with male selected, the second X homolog field is grayed out and auto-filled with Y. Switching back to female auto-resets it to +, avoiding invalid genotypes.

Q4 同染色体的两个元件怎么办？How do I handle two elements on the same chromosome?

assemble 任务会自动拒绝并提示 sameChromosomeWarning，请切到「重组 (recombine)」任务先合并到同一条染色体。Assemble tasks auto-reject with a sameChromosomeWarning. Switch to the "Recombine" task to merge the two elements onto a single chromosome first.

Q5 雄性致死或不育的 X 重组能设计吗？Can I design an X recombination with a male-lethal or male-sterile stock?

能。引擎会自动切到「♀ 亲本 = 致死品系」+「FM7a 保护」路径，Protocol 提示「重组染色体在 FM7a 保护下不再发生交换」。Yes. The engine auto-switches to the "♀-parent = lethal stock" + "FM7a protection" path, and the Protocol notes "the recombinant chromosome no longer recombines under FM7a protection."

Q6 杂交图上看不到致死个体是 bug 吗？Is it a bug that lethal individuals are missing from the cross diagram?

不是。画布只画活下来的个体（engine/PLAN_PROTOCOL.md 规则 Q7）。致死类按设计意图不出现在图上。Not a bug. The canvas only draws individuals that survive (per engine/PLAN_PROTOCOL.md rule Q7). Lethal classes are excluded by design.

Q7 节点上显示的是完整基因型吗？Does a node show the full genotype?

不是。节点显示简化名（剥 P{…} 行号），例如 P{w[+mC]=Act5C-GAL4}25F01 在 canvas 上显示为 Act5C-GAL4。悬停节点 tooltip 显示 full 全基因型 + 表型提示。No. Nodes show simplified names (with P{…} line numbers stripped). For example, P{w[+mC]=Act5C-GAL4}25F01 displays as Act5C-GAL4. Hover over a node to see the full genotype plus phenotype hints in the tooltip.

Q8 画布能缩放吗？Can the canvas be zoomed?

可以。右上角 − / ⤾ / ＋ 三个按钮，缩放范围 0.4× ~ 2×。按住背景左键可拖动平移。Yes. Three buttons in the top-right — − / ⤾ / ＋ — zoom from 0.4× to 2×. Hold the left mouse button on the background to pan.

Q9 保存 PDF 是导出图片吗？Does "Save PDF" export an image?

当前实现是触发浏览器打印对话框（window.print()，@media print 隐藏按钮与滚动条），选「另存为 PDF」即可。后续会换 html2pdf / jsPDF + html2canvas。Currently, it triggers the browser print dialog (window.print() with @media print hiding buttons and scrollbars) — pick "Save as PDF". A future version will switch to html2pdf or jsPDF + html2canvas.

Q10 染色体替换的回交对象有什么要求？What are the requirements for the backcross partner in chromosome replacement?

必须用「受体背景平衡系」（如 Sp/CyO 或 TM2/TM6B 品系雌性），不是普通 w[1118] 受体。警告框会自动提示。You must use a "recipient-background balanced stock" (for example, Sp/CyO or TM2/TM6B females), not a plain w[1118] recipient. The warning panel flags this automatically.

Q11 位点导入任务为什么禁用平衡子？Why are balancers disabled for introgression tasks?

平衡子会抑制交换，让侧翼供体片段无法削掉。平衡子只在终点（如目标位点为纯合致死时）才引入。Balancers suppress recombination, so they prevent the flanking donor segments from being shed. Balancers are introduced only at the final step — for example, when the target locus is homozygous lethal.

Q12 回交 N 代后受体背景占比怎么算？How is recipient-background fraction calculated after N backcross generations?

公式 (2^i − 1) / 2^i（i = 回交代数）。回交 5 代 → 受体背景 ≥ 31/32（≈ 96.9%）；回交 10 代 → ≥ 1023/1024（≈ 99.9%）。画布会显示「回交 N 代后受体背景 ≥xx/xx」。The formula is (2^i − 1) / 2^i (i = backcross generation). After 5 generations, recipient background ≥ 31/32 (≈ 96.9%); after 10, ≥ 1023/1024 (≈ 99.9%). The canvas shows "After N backcross generations, recipient background ≥ xx/xx."

Q13 输入「Tg1/FM7a」后致死 / 不育被自动改成「雌雄致死或不育」，是 bug 吗？I typed "Tg1/FM7a" and the Viability dropdown was auto-set to "both-sex lethal / sterile" — is this a bug?

不是。这是「维持系形态自动识别」（INF-A 规则）命中：X 上 FM7a 是平衡维持形态——元件挂在 FM7a 上就说明被平衡的 X 携带致死 / 不育突变，引擎保守按最严的 bothLethal 处理。如已实测雌雄可育，可在「致死 / 不育」下拉手动改回「雌雄可育」，该选择会被记为「用户已确认」并保留。No. The "maintenance-stock auto-detection" (INF-A) just fired: FM7a on X is a balancer-maintenance shape — anything over FM7a indicates the balanced X carries a lethal / sterile allele, and the engine conservatively forces bothLethal. If you've empirically validated viability, set the dropdown back to "viable" — that gets recorded as "user-confirmed" and sticks.

Q14 建系任务选了「2 号染色体」但解析出基因型在「3 号」，画布上方弹橙色横幅，是 bug 吗？Stock task: I picked "chr 2" but the parsed genotype sits on "chr 3" — an orange banner pops above the canvas. Is this a bug?

不是。这是建系任务的新校验——引擎会比对「参数面板选的染色体」与「品系基因型实际所在染色体」是否一致；如果对不上，引擎直接 throw，并在画布工具栏（缩放按钮行）之下、画布根节点之上弹出橙色横幅 #engine-error-banner（前缀 ⚠ 引擎异常： + 错误消息，例如 品系的 2 号染色体上未找到插入元件）。同时右栏 Protocol 显示「生成失败，请检查输入或联系开发者」。No. Stock now validates that the chromosome you selected in the parameter panel matches the chromosome the parsed genotype actually lives on. If they disagree, the engine throws and the UI renders an orange #engine-error-banner just below the canvas toolbar (the row with the zoom buttons) and above the canvas root — prefix ⚠ Engine error: + the error message (e.g. No insert found on chromosome 2 of this stock). The right-pane Protocol simultaneously shows "Generation failed, please check inputs or contact the developer."

常见原因：Common causes:

• BDSC / FlyBase / VDRC 解析出的完整基因型里，插入元件实际所在染色体与你在参数面板选的不一致（例如选「2 号」，但 BDSC #7018 解析出的是「3 号 tubP-GAL80[ts]」）。The chromosome the insert actually sits on in the resolved BDSC / FlyBase / VDRC genotype doesn't match the chromosome you picked in the parameter panel (e.g. you picked "chr 2", but BDSC #7018 resolves to "chr 3 tubP-GAL80[ts]").
• 手敲基因型时漏写了 semicolon 分隔，导致整段串被分到错误的染色体槽位。Manual genotype entry is missing a semicolon separator, so the whole string lands in the wrong chromosome slot.

处理：把参数面板的「染色体」下拉改到与解析结果一致的那一条，再点「生成杂交方案」即可。如果你的本意就是「另一条染色体」，请重新核对品系是否选错——建系任务只支持单条染色体上的插入元件。Fix: change the parameter panel's "Chromosome" dropdown to match the resolved genotype, then click "Generate cross plan" again. If you genuinely meant the other chromosome, double-check whether you picked the wrong strain — Stock tasks only support an insert on a single chromosome.