typshade:0.1.2 (#5076)

Author: rice8y

packages/preview/typshade/0.1.2/LICENSE

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+# Typshade
+
+![Typshade alignment overview](images/readme-overview.png)
+
+Typshade is a Typst package for visualizing multiple sequence alignments in bioinformatics.
+
+It provides a Typst-native interface centered on `shade(...)`, offering a readable and composable way to render alignments, add annotations, and incorporate logos, structure tracks, and graph tracks.
+
+Inspired by [TeXshade](https://ctan.org/pkg/texshade), Typshade rethinks alignment visualization with a focus on clarity, composability, and a Typst-native user experience.
+
+## Why Typshade?
+
+TeXshade is powerful, but its UI reflects TeX: many global commands, implicit state, and order-sensitive setup before the alignment is rendered. Typshade keeps the feature set while making the source read like a figure specification.
+
+TeXshade style:
+
+```latex
+\begin{texshade}{alignment.msf}
+  \shadingmode[similar]{identical}
+  \shadingcolors{blues}
+  \residuesperline{45}
+  \setends{1}{80..125}
+  \showruler{top}{1}
+  \rulersteps{10}
+  \showconsensus{bottom}
+  \showsequencelogo{top}
+  \shaderegion{1}{NPA}{White}{BrickRed}
+  \feature{top}{1}{NXX[ST]N}{box[Yellow]}{motif}
+\end{texshade}
+```
+
+Typshade style:
+
+```typst
+#let alignment = read("alignment.msf", encoding: none)
+
+#shade(
+  alignment,
+  format: "msf",
+  figure: publication(
+    similarity: "blues",
+    region: "80..125",
+    logo: "charge",
+    motifs: (
+      "NPA": (bg: "BrickRed", text: "active site"),
+      "NXX[ST]N": "motif",
+    ),
+  ),
+)
+```
+
+The lower-level helpers are still available through `commands:` when you need precise control, but new documents can usually start from the kind of figure you want: publication figure, motif map, structure map, or logo analysis.
+
+## Quick Start
+
+```typst
+#import "@preview/typshade:0.1.2": *
+
+#let alignment = read("alignment.msf", encoding: none)
+
+#shade(
+  alignment,
+  format: "msf",
+  theme: "screen",
+  figure: motif-map(auto),
+)
+```
+
+`read(..., encoding: none)` remains supported on Typst 0.15 and later. On Typst 0.15 or later, you can additionally pass a resolved project path and let Typshade read the source inside the package:
+
+```typst
+#shade(path("alignment.msf"), format: "msf", figure: motif-map(auto))
+```
+
+## Preview
+
+Protein alignment with similarity shading, motif annotations, a ruler,
+a conservation track, and a legend:
+
+![Protein alignment preview](images/readme-preview-1.png)
+
+Protein alignment with hydropathy-based functional coloring:
+
+![Hydropathy preview](images/readme-preview-2.png)
+
+Nucleotide alignment with DNA coloring, a sequence logo, a conservation track,
+and a ruler:
+
+![DNA alignment preview](images/readme-preview-3.png)
+
+## Typst-Native Helpers
+
+- `shade(...)`: Named-option alignment renderer for new documents.
+- `figure:`: Purpose-level recipe slot for complete figure designs.
+- `publication`, `motif-map`, `structure-map`, `logo-analysis`, `overview`: High-level recipes.
+- `similar`, `identical`, `diverse`, `functional`, `lines`, `window`, `ruler`, `consensus`, `logo`, `legend`: Compact command helpers.
+- `color-scheme`, `scoring-mode`, `sequence-window`: Small, readable option helpers.
+- `ruler-track`, `consensus-track`, `sequence-logo`, `subfamily-logo`, `legend-track`: Track helpers.
+- `structure-tracks(...)`: Adds topology/secondary-structure tracks from sidecar files.
+- `shade-preset("publication" | "overview" | "logo" | "functional" | "structure")`: Reusable command bundles.
+- `shade-theme("classic" | "print" | "screen" | "warm" | "nature")` and `visual-theme(...)`: Color/style bundles.
+- `highlight`, `tint`, `emphasize`, `mark`, `motif`, `graph`: Readable command builders for common annotations.
+- `pdb-point`, `pdb-line`, `pdb-plane`: Safer constructors for PDB selections.
+- `alignment-position("left" | "center" | "right")`: Overrides the default left-aligned block placement.
+- `alignment-summary(...)` and `selection-preview(...)`: In-document inspection helpers.
+- `sequence-list(...)` and `selection-table(...)`: Typst tables for data-aware reports.
+- `percent-identity(...)`, `percent-similarity(...)`, and `similarity-table(...)`: Pairwise identity/similarity analysis.
+- `alignment-data(...)` and `parse-alignment(...)`: Data access helpers for custom Typst logic.
+
+## TeXshade To Typshade
+
+| TeXshade idea | Typshade API |
+|---|---|
+| `texshade` environment | `shade(read("alignment.msf", encoding: none), format: "msf", figure: publication(...))`, or `shade(path("alignment.msf"), format: "msf", ...)` on Typst 0.15+ |
+| `shadingmode`, `shadingcolors`, `threshold` | `similar`, `identical`, `diverse`, `functional`, or `scoring-mode`, `color-scheme`, `threshold` |
+| `residuesperline`, `setends` | `lines`, `window`, or `residues-per-line`, `sequence-window` |
+| `shownames`, `shownumbering`, `showconsensus`, `showruler` | `names`, `numbers`, `consensus`, `ruler`, or the fine-grained track helpers |
+| `showsequencelogo`, `showsubfamilylogo`, `showlegend` | `logo`, `subfamily-logo`, `legend` |
+| `shaderegion`, `tintregion`, `emphregion`, `feature` | `highlight`, `tint`, `emphasize`, `mark`, `motif`, `graph` |
+| `includeDSSP`, `includeSTRIDE`, `includeHMMTOP`, `includePHD*` | `structure-tracks`, `dssp-track`, `stride-track`, `hmmtop-track`, `phd-topology-track`, `phd-secondary-track` |
+| font and spacing macros | `text-family`, `text-weight`, `text-posture`, `text-size`, `block-gap`, `feature-slot-space` |
+
+See [documentation](https://github.com/rice8y/typshade/blob/v0.1.2/docs/documentation.pdf) for the full guide and a larger correspondence table.
+
+## Smart Recipes
+
+Recipes inspect the alignment before rendering. For example, `motif-map(auto)` detects common motifs for the sequence type, focuses the region around them, chooses a readable line length, adds conservation when useful, and enables a logo only when the figure stays readable. Override any option when you need exact control.
+
+## Fine-Grained Control
+
+Macro-style command names are intentionally not part of the public API. Use Typst-shaped command helpers when you need detailed control:
+
+- Scoring: `threshold`, `weight-table`, `set-weight`, `gap-penalty`, `residue-style`, `functional-group`.
+- Tracks: `names-track`, `numbering-track`, `consensus-name`, `consensus-symbols`, `ruler-name`, `ruler-marker`, `logo-color`.
+- Sequence layout: `start-number`, `sequence-length`, `domain`, `hide-sequence`, `sequence-order`, `separation-line`.
+- Features and structure: `feature-rule`, `feature-text-label`, `backtranslation-label`, `show-structure-types`, `structure-appearance`, `stride-track`, `dssp-track`, `hmmtop-track`, `phd-topology-track`, `phd-secondary-track`.
+- Typography and spacing: `text-family`, `text-weight`, `text-posture`, `text-size`, `character-stretch`, `line-stretch`, `block-gap`, `feature-slot-space`.
+
+## Custom Control
+
+Use recipes when you know the purpose of the figure:
+
+```typst
+#let alignment = read("alignment.msf", encoding: none)
+
+#shade(
+  alignment,
+  format: "msf",
+  figure: publication(
+    region: "80..125",
+    logo: "charge",
+    motifs: (
+      "NPA": (bg: "BrickRed", text: "active site"),
+      "NXX[ST]N": "glycosylation",
+    ),
+  ),
+)
+```
+
+Use `commands:` when you want to assemble visible parts yourself:
+
+```typst
+#let alignment = read("alignment.msf", encoding: none)
+
+#shade(
+  alignment,
+  format: "msf",
+  preset: "publication",
+  theme: "screen",
+  commands: (
+    similar(colors: "blues", threshold: 45),
+    lines(45),
+    window(1, "80..125"),
+    ruler("top", sequence: 1, every: 10),
+    consensus("bottom", name: "conservation"),
+    logo("top", colors: "charge"),
+    legend(),
+    highlight(1, "NPA", bg: "BrickRed"),
+    motif(1, "NXX[ST]N", text: "motif"),
+    graph("bottom", 1, "all", "conservation", kind: "color", options: ("ColdHot",)),
+  ),
+)
+```
+
+You can also mix recipe output with explicit, reproducible helper lists:
+
+```typst
+#let alignment = read("alignment.msf", encoding: none)
+
+#shade(
+  alignment,
+  format: "msf",
+  figure: publication(region: "80..125"),
+  commands: (
+    highlight(1, "NXX[DE][KR]XXQ", fg: "White", bg: "BrickRed"),
+    sequence-logo(position: "top"),
+  ),
+)
+```
+
+# License
+
+This project is distributed under the GPL v2 License. See [LICENSE](LICENSE) for details.

packages/preview/typshade/0.1.2/README.md

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+// Copyright (C) 2026 Eito Yoneyama
+// SPDX-License-Identifier: GPL-2.0
+
+#let _add-command(out, value) = {
+  if value == none {
+    return out
+  }
+  if type(value) == array {
+    for item in value {
+      out = _add-command(out, item)
+    }
+  } else {
+    out.push(value)
+  }
+  out
+}
+
+#let command-pack(..items) = {
+  let out = ()
+  for item in items.pos() {
+    out = _add-command(out, item)
+  }
+  out
+}