varri-js 1.0.1 → 1.0.2

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/CITATION.bib CHANGED
@@ -1,10 +1,10 @@
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  @misc{raden_varrii_js_2026,
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- title = {vaRRI-js - Visual annotation of RNA-RNA interactions},
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+ title = {vaRRI - Visual annotation of RNA-RNA interactions},
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  author = {Raden, Martin and Ganter, Fabian},
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  year = {2026},
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- url = {https://backofenlab.github.io/vaRRI-js/},
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+ url = {https://backofenlab.github.io/vaRRI/},
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  note = {Web application and JavaScript library},
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- abstract = {vaRRI-js is a browser-based JavaScript library for visualizing RNA-RNA interactions (RRIs) as 2D diagrams with annotations such as base-pair highlights, probability profiles, subsequence highlights, and point mutation annotations.},
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+ abstract = {vaRRI is a browser-based JavaScript library for visualizing RNA-RNA interactions (RRIs) as 2D diagrams with annotations such as base-pair highlights, probability profiles, subsequence highlights, and point mutation annotations.},
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  keywords = {RNA, RNA-RNA interaction, visualization, JavaScript, bioinformatics},
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  version = {1.0.0},
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  license = {MIT},
package/CITATION.cff CHANGED
@@ -1,5 +1,5 @@
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  cff-version: 1.2.0
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- title: vaRRI-js - Visual annotation of RNA-RNA interactions
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+ title: vaRRI - Visual annotation of RNA-RNA interactions
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  message: >-
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  If you use this software in a publication, please cite it using the metadata
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  in this file.
@@ -17,10 +17,10 @@ authors:
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  website: 'https://www.bioinformatics.uni-freiburg.de/'
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  version: 1.0.0
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  date-released: '2026-07-31'
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- repository-code: 'https://github.com/BackofenLab/vaRRI-js'
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- url: 'https://backofenlab.github.io/vaRRI-js/'
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+ repository-code: 'https://github.com/BackofenLab/vaRRI'
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+ url: 'https://backofenlab.github.io/vaRRI/'
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  abstract: >-
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- vaRRI-js is a browser-based JavaScript library for visualizing RNA-RNA
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+ vaRRI is a browser-based JavaScript library for visualizing RNA-RNA
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  interactions (RRIs) as 2D diagrams with annotations such as base-pair
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  highlights, probability profiles, subsequence highlights, and point mutation
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  annotations.
package/README.html CHANGED
@@ -3,7 +3,7 @@
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  <head>
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  <meta charset="UTF-8">
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  <meta name="viewport" content="width=device-width, initial-scale=1.0">
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- <title>vaRRI-js README</title>
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+ <title>vaRRI README</title>
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  <link rel="icon" type="image/png" href="logo/vaRRI.logo.40x40.png">
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  <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/github-markdown-css/5.5.1/github-markdown.min.css">
@@ -107,7 +107,7 @@
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  if (isLocalFile && token.type === 'html' && typeof token.text === 'string' && token.text.includes('<iframe')) {
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  // Optionally extract the URL from the iframe if present
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  const srcMatch = token.text.match(/src=["']([^"']+)["']/);
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- const iframeUrl = srcMatch ? srcMatch[1] : 'https://backofenlab.github.io/vaRRI-js/index.html';
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+ const iframeUrl = srcMatch ? srcMatch[1] : 'https://backofenlab.github.io/vaRRI/index.html';
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  token.text = `
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  <div class="status-banner" style="margin: 16px 0;">
@@ -122,7 +122,7 @@
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  // 3. Define URLs
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  const localUrl = './README.md';
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- const remoteUrl = 'https://raw.githubusercontent.com/BackofenLab/vaRRI-js/main/README.md';
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+ const remoteUrl = 'https://raw.githubusercontent.com/BackofenLab/vaRRI/main/README.md';
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  // 4. Choose target URL
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  const targetUrl = isLocalFile ? remoteUrl : localUrl;
@@ -133,7 +133,7 @@
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  ⚠️ <strong>Note:</strong>
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  <blockquote style="margin: 8px;">
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  README.html was opened locally and cannot access the local README.md.<br>
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- Therefore, the README was loaded from the <a href="${remoteUrl}">vaRRI-js online repository</a>.
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+ Therefore, the README was loaded from the <a href="${remoteUrl}">vaRRI online repository</a>.
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  </blockquote>
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  </div>
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  `;
package/README.md CHANGED
@@ -1,13 +1,13 @@
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- # ![vaRRI-js](logo/vaRRI.logo.40x40.png) vaRRI-js - Visual Annotation of RNA–RNA Interactions
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+ # vaRRI - Visual Annotation of RNA–RNA Interactions
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- Visualise and annotate RNA–RNA interactions directly in the browser — no server or no command-line tools required.
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+ ![vaRRI](logo/vaRRI.logo.40x40.png) Visualise and annotate RNA–RNA interactions directly in the browser — no server or no command-line tools required.
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  ---
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  ## Table of Contents
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  1. [Overview](#overview-and-objective)
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- 2. [Examples from Literature](#examples-from-literature-reproduced-with-varri-js)
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+ 2. [Examples from Literature](#examples-from-literature-reproduced-with-varri)
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  3. [Project Structure](#project-structure)
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  4. [Quick Start](#quick-start)
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  5. [npm Package](#npm-package)
@@ -23,7 +23,7 @@ Visualise and annotate RNA–RNA interactions directly in the browser — no ser
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  ## Overview and Objective
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- vaRRI-js is a pure JavaScript library to visualize the base pairing of
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+ vaRRI is a pure JavaScript library to visualize the base pairing of
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  RNA-RNA interactions (RRIs) as 2D diagrams with additional annotation like
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  - coloring by sequence or loop type,
@@ -48,18 +48,18 @@ Use cases include
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  > If you like it, [please cite it!](citation.html)
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- Given two sequences and the RRI secondary-structure encoding in dot-bracket notation, vaRRI-js renders
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+ Given two sequences and the RRI secondary-structure encoding in dot-bracket notation, vaRRI renders
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  them with the [Fornac](https://github.com/ViennaRNA/fornac) library, and then
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  applies all of vaRRI's annotations and tweaks.
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- [![vaRRI-js example visualization](doc/vaRRI-UI-example.png)](https://backofenlab.github.io/vaRRI-js/)
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+ [![vaRRI example visualization](doc/vaRRI-UI-example.png)](https://backofenlab.github.io/vaRRI/)
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58
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  ---
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- ## Examples from Literature reproduced with vaRRI-js
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+ ## Examples from Literature reproduced with vaRRI
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- To showcase the capabilities of vaRRI-js, we provide a collection of examples from the literature that have been reproduced using vaRRI-js.
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+ To showcase the capabilities of vaRRI, we provide a collection of examples from the literature that have been reproduced using vaRRI.
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  The examples can be loaded directly in the input website via the **Example** dropdown.
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@@ -68,7 +68,7 @@ The examples can be loaded directly in the input website via the **Example** dro
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  ## Project Structure
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  ```
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- vaRRI-js/
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+ vaRRI/
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  │
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  ├── fornac/
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  │ ├── fornac.js # Fornac library (vaRRI dependency)
@@ -99,16 +99,16 @@ vaRRI-js/
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  > before using it in a production environment.
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- The easiest way to [**use vaRRI-js is via the GitHub pages website**](https://BackofenLab.github.io/vaRRI-js):
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+ The easiest way to [**use vaRRI is via the GitHub pages website**](https://BackofenLab.github.io/vaRRI):
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- - [https://BackofenLab.github.io/vaRRI-js](https://BackofenLab.github.io/vaRRI-js)
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+ - [https://BackofenLab.github.io/vaRRI](https://BackofenLab.github.io/vaRRI)
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- If you want to run the website locally or use the library in your own HTML page, clone the repository or download a ZIP of the project via the [Releases](https://github.com/BackofenLab/vaRRI-js/releases) section.
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+ If you want to run the website locally or use the library in your own HTML page, clone the repository or download a ZIP of the project via the [Releases](https://github.com/BackofenLab/vaRRI/releases) section.
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  Afterwards, open `index.html` directly in a browser — no build step or server needed:
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  ```bash
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- git clone https://github.com/BackofenLab/vaRRI-js.git
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- cd vaRRI-js
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+ git clone https://github.com/BackofenLab/vaRRI.git
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+ cd vaRRI
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  # simply open index.html in your browser, e.g.:
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  open index.html # macOS
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  xdg-open index.html # Linux
@@ -126,17 +126,18 @@ To use the library in your own HTML page, include the dependencies in the follow
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  ## npm Package
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- Install vaRRI-js in an application with:
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+ Install vaRRI in an application with:
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  ```bash
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  npm install varri-js
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  ```
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- Starting with version 1.0.1, the package includes the complete viewer as well as the library.
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+ The npm package remains `varri-js`; the GitHub repository and project branding are `vaRRI`.
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+ Version 1.0.2 includes the updated complete viewer as well as the library.
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  ### Open `index.html` in Browser
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- After installation via npm, you find the vaRRI-js user interface `index.html` in the following subfolder
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+ After installation via npm, you find the vaRRI user interface `index.html` in the following subfolder
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141
 
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  ```bash
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  node_modules/varri-js/index.html
@@ -311,8 +312,8 @@ These generated entries are shown in the same list but are **not removable or ed
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  Behaviour of generated list entries:
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  - When **RRI Background** is set to `nothing`, no generated region entry is shown.
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- - When set to `region`, vaRRI-js computes the overall intermolecular interaction region and displays it as a generated, non-removable region entry.
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- - When set to `basepairs`, vaRRI-js computes one or more generated region entries that correspond to intermolecular basepair stacks and displays them as non-removable entries.
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+ - When set to `region`, vaRRI computes the overall intermolecular interaction region and displays it as a generated, non-removable region entry.
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+ - When set to `basepairs`, vaRRI computes one or more generated region entries that correspond to intermolecular basepair stacks and displays them as non-removable entries.
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  - Generated entries are refreshed automatically from the current structure and settings; they are not exported as user-defined region highlights in share links.
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@@ -361,7 +362,7 @@ As separator, either space and tab is supported, and lines starting with `#` are
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  > [!TIP]
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  > - For convenience, respective text *files can be dragged and dropped* into the input fields to load the probability profiles.
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- > - vaRRI-js also supports CSV files with a header line, where the first column contains the nucleotide indices and the second column contains the probability values. Such data is automatically converted to the space-separated format above, and the header line is ignored.
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+ > - vaRRI also supports CSV files with a header line, where the first column contains the nucleotide indices and the second column contains the probability values. Such data is automatically converted to the space-separated format above, and the header line is ignored.
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366
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  Finally, the following fields are available to define the visualization of the probability profiles:
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@@ -377,7 +378,7 @@ Finally, the following fields are available to define the visualization of the p
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  ### Point Mutations
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  RNA-RNA interaction visualizations are often used to discuss the effect of point mutations on the interaction.
380
- To support this, vaRRI-js allows to define point mutations in the input sequences and visualizes them in the rendered structure.
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+ To support this, vaRRI allows to define point mutations in the input sequences and visualizes them in the rendered structure.
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  A point mutation is defined by the sequence (1 or 2), the index of the nucleotide to mutate, and the new nucleotide (or letter) to use for the mutation.
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  This information is provided in the following fields, and the "Add" button registers the mutation.
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@@ -389,7 +390,7 @@ This information is provided in the following fields, and the "Add" button regis
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  | **Color** | The color to use for highlighting the mutated nucleotide. |
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  > [!TIP]
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- > vaRRI-js allows to define arbitrary letters as mutations, i.e. the mutated nucleotide does not need to be a valid IUPAC character.
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+ > vaRRI allows to define arbitrary letters as mutations, i.e. the mutated nucleotide does not need to be a valid IUPAC character.
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  > That way, any kind of annotation can be added to the sequence, e.g. a letter representing a chemical modification, symbols for a certain type of mutation, or even a short word.
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  All registered mutations are shown in a list above the input fields, and can be removed by clicking the "🗑️" icon.
@@ -439,7 +440,7 @@ Details about URL encoding are given in the following section [URL Parameters &
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440
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  ## URL Parameters & Sharing
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442
 
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- **vaRRI-js** supports state persistence directly via URL parameters, allowing you to pre-fill inputs or share specific visualization configurations using the **🔗 Share Link** button in the export panel. Most parameter names map directly to their corresponding HTML element IDs.
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+ **vaRRI** supports state persistence directly via URL parameters, allowing you to pre-fill inputs or share specific visualization configurations using the **🔗 Share Link** button in the export panel. Most parameter names map directly to their corresponding HTML element IDs.
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444
 
444
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  ### Key Parameters
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446
 
@@ -473,12 +474,25 @@ To simplify sequence and structure input validation, sequence and structure inpu
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474
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  You can embed the visualization directly into external web pages (e.g., in documentation, blogs, or web tools) using an `<iframe>`.
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476
 
477
+ ### Embeddings in Existing Web Applications
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+
479
+ Currently, vaRRI is already available as an RRI visualizer in the the following web applications:
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+
481
+ - Freiburg RNA Tools: [https://rna.informatik.uni-freiburg.de/](https://rna.informatik.uni-freiburg.de/)
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+ - IntaRNA - RNA-RNA interaction prediction server
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+ - [Example visualization](https://rna.informatik.uni-freiburg.de/IntaRNA/Result.jsp?toolName=IntaRNA&jobID=4267751)
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+ - CopomuS - Compensatory Mutation Designer for RNA-RNA interactions
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+ - [Example visualization](https://rna.informatik.uni-freiburg.de/CopomuS/Result.jsp?toolName=CopomuS&jobID=1595284)
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+ - Galaxy Visualizer: [https://usegalaxy.eu/](https://usegalaxy.eu/)
487
+ - vaRRI is available as a visualization tool for RNA-RNA interactions in the Galaxy workflow system
488
+
489
+
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  ### Query Parameter
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491
 
478
492
  Use the `showRenderingOnly=true` URL parameter to hide all surrounding UI elements (header, controls panel, footer) and display only the visualization result panel.
479
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480
494
  ```text
481
- https://backofenlab.github.io/vaRRI-js/index.html?showRenderingOnly=true&<remaining_parameters...>
495
+ https://backofenlab.github.io/vaRRI/index.html?showRenderingOnly=true&<remaining_parameters...>
482
496
  ```
483
497
 
484
498
  For embedding without header and footer, you can also use the `hideFooterAndHeader=true` parameter, which will hide the header and footer but keep the controls panel visible, i.e. this checks the "Full screen UI" checkbox in the controls panel.
@@ -487,34 +501,35 @@ For embedding without header and footer, you can also use the `hideFooterAndHead
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488
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  ```html
489
503
  <iframe
490
- src="https://backofenlab.github.io/vaRRI-js/?sequence=ACGAUCAUGGAUUAGAGCAUUCGACAGCAG%26ACGAAAAAAAGAGCAUACGACAGUAG&colorSeq1=%23add8e6&startIndex1=-6&colorSeq2=%23f4bb44&startIndex2=100&structure=..%3C%3C%3C%3C...%3E%3E%3E%3E...%28%28..%28%28%28...%28%28..%26............%29%29...%29%29%29..%29%29..&coloring=strand&highlighting=region&colorRriNodes=%23ff0000&backgroundhighlighting=basepairs&colorRriRegion=%23ff0000&colorBasepair=%23ff0000&distinctBpTypes=on&forceLayout=on&profileColor1=%23800080&profileColorRepresentsOne1=on&profileColor2=%23ff0000&profileData1=%23+unpaired+probabilities%0A1+0.9%0A2+0.7%0A3+0.3%0A4+0.1%0A7+0.3%0A8+0.7%0A9+0.6&profileIdxRef1=1&profileIdxRef2=1&cropping=2&mutations=1%3A16G%3A338a29%2C2%3A118C%3A338a29&highlights=1%3A18-20%3A338a29%2C2%3A114-116%3A338a29&showRenderingOnly=true"
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+ src="https://backofenlab.github.io/vaRRI/?sequence=ACGAUCAUGGAUUAGAGCAUUCGACAGCAG%26ACGAAAAAAAGAGCAUACGACAGUAG&colorSeq1=%23add8e6&startIndex1=-6&colorSeq2=%23f4bb44&startIndex2=100&structure=..%3C%3C%3C%3C...%3E%3E%3E%3E...%28%28..%28%28%28...%28%28..%26............%29%29...%29%29%29..%29%29..&coloring=strand&highlighting=region&colorRriNodes=%23ff0000&backgroundhighlighting=basepairs&colorRriRegion=%23ff0000&colorBasepair=%23ff0000&distinctBpTypes=on&forceLayout=on&profileColor1=%23800080&profileColorRepresentsOne1=on&profileColor2=%23ff0000&profileData1=%23+unpaired+probabilities%0A1+0.9%0A2+0.7%0A3+0.3%0A4+0.1%0A7+0.3%0A8+0.7%0A9+0.6&profileIdxRef1=1&profileIdxRef2=1&cropping=2&mutations=1%3A16G%3A338a29%2C2%3A118C%3A338a29&highlights=1%3A18-20%3A338a29%2C2%3A114-116%3A338a29&showRenderingOnly=true"
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  width="100%"
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  height="600"
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  style="border: none;"
494
- title="vaRRI-js Visualization">
508
+ title="vaRRI Visualization">
495
509
  </iframe>
496
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  ```
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  > [!IMPORTANT]
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  > Ensure special characters in URL parameters (such as `&` separating two RNA strands) are properly URL-encoded as `%26` when constructing embedding links manually. Also `()` have to be encoded using `%28` and `%29` respectively, as they are not encoded by default by URL encoders following RFC 3986.
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501
- Valid embedding links can be generated using the "🔗 Share Link" button in the vaRRI-js interface but have to extended with `&showRenderingOnly=true`.
515
+ Valid embedding links can be generated using the "🔗 Share Link" button in the vaRRI interface but have to extended with `&showRenderingOnly=true`.
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503
517
  ----
504
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505
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  <iframe
506
- src="https://backofenlab.github.io/vaRRI-js/?showRenderingOnly=true&sequence=ACGAUCAUGGAUUAGAGCAUUCGACAGCAG%26ACGAAAAAAAGAGCAUACGACAGUAG&colorSeq1=%23add8e6&startIndex1=-6&colorSeq2=%23f4bb44&startIndex2=100&structure=..%3C%3C%3C%3C...%3E%3E%3E%3E...%28%28..%28%28%28...%28%28..%26............%29%29...%29%29%29..%29%29..&coloring=strand&highlighting=region&colorRriNodes=%23ff0000&backgroundhighlighting=basepairs&colorRriRegion=%23ff0000&colorBasepair=%23ff0000&distinctBpTypes=on&forceLayout=on&profileColor1=%23800080&profileColorRepresentsOne1=on&profileColor2=%23ff0000&profileData1=%23+unpaired+probabilities%0A1+0.9%0A2+0.7%0A3+0.3%0A4+0.1%0A7+0.3%0A8+0.7%0A9+0.6&profileIdxRef1=1&profileIdxRef2=1&cropping=2&mutations=1%3A16G%3A338a29%2C2%3A118C%3A338a29&highlights=1%3A18-20%3A338a29%2C2%3A114-116%3A338a29"
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+ src="https://backofenlab.github.io/vaRRI/?showRenderingOnly=true&sequence=ACGAUCAUGGAUUAGAGCAUUCGACAGCAG%26ACGAAAAAAAGAGCAUACGACAGUAG&colorSeq1=%23add8e6&startIndex1=-6&colorSeq2=%23f4bb44&startIndex2=100&structure=..%3C%3C%3C%3C...%3E%3E%3E%3E...%28%28..%28%28%28...%28%28..%26............%29%29...%29%29%29..%29%29..&coloring=strand&highlighting=region&colorRriNodes=%23ff0000&backgroundhighlighting=basepairs&colorRriRegion=%23ff0000&colorBasepair=%23ff0000&distinctBpTypes=on&forceLayout=on&profileColor1=%23800080&profileColorRepresentsOne1=on&profileColor2=%23ff0000&profileData1=%23+unpaired+probabilities%0A1+0.9%0A2+0.7%0A3+0.3%0A4+0.1%0A7+0.3%0A8+0.7%0A9+0.6&profileIdxRef1=1&profileIdxRef2=1&cropping=2&mutations=1%3A16G%3A338a29%2C2%3A118C%3A338a29&highlights=1%3A18-20%3A338a29%2C2%3A114-116%3A338a29"
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  width="100%"
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522
  height="600"
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  style="border: 2px solid #333333; border-radius: 6px;"
510
- title="vaRRI-js Visualization">
524
+ title="vaRRI Visualization">
511
525
  </iframe>
512
526
 
513
527
  ----
514
528
 
515
529
  > [!NOTE]
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  > GitHub repository preview strips embedded `<iframe>` elements as above for security reasons.
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- > * If you are viewing [this page on **GitHub Pages**](https://backofenlab.github.io/vaRRI-js/README.html), the live widget will render directly below.
531
+ > * If you are viewing [this page on **GitHub Pages**](https://backofenlab.github.io/vaRRI/README.html), the live widget will render directly below.
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+
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519
534
  ## Input Format Reference
520
535
 
@@ -528,7 +543,7 @@ Valid embedding links can be generated using the "🔗 Share Link" button in the
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543
 
529
544
  ### Dot-Bracket Notation
530
545
 
531
- vaRRI-js accepts standard dot-bracket secondary structure notation with the following characters:
546
+ vaRRI accepts standard dot-bracket secondary structure notation with the following characters:
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547
 
533
548
  | Character | Meaning |
534
549
  |---|---|
@@ -543,7 +558,7 @@ You can use any of the four bracket types to represent basepairs, and they can b
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558
  The only restriction is that the brackets must be balanced, i.e. every opening bracket must have a corresponding closing bracket of the same type.
544
559
 
545
560
  > [!IMPORTANT]
546
- > Since vaRRI-js is based on the fornac library, its underlying layout algorithm does not support pseudoknots, i.e. basepairs that cross each other.
561
+ > Since vaRRI is based on the fornac library, its underlying layout algorithm does not support pseudoknots, i.e. basepairs that cross each other.
547
562
  > In that case, the primary layout will be based on a reduced set of basepairs that do not cross each other, and the remaining basepairs are added subsequently.
548
563
  > Therefore, the layout of pseudoknotted structures may not be optimal, and the visualisation may be less clear than for non-pseudoknotted structures.
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564
 
@@ -610,20 +625,23 @@ position-based annotations, including highlightings, point mutations, and probab
610
625
  Include `src/vaRRI.js` after the Fornac dependencies.
611
626
  The library exposes a single global object `vaRRI` with the a set of respective functions.
612
627
 
613
- The `src` directory provides a [detailed vaRRI-js Library API documentation](src/README.md)
628
+ The `src` directory provides a [detailed vaRRI Library API documentation](src/README.md)
614
629
 
615
630
 
616
631
  ---
617
632
 
618
633
  ## Release Process
619
634
 
620
- Publishing is automated by [`.github/workflows/publish-npm.yml`](https://github.com/BackofenLab/vaRRI-js/blob/main/.github/workflows/publish-npm.yml).
621
- The initial `varri-js@1.0.0` publication was manual. Before automated releases, an npm package
622
- owner must configure a **GitHub Actions trusted publisher** in the package's npm settings:
623
- organization `BackofenLab`, repository `vaRRI-js`, workflow filename `publish-npm.yml`, no
635
+ Publishing is automated by [`.github/workflows/publish-npm.yml`](https://github.com/BackofenLab/vaRRI/blob/main/.github/workflows/publish-npm.yml).
636
+ Releases continue to update the existing `varri-js` npm package. The npm package name is
637
+ independent of the GitHub repository name; no source files need to be renamed.
638
+ An owner must configure a **GitHub Actions trusted publisher** in the `varri-js` package's npm settings:
639
+ organization `BackofenLab`, repository `vaRRI`, workflow filename `publish-npm.yml`, no
624
640
  environment name, with direct `npm publish` allowed. This one-time account action may request
625
641
  2FA. The workflow uses OIDC and does not require an `NPM_TOKEN` secret or interactive 2FA for
626
642
  each release. See [npm trusted publishing](https://docs.npmjs.com/trusted-publishers/).
643
+ After the GitHub repository rename, update any existing trusted publisher that still names
644
+ the old repository to `vaRRI`. The repository name is case-sensitive.
627
645
 
628
646
  Merge the workflow changes before creating a release tag on a commit containing them.
629
647
  Every published GitHub release runs the tests, derives the npm version from the release tag,
package/citation.html CHANGED
@@ -3,7 +3,7 @@
3
3
  <head>
4
4
  <meta charset="utf-8" />
5
5
  <meta name="viewport" content="width=device-width, initial-scale=1" />
6
- <title>Citation — vaRRI-js</title>
6
+ <title>Citation — vaRRI</title>
7
7
  <link rel="icon" type="image/png" href="logo/vaRRI.logo.40x40.png">
8
8
 
9
9
  <!-- External Stylesheets (matching index.html) -->
@@ -79,9 +79,9 @@
79
79
  <a class="group-logo-link" href="https://www.bioinf.uni-freiburg.de" target="_blank" rel="noopener noreferrer" aria-label="Visit the Bioinformatics Group Freiburg website">
80
80
  <img class="group-logo" src="https://www.bioinf.uni-freiburg.de/assets/images/bioinf-fr-logo-blau.png" alt="Bioinformatics Group Freiburg logo" />
81
81
  </a>
82
- <img class="varri-logo" src="logo/vaRRI.logo.200x200.png" alt="vaRRI-js logo">
82
+ <img class="varri-logo" src="logo/vaRRI.logo.200x200.png" alt="vaRRI logo">
83
83
  <div class="header-title">
84
- <h1>vaRRI-js</h1>
84
+ <h1>vaRRI</h1>
85
85
  <p>Visual Annotation of RNA–RNA Interactions</p>
86
86
  </div>
87
87
  <div class="uni-logo-wrap">
@@ -142,14 +142,14 @@
142
142
  </p>
143
143
  <p>
144
144
  The source code for this service is freely available on
145
- <a href="https://github.com/BackofenLab/vaRRI-js" target="_blank" rel="noopener noreferrer">GitHub</a>.
145
+ <a href="https://github.com/BackofenLab/vaRRI" target="_blank" rel="noopener noreferrer">GitHub</a>.
146
146
  </p>
147
147
  </div>
148
148
  </footer>
149
149
 
150
150
  <!-- JavaScript Logik -->
151
151
  <script>
152
- const GITHUB_RAW_BASE = 'https://raw.githubusercontent.com/BackofenLab/vaRRI-js/main/';
152
+ const GITHUB_RAW_BASE = 'https://raw.githubusercontent.com/BackofenLab/vaRRI/main/';
153
153
 
154
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  const TABS_CONFIG = {
155
155
  bibtex: { label: 'BibTeX', filename: 'CITATION.bib', mime: 'text/plain', source: 'CITATION.bib', type: 'raw' },
Binary file
@@ -1,12 +1,12 @@
1
1
  # "Free trailing ends" feature — documentation
2
2
 
3
- This document describes the "Free trailing ends" feature of vaRRI-js: what it
3
+ This document describes the "Free trailing ends" feature of vaRRI: what it
4
4
  does, the relevant parts of Fornac's internal force-layout architecture it
5
5
  depends on, and the exact steps taken to implement it.
6
6
 
7
7
  ## 1. What the feature does
8
8
 
9
- vaRRI-js renders RNA/RNA-RNA-interaction structures using
9
+ vaRRI renders RNA/RNA-RNA-interaction structures using
10
10
  [Fornac](https://github.com/ViennaRNA/fornac)'s force-directed layout
11
11
  (`options.forceLayout = true`, i.e. the "Enable Fornac force-layout animation"
12
12
  checkbox). Fornac's layout algorithm pulls every *loop* of the structure
@@ -20,7 +20,7 @@ the two free/dangling ends of the sequence(s) toward each other into a closed
20
20
  ring — even though these ends have no real base-pairing there.
21
21
 
22
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  When the **"Free trailing ends"** checkbox is enabled (only selectable while
23
- "Enable Fornac force-layout animation" is also enabled), vaRRI-js removes this
23
+ "Enable Fornac force-layout animation" is also enabled), vaRRI removes this
24
24
  artificial circularisation from the force simulation:
25
25
 
26
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  - The two sequence ends are released from being pulled together.
package/example-data.js CHANGED
@@ -114,7 +114,7 @@
114
114
  name: 'RNA–RNA interaction feature overview',
115
115
  nameShort: 'All feature showcase',
116
116
  description: 'Demonstrates cropping, probability profiles, region and subsequence highlights, and point mutations in one interaction.',
117
- descriptionShort: 'Showcases all features of vaRRI-js.',
117
+ descriptionShort: 'Showcases all features of vaRRI.',
118
118
  vaRRIParams: {
119
119
  sequence: 'ACGAUCAUGUGGUUUAGAGCAUUUUCGACAGCAG&ACGAAAAAAAGAGCAGACAGUAG',
120
120
  structure: '..<<..<<...>>>>...((....(((...((..&............)))))..))..',
package/index.html CHANGED
@@ -3,7 +3,7 @@
3
3
  <head>
4
4
  <meta charset="utf-8">
5
5
  <meta name="viewport" content="width=device-width, initial-scale=1">
6
- <title>vaRRI-js — Visual Annotation of RNA-RNA Interactions</title>
6
+ <title>vaRRI — Visual Annotation of RNA-RNA Interactions</title>
7
7
  <link rel="icon" type="image/png" href="logo/vaRRI.logo.40x40.png">
8
8
 
9
9
  <!-- Fornac dependencies -->
@@ -18,7 +18,7 @@
18
18
  <!-- Marked synchron laden -->
19
19
  <script src="https://cdn.jsdelivr.net/npm/marked/marked.min.js"></script>
20
20
 
21
- <!-- vaRRI-js UI -->
21
+ <!-- vaRRI UI -->
22
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  <script src="example-data.js" defer></script>
23
23
  <script src="index.js" defer></script>
24
24
  </head>
@@ -28,9 +28,9 @@
28
28
  <a class="group-logo-link" href="https://www.bioinf.uni-freiburg.de" target="_blank" rel="noopener noreferrer" aria-label="Visit the Bioinformatics Group Freiburg website">
29
29
  <img class="group-logo" src="https://www.bioinf.uni-freiburg.de/assets/images/bioinf-fr-logo-blau.png" alt="Bioinformatics Group Freiburg logo">
30
30
  </a>
31
- <img class="varri-logo" src="logo/vaRRI.logo.200x200.png" alt="vaRRI-js logo">
31
+ <img class="varri-logo" src="logo/vaRRI.logo.200x200.png" alt="vaRRI logo">
32
32
  <div class="header-title">
33
- <h1>vaRRI-js</h1>
33
+ <h1>vaRRI</h1>
34
34
  <p>Visual Annotation of RNA–RNA Interactions</p>
35
35
  </div>
36
36
  <div class="uni-logo-wrap">
@@ -368,10 +368,10 @@
368
368
  <button id="exportSvgBtn" class="btn btn-success btn-sm" type="button" title="Download rendering in SVG format.">⬇ SVG</button>
369
369
  <button id="exportPngBtn" class="btn btn-info btn-sm" type="button" title="Download rendering in PNG format.">⬇ PNG</button>
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  <button id="shareLinkBtn" class="btn btn-shareLink btn-sm" type="button" title="Copy shareable link to clipboard">🔗 Share</button>
371
- <button id="openVarriBtn" class="btn btn-openVarri btn-sm" type="button" title="Show this in a new vaRRI-js browser window">Full Page</button>
371
+ <button id="openVarriBtn" class="btn btn-openVarri btn-sm" type="button" title="Show this in a new vaRRI browser window">Full Page</button>
372
372
  <!-- right-aligned note to cite varri-->
373
373
  <span class="cite-note">Please
374
- <a href="citation.html" class="btn btn-cite btn-sm">🔖 cite vaRRI-js</a></span>
374
+ <a href="citation.html" class="btn btn-cite btn-sm">🔖 cite vaRRI</a></span>
375
375
  </div>
376
376
 
377
377
  </section>
@@ -387,7 +387,7 @@
387
387
  </p>
388
388
  <p>
389
389
  The source code for this service is freely available on
390
- <a href="https://github.com/BackofenLab/vaRRI-js" target="_blank" rel="noopener noreferrer">GitHub</a>.
390
+ <a href="https://github.com/BackofenLab/vaRRI" target="_blank" rel="noopener noreferrer">GitHub</a>.
391
391
  </p>
392
392
  </div>
393
393
  </footer>
@@ -14,7 +14,7 @@
14
14
  id="svg871"
15
15
  sodipodi:docname="vaRRI.logo.svg"
16
16
  inkscape:version="1.0.2 (e86c870879, 2021-01-15)"
17
- inkscape:export-filename="C:\Research\vaRRI-js\logo\vaRRI.logo.40x40.png"
17
+ inkscape:export-filename="vaRRI.logo.40x40.png"
18
18
  inkscape:export-xdpi="19.200001"
19
19
  inkscape:export-ydpi="19.200001">
20
20
  <metadata
@@ -38,8 +38,8 @@
38
38
  guidetolerance="10"
39
39
  inkscape:pageopacity="0"
40
40
  inkscape:pageshadow="2"
41
- inkscape:window-width="1812"
42
- inkscape:window-height="1057"
41
+ inkscape:window-width="2452"
42
+ inkscape:window-height="1417"
43
43
  id="namedview873"
44
44
  showgrid="false"
45
45
  showguides="true"
@@ -128,17 +128,25 @@
128
128
  style="fill:#4d4d4d;stroke-width:0.868952"
129
129
  inkscape:export-xdpi="96"
130
130
  inkscape:export-ydpi="96">
131
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132
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133
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131
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132
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135
133
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136
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- <text
138
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141
143
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150
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143
151
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144
152
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package/package.json CHANGED
@@ -1,16 +1,16 @@
1
1
  {
2
2
  "name": "varri-js",
3
- "version": "1.0.1",
3
+ "version": "1.0.2",
4
4
  "description": "Browser viewer and JavaScript library for visualising and annotating RNA-RNA interactions",
5
5
  "license": "MIT",
6
6
  "author": "Bioinformatics Group, University of Freiburg",
7
- "homepage": "https://backofenlab.github.io/vaRRI-js/",
7
+ "homepage": "https://backofenlab.github.io/vaRRI/",
8
8
  "repository": {
9
9
  "type": "git",
10
- "url": "git+https://github.com/BackofenLab/vaRRI-js.git"
10
+ "url": "git+https://github.com/BackofenLab/vaRRI.git"
11
11
  },
12
12
  "bugs": {
13
- "url": "https://github.com/BackofenLab/vaRRI-js/issues"
13
+ "url": "https://github.com/BackofenLab/vaRRI/issues"
14
14
  },
15
15
  "keywords": [
16
16
  "bioinformatics",
package/src/README.md CHANGED
@@ -1,4 +1,4 @@
1
- # vaRRI-js JavaScript API
1
+ # vaRRI JavaScript API
2
2
 
3
3
  `src/vaRRI.js` exposes one global object, `window.vaRRI`. In CommonJS test
4
4
  code, `require('./src/vaRRI.js')` returns the same object.
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