diff --git a/docs/wiki-Home.md b/docs/wiki-Home.md index 7568f4b7..a08ba8ad 100644 --- a/docs/wiki-Home.md +++ b/docs/wiki-Home.md @@ -1,201 +1,106 @@ -Welcome to the DNAnalyzer wiki! +# Welcome to the DNAnalyzer Wiki! ![](https://user-images.githubusercontent.com/96280466/186224441-46dd2029-b9dc-4b3d-aad8-bfd1e1e62f2e.png) -> DNAnalyzer identifies proteins, amino acids, start and stop codons, high coverage regions, regions susceptible to -> neurodevelopmental disorders, transcription factors, and regulatory elements. Researchers are working to extract -> valuable information from such software to better understand human health and disease. Currently, we are working on -> developing a Command-Line-Interface (CLI) and Graphical User Interface (GUI) that will enable physicians to quickly and -> more easily interact with the software, enabling them to identify genetic mutations that may cause disease. +> DNAnalyzer identifies proteins, amino acids, start and stop codons, high coverage regions, and regulatory elements. +> Researchers are working to extract valuable information to better understand human health and disease. +> Currently, we are developing a Command-Line Interface (CLI) and a Graphical User Interface (GUI) to enable physicians +> to quickly identify genetic mutations. -# [Documents](https://github.com/VerisimilitudeX/DNAnalyzer/tree/main/docs) +## Documents +[View Documents](https://github.com/VerisimilitudeX/DNAnalyzer/tree/main/docs) ## Contributing ### Steps to follow 📜 -#### 1. Fork it 🍴 - -You can get your own fork (copy) of [DNAnalyzer](https://github.com/VerisimilitudeX/DNAnalyzer) by using the `Fork` -button at the top right of this page. - -![Fork Button](https://github-images.s3.amazonaws.com/help/bootcamp/Bootcamp-Fork.png) - -#### 2. Clone it 👥 - -You must move to your fork of the repository and clone (download) it to your local machine using - -`$ git clone https://github.com/Your_Username/DNAnalyzer.git` - -This creates a local copy of the repository on your machine. - -After cloning the `DNAnalyzer` repository on GitHub, use the change directory command on Linux and Mac to go to that -folder. - -```python -# This will change directory to a folder DNAnalyzer -$ cd -DNAnalyzer -``` - -Move to this folder for all other commands. - -Let us now add a reference to the original 'DNAnalyzer' repository using: - -`$ git remote add upstream https://github.com/theabhishek07/DNAnalyzer.git` - -This adds a new remote named **_upstream_**. - -Examine the modifications using: - -```git - $ git remote -v - origin https://github.com/Your_Username/DNAnalyzer.git (fetch) - origin https://github.com/Your_Username/DNAnalyzer.git (push) - upstream https://github.com/theabhishek07/DNAnalyzer.git (fetch) - upstream https://github.com/theabhishek07/DNAnalyzer.git (push) - ``` - -#### 3. Sync with the Remote 🔄 - -Remember to keep your local repository up to date with the remote repository. - -```python -# Fetch all remote repositories and delete any deleted remote branches -$ git -fetch - -all - -prune -# Switch to main branch -$ git -checkout -main -# Reset local main branch to match upstream repository's main branch -$ git -reset - -hard -upstream / main -# Push changes to your forked DNAnalyzer repo -$ git -push -origin -main -``` - -#### 4. Create a new branch - -Whenever you want to make a contribution, use the following command to establish a new branch and keep your `main` -branch uncluttered (i.e. synced with remote branch). - -```python -# It will create a new branch with name and switch to branch -$ git -checkout - b < branchname > -``` - -To switch to desired branch - -```python -# To switch from one folder to other -$ git -checkout < branchname > -``` - -To add the changes to the branch. Use - -```python -# To add all files to branch -$ git -add. -``` - -Type in a message relevant for the code reviewer using - -```python -# This message get associated with all files you have changed -$ git -commit - m -"relevant message" -``` - -Now, Push your awesome work to your remote repository using - -```python -# To push your work to your remote repository -$ git -push - u -origin < branchname > -``` - -Finally, in your browser, navigate to your repository and click `Contribute` amd then `Open Pull Request`. There, please -provide a title and description, with brevity, that describe your much-appreciated effort. - -## Contribution Guideline - -- Drop a :star: on the GitHub repository (It's optional)
- -- Before Contribute Please - read `Contributing_Guidelines.md` - and `CODE_OF_CONDUCT.md` - -- Create an issue of the project or a feature you would like to add in the project and get the task assigned for - yourself.(Issue can be any bug fixes or any feature you want to add in this project). - -- Fork the repo to your Github.
- -- Clone the Repo by going to your local Git Client in a particular local folder in your local machine by using this - command with your forked repository link in place of below given link:
- `git clone https://github.com/VerisimilitudeX/DNAnalyzer` -- Create a branch using below command. - `git branch ` -- Checkout to your branch. - `git checkout ` -- Add your code in your local machine folder. - `git add . ` -- Commit your changes. - `git commit -m""` -- Push your changes. - `git push --set-upstream origin ` - -- Make a pull request! (compare your branch with the owner main branch) +1. **Fork it 🍴** + Get your own fork of [DNAnalyzer](https://github.com/VerisimilitudeX/DNAnalyzer) by using the `Fork` button at the top right of this page. + ![](https://github-images.s3.amazonaws.com/help/bootcamp/Bootcamp-Fork.png) + +2. **Clone it 👥** + Clone your fork to your local machine: + ```bash + git clone https://github.com/Your_Username/DNAnalyzer.git + cd DNAnalyzer + ``` + Then, add a reference to the original repository: + ```bash + git remote add upstream https://github.com/theabhishek07/DNAnalyzer.git + git remote -v + ``` + +3. **Sync with the Remote 🔄** + Keep your local repository up-to-date: + ```bash + git fetch --all --prune + git checkout main + git reset --hard upstream/main + git push origin main + ``` + +4. **Create a new branch** + Create a new branch for your contribution: + ```bash + git checkout -b + ``` + To switch branches later: + ```bash + git checkout + ``` + Add changes and commit: + ```bash + git add . + git commit -m "your commit message" + ``` + Push your branch: + ```bash + git push -u origin + ``` + Finally, in your browser, navigate to your repository, click **Contribute**, and then **Open Pull Request**. Provide a concise title and description describing your contribution. + +### Contribution Guideline + +- ⭐ Drop a star on the GitHub repository (optional). +- Before contributing, please read [`Contributing_Guidelines.md`](Contributing_Guidelines.md) and [`CODE_OF_CONDUCT.md`](CODE_OF_CONDUCT.md). +- Create an issue or propose a feature/bug fix. +- Fork the repo, clone it, create a branch, add your changes, commit, and push. +- Make a pull request comparing your branch with the main branch of the repository. ## Usage -#### Command-Line Interface (CLI) Usage - -DNAnalyzer uses CLI arguments instead of `stdin`. For example, you can do: +### Command-Line Interface (CLI) Usage -``` +DNAnalyzer uses CLI arguments instead of standard input. For example: +```bash assets/dna/random/dnalong.fa --amino=ser ``` - or - -``` +```bash assets/dna/random/dnalong.fa --amino=ser --min=0 --max=100 ``` - -Help message (--help): - +To view the help message: +```bash + --help + +# Output: +Usage: DNAnalyzer [-hrV] --amino= [--find=] [--max=] [--min=] DNA + DNA The FASTA file to be analyzed. + --amino= The amino acid representing the start of a gene. + --find= The DNA sequence to be found. + -h, --help Show this help message and exit. + --max= Maximum count of the reading frame. + --min= Minimum count of the reading frame. + -r, --reverse Reverse the DNA sequence before processing. + -V, --version Print version information and exit. ``` -Usage: DNAnalyzer [-hrV] --amino= [--find=] - [--max=] [--min=] DNA -A program to analyze DNA sequences. - DNA The FASTA file to be analyzed. - --amino= The amino acid representing the start of a gene. - --find= The DNA sequence to be found within the FASTA file. - -h, --help Show this help message and exit. - --max= The maximum count of the reading frame. - --min= The minimum count of the reading frame. - -r, --reverse Reverse the DNA sequence before processing. - -V, --version Print version information and exit. - ``` ## Reports -[Key Personnel and Knowledge Distribution](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/key-personnel-and-and-knowledge-distribution.pdf) - -[Technical Health Overview](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/technical-health-overview.pdf) - -[Trend Report](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/trend-report.pdf) +- [Key Personnel and Knowledge Distribution](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/key-personnel-and-and-knowledge-distribution.pdf) +- [Technical Health Overview](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/technical-health-overview.pdf) +- [Trend Report](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/trend-report.pdf) ## Samples -[Serine DNAlong](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/samples/serine-dnalong.md) \ No newline at end of file +- [Serine DNAlong](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/samples/serine-dnalong.md) \ No newline at end of file diff --git a/web/docs/docs.css b/web/docs/docs.css index 1fbc1021..f75c3690 100644 --- a/web/docs/docs.css +++ b/web/docs/docs.css @@ -1,9 +1,27 @@ +html { + scroll-behavior: smooth; +} + /* Documentation Layout */ .container { + max-width: 1200px; + margin: 80px auto 0; + padding: 2rem; + width: 100%; +} + +/* Docs Container Layout */ +.docs-container { display: grid; - grid-template-columns: 280px 1fr; + grid-template-columns: 250px minmax(0, 1fr); gap: 2rem; - padding-top: 2rem; + width: 100%; + max-width: 100%; +} + +/* Adjust main container margin to offset the fixed header */ +main.container { + margin-top: 80px; } /* Sidebar */ @@ -13,9 +31,11 @@ border: 1px solid rgba(255, 255, 255, 0.1); padding: 2rem; position: sticky; - top: 6rem; - height: calc(100vh - 8rem); + top: 80px; /* Match the header height */ + align-self: start; + height: calc(100vh - 100px); overflow-y: auto; + -webkit-overflow-scrolling: touch; } .docs-sidebar::-webkit-scrollbar { @@ -83,7 +103,14 @@ /* Search */ .search-container { - margin-bottom: 2rem; + position: sticky; + top: 0; + background: rgba(0, 0, 0, 0.2); + padding: 1rem; + margin: -2rem -2rem 1rem -2rem; + border-bottom: 1px solid rgba(255, 255, 255, 0.1); + backdrop-filter: blur(10px); + z-index: 10; } .search-input { @@ -108,13 +135,17 @@ background: rgba(0, 0, 0, 0.2); border-radius: 12px; border: 1px solid rgba(255, 255, 255, 0.1); - padding: 2rem; + padding: 3rem; min-height: calc(100vh - 8rem); + width: 100%; + margin: 0; } .content-section { margin-bottom: 4rem; - scroll-margin-top: 6rem; + max-width: 800px; + margin-left: auto; + margin-right: auto; } .content-section:last-child { @@ -123,8 +154,9 @@ .content-section h2 { font-size: 2.5rem; - margin-bottom: 2rem; + margin-bottom: 1.5rem; color: var(--gradient-end); + text-align: left; } .content-section h3 { @@ -265,7 +297,12 @@ mark { /* Responsive Design */ @media screen and (max-width: 1024px) { .container { + padding: 2rem; + } + + .docs-container { grid-template-columns: 1fr; + gap: 2rem; } .docs-sidebar { @@ -277,9 +314,31 @@ mark { .content-section { scroll-margin-top: 2rem; } + + .docs-content { + max-width: 100%; + } } @media screen and (max-width: 768px) { + .container { + margin-top: 120px; + padding: 1rem; + } + + .search-container { + margin: -1rem -1rem 1rem -1rem; + padding: 0.75rem; + } + + .docs-content { + padding: 1.5rem; + } + + .content-section { + margin-bottom: 2rem; + } + .docs-content { padding: 1.5rem; } @@ -296,4 +355,18 @@ mark { display: block; overflow-x: auto; } + + .docs-container { + display: block; + } + .docs-sidebar { + position: relative; + height: auto; + width: 100%; + margin-bottom: 1rem; + } + .docs-content { + width: 100%; + padding: 1rem; + } } \ No newline at end of file diff --git a/web/docs/docs.html b/web/docs/docs.html index 4ae955a1..4023d52d 100644 --- a/web/docs/docs.html +++ b/web/docs/docs.html @@ -20,6 +20,9 @@ + About Features Analyzer @@ -267,6 +270,11 @@

Development Setup

+ \ No newline at end of file diff --git a/web/index.js b/web/index.js index 4ee64956..c002f286 100644 --- a/web/index.js +++ b/web/index.js @@ -181,4 +181,21 @@ document.addEventListener('DOMContentLoaded', function() { } }); }); + + // Menu toggle functionality + const menuToggle = document.querySelector('.menu-toggle'); + const nav = document.querySelector('.floating-nav'); + + if (menuToggle) { + menuToggle.addEventListener('click', function() { + nav.classList.toggle('responsive'); + }); + } + + // Close menu when clicking outside + document.addEventListener('click', function(e) { + if (!nav.contains(e.target) && nav.classList.contains('responsive')) { + nav.classList.remove('responsive'); + } + }); }); \ No newline at end of file diff --git a/web/style.css b/web/style.css index 0988849c..29038ccc 100644 --- a/web/style.css +++ b/web/style.css @@ -786,6 +786,87 @@ body { grid-template-columns: repeat(2, 1fr); gap: 2rem; } + + /* Improve navbar for mobile view */ + .floating-nav { + flex-direction: column; + align-items: center; + gap: 0.5rem; + padding: 0.5rem; + height: auto; + } + .nav-link { + width: 100%; + text-align: center; + padding: 1rem 0; + border-top: 1px solid rgba(255, 255, 255, 0.1); + margin: 0; + } + .nav-link:first-child { + border-top: none; + } + .right-links { + width: 100%; + flex-direction: column; + margin-top: 1rem; + gap: 0.5rem; + } + + .floating-header { + position: fixed; + height: auto; + } + + .floating-nav { + flex-wrap: wrap; + justify-content: space-between; + padding: 0.75rem; + } + + .nav-logo { + margin-right: auto; + } + + .nav-link:not(:first-child) { + display: none; + } + + .right-links { + display: none; + } + + .floating-nav.responsive .nav-link:not(:first-child), + .floating-nav.responsive .right-links { + display: flex; + width: 100%; + padding: 0.75rem; + border-top: 1px solid rgba(255, 255, 255, 0.1); + } + + .floating-nav.responsive { + flex-direction: column; + } + + .floating-nav.responsive .right-links { + flex-direction: column; + gap: 0.5rem; + } + + .menu-toggle { + display: block; + background: none; + border: none; + color: var(--text-color); + font-size: 1.5rem; + cursor: pointer; + padding: 0.5rem; + } +} + +@media screen and (min-width: 769px) { + .menu-toggle { + display: none; + } } @media screen and (max-width: 480px) { @@ -806,3 +887,10 @@ body { width: 100%; } } + +.hero-text h1, .stat-number, .cta-container h2, .security-content h2, .content-wrapper h2 { + background: linear-gradient(45deg, var(--gradient-start), var(--gradient-end)); + background-clip: text; + -webkit-background-clip: text; + -webkit-text-fill-color: transparent; +}