Developer Guide

Developer Guide

This page summarizes the current project structure and points developers to the detailed Wiki pages.

Developer pages

• Architecture
• Runtime Layout
• Build System
• Release Pipeline
• Contributing
• Publishing to GitHub Wiki

Requirements

• Java 26
• Maven wrapper included in the repository
• Git
• Platform runtime assets for release packaging

Build

./mvnw clean package

The packaged JAR is created under target/.

Run CLI from source build

java -jar target/insilicoPCR.jar -h

Main entry points

Area	Entry point
Dispatcher	ca.canada.inspection.dispatchpcr.Dispatcher
GUI	ca.canada.inspection.insilicopcr.MainRun
CLI	ca.canada.inspection.commandpcr.CommandMain
Pipeline	ca.canada.inspection.pipeline.InSilicoPcrPipeline

The dispatcher starts the GUI when no arguments are provided and starts the CLI pipeline when command-line arguments are present.

Documentation approach

Keep the README compact. Use the GitHub Wiki as the user-facing manual.

The docs/wiki/ directory is a source-controlled mirror that can be pushed into the actual GitHub Wiki repository after the Wiki has been initialized.

When adding a feature, update:

• README only if the feature changes the project overview or quick start
• relevant Wiki page for full details
• SVG diagrams under docs/assets/ if the architecture, workflow, or release process changes
• screenshots under docs/screenshots/ when available

Notes for future improvements

Potential future work:

• add tests for primer FASTA validation
• enforce the standard PCR vs qPCR mode limitation earlier in the run
• improve synthetic gel export options
• add screenshots to the README and Wiki
• publish docs/wiki/ pages into the GitHub Wiki after initialization