Architecture

Architecture

insilicoPCR uses a shared pipeline behind both the graphical interface and command-line interface.

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 command-line arguments are provided. When CLI arguments are present, it runs the command-line pipeline.

High-level layers

GUI / CLI
   ↓
Dispatcher
   ↓
Shared pipeline
   ↓
Input services, primer service, FASTQ processing, BLAST database building
   ↓
BBMap / BLAST+ runners
   ↓
Parsers and domain model
   ↓
Reports and synthetic gel visualization

Design goals

• Keep GUI and CLI behavior consistent.
• Keep runtime discovery centralized.
• Keep external tool execution isolated from UI code.
• Keep reports and synthetic gel visualization based on structured pipeline output.
• Preserve portable release behavior across Windows and Linux.