Welcome to JABAWS’s documentation!

Read on these documentation pages or go back to the JABAWS homepage!

JABAWS documentation is also available in pdf. Download it here!

Contents:

• Getting Started
  • JABAWS Benefits
  • JABAWS Distributions
    • Jalview and the JABAWS Public Server
    • Command Line Client (CLI)
    • Web Application aRchive (WAR)
    • Virtual Appliance (VA)
• Included Tools
  • Multiple Sequence Alignment
  • Protein Disorder Prediction
  • Amino Acid Conservation
  • RNA Secondary Structure
• Command Line Client (CLI)
  • Installing
  • Usage
  • Example Usage
• Web Application Archive (WAR)
  • Installing
  • Usage
  • Troubleshooting
• Virtual Appliance (VA)
  • Installing
  • Usage
  • Configuration
    • VM configuration
    • JABAWS configuration
• Advanced Usage
  • Valid WSDL
  • JABAWS Configuration
    • Local Engine Configuration
    • Cluster Engine Configuration
    • Executable Configuration
    • Defining Environment Variables for Executables
    • Configure JABAWS to Work with Mafft
    • Limiting the size of the job accepted by JABAWS
    • Pre-compiled binaries
    • Recompiling binaries for your system
    • Obtaining or reusing binaries
  • Load balancing
  • Testing the JABAWS Server
  • JABAWS internal logging
    • JABAWS requests logging
  • JABAWS and Google Analytics
  • JABAWS War File Content
• For Developers
  • Source Code
  • The API
  • Structure of the project
  • The code structure
  • Unit Testing
  • Accessing JABAWS from your program
    • Web services functions overview
    • Structure of the template command line client
    • Connecting to JABAWS
    • Aligning Sequences
    • Checking the status of the calculation
    • Aligning with presets
    • Aligning with custom parameters
    • Writing alignments to a file
    • A complete client example
  • Adding new web-services
    • Brief Guide
    • Building web services artifacts
    • Preparing Distributives
• Usage Statistics
  • Detailed View
  • Job List
  • Job Directory Contents
  • Configuring JABAWS execution statistics
  • Configuring a privileged access for Tomcat web application server
• Citations
• Changelog
  • Version 2.2 (Released 12 April 2017)
  • Version 2.1 (Released 1st Oct 2013)
  • Version 2.0.1 (Released 2nd Jul 2013)
  • Version 2 (Released 16th Dec 2011)

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Note

This is an open source project. If you want to contribute or report an issue have a look at our Git-tracker.