About MSDK
Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing mass spectrometry data. The goals of the library are to provide a flexible data model with Java interfaces for mass-spectrometry related objects (including raw spectra, processed data sets, identification results etc.) and to integrate the existing algorithms that are currently scattered around various Java-based graphical tools.
Java version
MSDK requires Java runtime (JRE) version 8 or newer.
Usage
API
Please see the complete MSDK API.
Maven artifacts
MSDK jars are automatically deployed to Maven Central. In order to use MSDK, simply add the following dependency to your pom.xml:
<dependency>
<groupId>io.github.msdk</groupId>
<artifactId>msdk-all</artifactId>
<version>0.0.27</version>
</dependency>
Development
Tutorial
Please read our brief tutorial on how to contribute new code to MSDK.
Code style
- We use the Google Java Style Guide (https://github.com/google/styleguide)
- You can use the
eclipse-java-google-style.xml
file to automatically format your code in the Eclipse IDE - Please write JavaDoc comments as full sentences, starting with a capital letter and ending with a period. Brevity is preferred (e.g., "Calculates standard deviation" instead of "This method calculates and returns a standard deviation of given set of numbers").
Logging
MSDK uses the SLF4J library for logging. This library can forward all logging calls to your favorite logging framework (java.util.logging, Apache log4j, or others). Please see SLF4J documentation for details.
Building
See the BUILD.md file