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msdk-alignment-joinaligner
msdk-alignment-ransac
msdk-all Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-datamodel Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-db-gnps Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-db-kegg
msdk-db-mona
msdk-featuredetection-adap3d
msdk-featuredetection-chromatogrambuilder
msdk-featuredetection-gridmass
msdk-featuredetection-msms
msdk-featuredetection-openms Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-featuredetection-srm Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-featuredetection-targeted Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-id-localdatabase Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-id-metfrag Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-id-sirius Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-io-chromatof
msdk-io-fileimport
msdk-io-filetypedetection
msdk-io-mgf Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-io-msp Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-io-mzdata
msdk-io-mzdb Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-io-mzml Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-io-mztab Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-io-mzxml Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-io-nativeformats Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-io-netcdf Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-io-txt Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-isotopes-isotopegrouper Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-isotopes-isotopepattern
msdk-normalization-stdcompound
msdk-rawdata-baselinecorrection Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-rawdata-filters Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-spectra-centroiding
msdk-spectra-centroidprofiledetection Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-spectra-peakinvestigator Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-spectra-similarity Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018
msdk-spectra-splash
.gitattributes
.gitignore Added code and test data from Maltcms for ChromaTof Import. Added Rul… Jan 7, 2016
.travis.yml
BUILD.md
LICENSE Merged license header with comments into LICENSE. Jan 7, 2016
README.md
eclipse-java-google-style.xml Adopted Google Code Style Apr 24, 2017
nb-configuration.xml Merged license header with comments into LICENSE. Jan 7, 2016
nbactions.xml Updated versions for development to 0.0.5-SNAPSHOT. Jan 24, 2016
pom.xml Updated version number to 0.0.15-SNAPSHOT Jul 19, 2018

README.md

About MSDK

Build Status Maven Central

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 1.8 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>0.0.12</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