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Group: EBI PRIDE Tools

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1. JMzReader Core Library16 usages

uk.ac.ebi.pride.tools » jmzreaderApache

Interfaces for the peak list parsers developed by the PRIDE team.
Last Release on Sep 22, 2015

2. BufferedRandomAccessFile8 usages

uk.ac.ebi.pride.tools » brafApache

This is an optimized version of the RandomAccessFile class as described by Nick Zhang on JavaWorld.com. The article can be found at http://www.javaworld.com/javaworld/javatips/jw-javatip26.html
Last Release on Sep 22, 2015
A tool to validate a XMl file against a provided XML schema (XSD) file.
Last Release on Mar 26, 2012

4. MGF Parser7 usages

uk.ac.ebi.pride.tools » mgf-parserApache

A parser library for Matrix Science's mgf file format.
Last Release on Jul 3, 2016

5. JMzParser Core Library7 usages

uk.ac.ebi.pride.tools » jmzparserApache

Interfaces for the peak list parsers developed by the PRIDE team.
Last Release on Oct 4, 2011
Package to clean up submitted accessions into something that makes sense
Last Release on May 23, 2014

7. Mzxml Parser5 usages

uk.ac.ebi.pride.tools » mzxml-parserApache

A read-only parser library to parse mzXML files. This library was build based on mzXML version 3.2 but should work for any mzXML file version >= 2.0.
Last Release on Sep 22, 2015

8. Buffered Line Reader4 usages

uk.ac.ebi.pride.tools » buffered-line-readerApache

An efficient class to read files line-by-line. Compared to using RandomAccessFile's readLine function this class is 10 fold faster.
Last Release on Oct 6, 2011
Group EBI PRIDE Tools Converter


10. Pkl Parser3 usages

uk.ac.ebi.pride.tools » pkl-parserApache

A parser library for the pkl file format.
Last Release on Sep 22, 2015

11. Mzdata Parser3 usages

uk.ac.ebi.pride.tools » mzdata-parserApache

A read-only library to parse mzData files. This library implements the PeakListParser interface.
Last Release on Sep 22, 2015

12. MS2 Parser3 usages

uk.ac.ebi.pride.tools » ms2-parserApache

A parser library for the .ms2 file format.
Last Release on Sep 22, 2015

13. DTA Parser3 usages

uk.ac.ebi.pride.tools » dta-parserApache

A parser library for dta peak list files. This library supports two options: 1.) A directory containing a single dta file for every spectrum and 2.) a single file containing multiple concatenated dta files (must be sperated by an empty line).
Last Release on Sep 22, 2015

14. APL Peak List File Reader2 usages

uk.ac.ebi.pride.tools » apl-parserApache

This is apl peak list file reader
Last Release on Sep 22, 2015
Protein Details Fetcher
Last Release on Dec 4, 2015

16. MzML Wrapper2 usages

uk.ac.ebi.pride.tools » mzml-wrapperApache

A wrapper class around the jmzml parser library implementing the PeakListParser interface.
Last Release on Jul 17, 2012

17. PRIDE ID Fetcher1 usages

uk.ac.ebi.pride.tools » pride-id-fetcher

Used to fetch ids for new objects in the PRIDE database.
Last Release on Jan 31, 2013

18. PRIDE Wrapper1 usages

uk.ac.ebi.pride.tools » pride-wrapperApache

PRIDE Wrapper
Last Release on Dec 9, 2014

19. PRIDE XML File Dump

uk.ac.ebi.pride.tools » pride-xmldump

This produces the PRIDE XML file dumps for experiments in the PRIDE database.
Last Release on Mar 1, 2012

20. PRIDE Specta Clustering

uk.ac.ebi.pride.tools » pride-spectra-clusteringApache

API to cluster MS/MS spectra developed by the PRIDE team.
Last Release on Jun 15, 2012