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PRIDE-Utilities / ms-data-core-api

Open-source java library to handle different file format standards for proteomics. Specially ms-data-core-api is good for MetaData representation.
Apache License 2.0
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Using this API in MATLAB #31

Open kaichengub opened 6 years ago

kaichengub commented 6 years ago

Hello, I've been trying to use ms-data-core-api in MATLAB to process mzXML and mzML data but have been unsucessful.

I downloaded the newest version from Github and built it with Maven in Eclipse, goal was set to "assembly:assembly". It seems that log4j was not included in the POM so I added it in the "dependency" section.

MATLAB version is R2017b, running "Java 1.8.0_121-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode".

The issues I encountered are:

  1. When reading a mzML file (MzMLFile_7_compressed.mzML in \test\resources), in MATLAB I imported "java.io.File" and "uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl". When running "MzMLControllerImpl(file)", the error appeared as "java.lang.NoClassDefFoundError: Could not initialize class uk.ac.ebi.jmzml.xml.Constants".

  2. When reading a mzXML file (our own data), after following a similar routine, when running "MzXmlControllerImpl(file)", the error appeared as "java.lang.IllegalStateException: Could not initialize unmarshaller".

Please don't hesitate to ask if you need any more information to help me solve this problem.

I sincerely appreciate your kindly help. Thank you very much!

sureshhewabi commented 6 years ago

Which version of ms-data-core-api used? I don't see any MzMLFile_7_compressed.mzML file in version 2.0.21 which is the latest release. Could you please provide the input files for investigation?