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abterrabio / dp-mzml

A java-based streaming parser for mzml files
Apache License 2.0
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When Parsing using MzMLChromatogramStAXParser, the parser only returns the value null #12

Open jlcdaluz opened 2 months ago

jlcdaluz commented 2 months ago

Hello Digital Proteomics team,

I would like to ask about the MzMLChromatogramStAXParser. I am currently trying to parse through Chromatogram tags with the dp-mzml library, however, I keep getting null values whenever I use the MzMLChromatogramStAXParser. I tried implementing the MzMLChromatogramStAXParser using the code below.

image

However, whenever I try to run this code, I only get the following message in my log files:

image

I don't think the issue is caused by the file I am using since it contains chromatogram tags that are being used by the code, as seen in the image below.

image

If there is anything wrong with how I am creating the parser, please let me know. Your help would be greatly appreciated. Thank you, and I look forward to your response.

l337x911 commented 2 months ago

It looks like you are calling everything correctly. Are you able to share your mzML file?

There is a unit test com.digitalproteomics.oss.parsers.mzml.MzMLChromatogramStAXParserTest that shows the chromatogram parsing is working with small.pviz.1.1.mzML, which is found in the src/main/resources directory. The chromatogram list is similar, as shown here: image