Re: [chemclipse-dev] NPE in reading mzXML file

[Trig Chen <trigchen@xxxxxxxxx>]

There might be a problem in line 91 of org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.io.ReaderVersion20.java: 

ByteBuffer byteBuffer = ByteBuffer.wrap(peaks.getValue());

The peaks of mz-intensity pairs are encoded in Base64 and stored in mzXML, so restoring the peaks should decode it firstly.

There is an sample mzXML 2.1 file "Chromatogram1.mzXML" in OpenChrom's sample data package, OpenChrom can open it properly. I checked the org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.io.ReaderVersion21.java, the line 90 is the same: 

ByteBuffer byteBuffer = ByteBuffer.wrap(peaks.getValue());

It seems strange.

Best regards,

Trig

2016-12-08 17:55 GMT+08:00 Philip Wenig <philip.wenig@xxxxxxxxxxxxx>:

Hi Trig,

feel free to fix it.


Best,
Philip

Am 08.12.2016 um 10:54 schrieb Trig Chen:

In the definition of mzXML, the retentionTime of scan element is optional, if retentionTime is omitted, an NPE will throw in line 84 in org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.io.ReaderVersion20.java. 

Best regards,

Trig

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