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

Hi Trig,

each file format converter has to define its own limits. Itcan be adjusted for the mzXML reader if needed. The reason why we have this is that we support various vendor formats. It depends on the format, but sometimes it only allows to store e.g. a mass range of m/z 18 to 2000.

Please setup Gerrit when pushing changes to our Eclipse repos.

Best,
Philip


Am 09.12.2016 4:19 vorm. schrieb Trig Chen <trigchen@xxxxxxxxx>:
IonLimitExceededException：

WARN  io.ReaderVersion20.read (ReaderVersion20.java:134) org.eclipse.chemclipse.msd.model.exceptions.IonLimitExceededException: The value ion: 68780.6893 is out of limit 1.0 - 65535.0

I encounter many data which abundances are zero and m/z values greater than 66000, but there are many files that define  "MIN_ABUNDANCE = Float.MIN_VALUE" and "MAX_Ion = 65535.0d" in OpenChrom.  Are these limitations necessary or not enough? 

Best regards,

Trig

2016-12-09 10:29 GMT+08:00 Trig Chen <trigchen@gmail.com>:
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@openchrom.net>:
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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OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Philip Wenig » Founder » philip.wenig@openchrom.net » http://www.openchrom.net
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