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

[Alexander Kerner <alexander.kerner@xxxxxxxxxxxxx>]

Hi,

please be aware that the maximum number for Float is -Float.MAX_VALUE and for Double is -Double.MAX_VALUE.

http://stackoverflow.com/questions/7071457/maximum-value-for-float-in-java

Best,

Alex

~~~~~~~~~~~~~~~~~~~~~~~~
OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Alexander Kerner » Software developer » alexander.kerner@xxxxxxxxxxxxx » http://www.openchrom.net
~~~~~~~~~~~~~~~~~~~~~~~~

On 12/09/2016 04:19 AM, Trig Chen wrote:

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@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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OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Philip Wenig » Founder » philip.wenig@xxxxxxxxxxxxx » http://www.openchrom.net
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