Chemical notation peak name tags in 5.2

[Ronald Ouwerkerk]

Some of the starting value files for AMARES I created in ver.5.0 no longer work. This failure was related to the peak name tags I have used in ver5.0. I found that names like “H-C=C-H” will cause the AMARES plugin to not produce output. You can only discover the cause of failure by examining the log file created by java. I examined the file C:\Program Files\jmrui-5.2\log\out.log and found that names with math symbols like ‘-‘, ‘=’ are apparently parsed as variable names containing numbers:
clicked on 999999mrui.quantitation.amares.view.Amares
11-Jun-2015 11:32:35 INFO mrui.quantitation.amares.controler.GUISV actionPerformed The file contained 7 peaks.
11-Jun-2015 11:32:37 INFO mrui.quantitation.amares.controler.GUIPK actionPerformed C:\Documents and Settings\All Users\Documents\MRdata\default.pk
11-Jun-2015 11:32:39 INFO mrui.quantitation.amares.controler.GUIPhase actionPerformed value1=0.0
peakSet.getNbPeak() == 7
Quantifying signal 1 out of 2…
java.lang.NumberFormatException: For input string: “C-H”
at java.lang.NumberFormatException.forInputString(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at java.lang.Integer.valueOf(Unknown Source)
at mrui.quantitation.amares.view.Amares.getHasMapLowerCase(Unknown Source)
at mrui.quantitation.amares.view.Amares.quantifyFid(Unknown Source)
at mrui.plugin.quantitation.QuantitationPlugin.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

• This topic was modified 9 years ago by MRUI webmaster. Reason: Moved to bug reports

Ronald Ouwerkerk
National Institutes of Health (NIH)

[Miquel]

This is clearly a bug. Text fields meant for tags & labels shouldn’t be parsed.

Thanks for reporting it.

Miquel Cabanas, SeRMN
Universitat Autònoma de Barcelona

[Jana]

I will fix the bug as soon as possible. Thanks for reporting. Once I have it fixed I will post a message here with a link on the new patch.

Jana

[Author]

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