Clean build of BatMass fails with three errors

[etrh]

I want to read CEF files using BatMass and as I understand, this functionality is not provided by default in BatMass. So I am going through this tutorial in order to be able to add the umich.ms.batmass.filesupport.files.types.agilent.cef.data module to BatMass in this way.

While going through this tutorial, I get stuck in the very last step, i.e. clean build BatMass. Clean build of MSFTBX, BatMassLibs, and BatMassExternalSuite are all successful, but when I try to Clean and Build BatMass, I get 3 errors:

Desktop\batmass-projects\batmass-master\FileSupport\src\umich\ms\batmass\filesupport\files\types\mzml\MzMLLCMSDataProvider.java:42: error: cannot access AbstractFile LCMSData lcmsData = new LCMSData(lcmsDataSource, scans); class file for umich.ms.util.file.AbstractFile not found

Desktop\batmass-projects\batmass-master\FileSupport\src\umich\ms\batmass\filesupport\files\types\pepxml\data\PepxmlFeature.java:53: error: incompatible types: possible lossy conversion from double to float float dm = Math.abs(sh.getMassdiff());

Desktop\batmass-projects\batmass-master\FileSupport\src\umich\ms\batmass\filesupport\files\types\pepxml\providers\PepxmlFeaturesDataSource.java:54: error: incompatible types: Double cannot be converted to Float Float rt = sum.getSpectrumQuery().get(0).getRetentionTimeSec();

Windows 10 NetBeans IDE 8.2 Java Version 8 Update 172 (build 1.8.0_172-b11) jdk1.8.0_172 jre1.8.0_172

[chhh]

@etrh Sorry, was away, didn't see your post.

Are you looking for a library to read CEF files? Or you want to visualize them with batmass? By default IIRC you can right click the "Features" folder in the project explorer and it should be able to pull in CEF files.

Those errors crop up because of recent updates to MSFTBX, I'll fix the build.

[etrh]

Thank you for getting back to me.

Yes. I want to read CEF files. I do not want to visualize them. I only want to see them in human-readable format.

I just tried the default BatMass installation and indeed I could load CEF files as "Features". But when I choose any CEF file to be loaded, nothing happens, I just see a new tab open up and a loading circle moving forever. Any idea what is happening?

[chhh]

@etrh Not yet, I've only dealt with CEF files once several years ago and thats when I wrote support for it. Would you mind sharing a sample file that doesn't want to open for you, then I can quickly debug and fix. Maybe they've changed the format since then, maybe there's something in the files that was not anticipated back then etc.

[etrh]

Thanks for devoting your time to this. I just sent you two CEF files by email.

[chhh]

Thanks, I'm finally back home from ASMS, so will take a look

[chhh]

Ok, I think I know what the problem is - your CEF files don't have "RTRanges" tags for compounds. When the original version was written I've only seen files with those tags, so I thought they were mandatory. I'll try to update it to use a single RT value for the whole compound. I've fixed the other build errors.

[chhh]

@etrh Ok, everything has been updated, you can start batmass and you'll get the prompt to auto-update several modules. CEF support is most likely not exactly what you're expecting, but it works and navigation when the list of features is synced to 2d view also works.