Monday, May 23, 2011

If you build it... can finally get started! So my code base is built (kinda--more in a minute) and just in time to get down to real work. But boy was that a challenge. My only error that occurs when I build it is:

The markup in the document following the root element must be well-formed. styles.xml

So not really sure what is going on, but if I comment out line 3 and 4, the code builds. So moving on now....

To kick every thing off, I am going to be expressing CHARSET free text and expressing the row-segment metadata (Genbank accession number) for NeXML. Right now, it only seems to be working for NEXUS. And don't worry...I am working on my directions for setting up the code base as well so more to come.

Okay back to work. Bye bye.

1 comment:

  1. Don't worry about the error - it is complaining about some wonky xml that mesquite uses internally. As you can see, the styles.xml file has two root elements whereas well-formed xml can only have one. If it annoys you, maybe you can turn off the errors emanating out of mesquite, or turn xml validation off (though you might want to keep that turned on just in case you want to check nexml documents you're producing). In any case, nothing to worry about.

    By the way, there will also be many instances of warnings coming out of the code base, but for the most part these are unused java imports, unchecked conversions or non-parameterized generics. Whenever I see these in code I'm working on I'll fix it but there's really no point in trying to tackle all of them. Just ignore.