How can I get the output of a pipeline built in java as an XMI file similar
to how piper files output extracted annotation information in form of XMI
files? Eg. I have the code

AggregateBuilder builder = new AggregateBuilder();
builder.add( ClinicalPipelineFactory.getDefaultPipeline() );
SimplePipeline.runPipeline( jcas, builder.createAggregateDescription() );

But how do I get all of the annotation info in XMI form from the jcas after
this (like what gets generated in outputDirectory when doing
bin/*runClinicalPipeline * -i *inputDirectory*  --xmiOut *outputDirectory*
--user *umlsUsername*  --pass *umlsPassword*
)? Also, what class can be used to read existing XMI output files?
Thank you.

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