Categorical data enhancements#5

Merged

rvosa merged 8 commits intonexml:masterfrom

balhoff:categorical-data-enhancements

Sep 1, 2012

Commits on May 22, 2012

Added parsing of input matrix cells. Values seem to have been ignored previously.
balhoff
committed

Commits on Aug 21, 2012

Commits on Aug 27, 2012

Completed updates to output for categorical data.
balhoff
committed

Commits on Aug 31, 2012

Fixed reading of character state labels for categorical data.
balhoff
committed
Handling of uncertainties and polymorphisms in categorical data read.
balhoff
committed
Fixed exception due to improper use of DOM node in two documents.
balhoff
committed