Several small changes to TreeLoggerParser that structure it in a way that allows subclasses to use much of its functionality without reimplementing or copying code. --------------- Adding a new model of hidden linkage among reads in a metagenomic dataset.  The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen.  This is one part of commit phase 2.  
Several small changes to TreeLoggerParser that structure it in a way that allows subclasses to use much of its functionality without reimplementing or copying code.
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Adding a new model of hidden linkage among reads in a metagenomic dataset.  The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen.  This is one part of commit phase 2.  

git-svn-id: 67bc77c75b8364e4e9cdff0eb6560f5818674cd8@3593 ca793f91-a31e-0410-b540-2769d408b6a1

armanbilge/BEAST_sandbox,svn2github/beast-mcmc,svn2github/beast-mcmc,armanbilge/BEAST_sandbox,svn2github/beast-mcmc,armanbilge/BEAST_sandbox,armanbilge/BEAST_sandbox,armanbilge/BEAST_sandbox,svn2github/beast-mcmc,svn2github/beast-mcmc