def run(self):
#---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
Computes the log-likelihood based on the current tree and current
model.
"""
ds = self.opts.data_source
mat = ds and ds.getMatrix() or None
self.phycassert(self.opts.data_source is not None, "specify data_source before calling like()")
self._loadData(mat)
self.starting_tree = self.getStartingTree()
if self.opts.preorder_edgelens is not None:
self.starting_tree.replaceEdgeLens(self.opts.preorder_edgelens)
print '@@@@@@@@@@ self.starting_tree.makeNewick() =',self.starting_tree.makeNewick()
core = LikelihoodCore(self)
core.setupCore()
core.prepareForLikelihood()
if self.opts.store_site_likes:
core.likelihood.storeSiteLikelihoods(True)
self.opts.pattern_counts = None
self.opts.char_to_pattern = None
self.opts.site_likes = None
self.opts.site_uf = None
else:
core.likelihood.storeSiteLikelihoods(False)
lnL = core.calcLnLikelihood()
if self.opts.store_site_likes:
self.opts.pattern_counts = core.likelihood.getPatternCounts()
self.opts.char_to_pattern = core.likelihood.getCharIndexToPatternIndex()
self.opts.site_likes = core.likelihood.getSiteLikelihoods()
self.opts.site_uf = core.likelihood.getSiteUF()
return lnL
