def __init__(self, registry):
_LOG.info('Initializing Phycas')
Phycas.__init__(self)
self.data_source = 'memory'
SimpleServer.__init__(self, registry)
self.registry = registry
self.trees = []
self.treesLock = threading.Lock()
self.curr_tree_pos = None
self.phycasIDLishMatrix = None
self.ntax = 0
self.leafSet = []
self.serverRefCount = 1
self.settings = {}
def recordSample(self, cycle, lnL = 0.0):
#---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
Calls base class version, then stores tree description in list so that
trees can be supplied when requested.
"""
Phycas.recordSample(self, cycle, lnL)
t = (cycle + 1, lnL, self.tree.makeNewick())
_LOG.debug(str(t))
self.treesLock.acquire()
try:
self.trees.append(t)
if not self.curr_tree_pos:
self.curr_tree_pos = 0
finally:
self.treesLock.release()