#NEWLINE# def setUp( self ) : #NEWLINE# #INDENT# self . b1 = np . array ( [ [ 1 , 3 , 0 , 1 , 0 ] , [ 0 , 2 , 0 , 4 , 4 ] , [ 0 , 0 , 6 , 2 , 1 ] , [ 0 , 0 , 1 , 1 , 1 ] , [ 5 , 3 , 5 , 0 , 0 ] , [ 0 , 0 , 0 , 3 , 5 ] ] ) #NEWLINE# self . sids1 = list ( 'ABCDEF' ) #NEWLINE# self . oids1 = [ ( 'OTU%d' % i ) for i in range ( 1 , 6 ) ] #NEWLINE# self . t1 = TreeNode . read ( StringIO ( '(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:0.75,OTU5:0.75):1.25):0.0)root;' ) ) #NEWLINE# self . t1_w_extra_tips = TreeNode . read ( StringIO ( '(((((OTU1:0.5,OTU2:0.5):0.5,OTU3:1.0):1.0):0.0,(OTU4:0.75,(OTU5:0.25,(OTU6:0.5,OTU7:0.5):0.5):0.5):1.25):0.0)root;' ) ) #NEWLINE# self . t2 = TreeNode . read ( StringIO ( '((OTU1:0.1, OTU2:0.2):0.3, (OTU3:0.5, OTU4:0.7):1.1)root;' ) ) #NEWLINE# self . oids2 = [ ( 'OTU%d' % self ) for i in range ( 1 , 5 ) ]