def checkSanity(self):
"""
Place asserts in this function that should be checked before anything substantive
is done during a call of a SS object.
"""
cf = CommonFunctions(self)
cf.phycassert(mcmc.ncycles > 0, 'mcmc.ncycles cannot be less than 1 for path sampling')
def __init__(self, opts):
#---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
Initializes ParamSummarizer object.
"""
CommonFunctions.__init__(self, opts)
def __init__(self, opts):
#---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
"""
CommonFunctions.__init__(self, opts)
self.opts = opts
self.detailsf = None
def checkSanity(self):
"""
Place asserts in this function that should be checked before anything substantive
is done during a call of a SS object.
"""
cf = CommonFunctions(self)
cf.phycassert(mcmc.ncycles > 0, 'mcmc.ncycles cannot be less than 1 for the stepping-stone method')
if not self.override_fixed_topology_restriction:
cf.phycassert(mcmc.fix_topology == True, "mcmc.fix_topology must be True to use the stepping-stone method (we're working on relaxing this requirement)")
def __init__(self, opts):
#---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
Initializes MCMCImpl object by assigning supplied phycas object
to a data member variable.
"""
CommonFunctions.__init__(self, opts)
self.opts = opts
self.sitelikef = None
def __init__(self, opts):
#---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
Initializes the SimulateImpl object by assigning supplied phycas object
to a data member variable.
"""
CommonFunctions.__init__(self, opts)
self.starting_tree_source = None
self.starting_tree = None
#self.ntax = None
self.sim_model_tree = None
self.data_matrix = None
def __init__(self, opts):
#---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
Initializes the LikeImpl object by assigning supplied phycas object
to a data member variable.
"""
CommonFunctions.__init__(self, opts)
self.starting_tree = None
self.taxon_labels = None
self.data_matrix = None
self.ntax = None
self.nchar = None
self.reader = NexusReader()
self.npatterns = [] # Will hold the actual number of patterns for each subset after data file has been read
def __init__(self, opts):
#---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
Initializes TreeSummarizer object.
"""
CommonFunctions.__init__(self, opts)
self.pdf_page_width = 8.5 # should be an option
self.pdf_page_height = 11.0 # should be an option
self.pdf_ladderize = 'right' # should be an option - valid values are 'right', 'left' or None
self.rooted_trees = opts.rooted
self.outgroup = opts.outgroup_taxon
if self.rooted_trees and opts.outgroup_taxon:
self.outgroup = None
self.warning('Specifying True for sumt_rooted is incompatible with specifying\nsumt_outgroup_taxon; I will pretend that you set sumt_outgroup_taxon to None')
def __init__(self, opts):
# ---+----|----+----|----+----|----+----|----+----|----+----|----+----|
"""
Initializes TreeSummarizer object by assigning supplied phycas object
to a data member variable.
"""
CommonFunctions.__init__(self, opts)
self.r = self._getLot()
eld = self.edgelen_dist
self._current = 0
self.trees = []
if eld is None:
if self.distribution.lower() != "yule":
raise ValueError("edgelen_dist must be set if the tree simulator's distribution is not Yule")
if self.speciation_rate is None:
raise ValueError(
"edgelen_dist or the speciation_rate must be set to generate trees from the Yule process"
)
else:
eld.setLot(self.r)
self.stdout.debugging("Generating %s" % str(self))
def __init__(self):
CommonFunctions.__init__(self, None)
self.pdf_splits_to_plot = None
# Variables associated with PDF tree drawing (used in pdftree() function)
# The 14 standard fonts guaranteed to be available in all PDF consumer applications:
# Times-Roman Helvetica Courier Symbol
# Times-Bold Helvetica-Bold Courier-Bold ZapfDingbats
# Times-Italic Helvetica-Oblique Courier-Oblique
# Times-BoldItalic Helvetica-BoldOblique Courier-BoldOblique
self.pdf_filename = 'trees.pdf' # Set to desired name of pdf file to create
self.pdf_edge_support_file = None # File containing PAUP* output with table of support values; if specified, the support values will be shown on trees plotted
self.pdf_tip_label_font = 'Times-Italic' # Font used for tip node names; should be one of the 14 standard fonts listed above
self.pdf_tip_label_height = 12 # Height in points of tip node name font
self.pdf_plot_label_font = 'Helvetica' # Font used for plot axis labels; should be one of the 14 standard fonts listed above
self.pdf_plot_label_height = 12 # Height in points of plot axis label font
self.pdf_title_font = 'Helvetica' # Font used for scalebar text; should be one of the 14 standard fonts listed above
self.pdf_title_height = 14 # Height in points of scalebar text font
self.pdf_scalebar_position = 'bottom' # Valid values are 'top', 'bottom' or None
self.pdf_scalebar_label_font = 'Helvetica' # Font used for scalebar text; should be one of the 14 standard fonts listed above
self.pdf_scalebar_label_height = 10 # Height in points of scalebar text font
self.pdf_support_label_font = 'Times-Roman' # Font used for edge support values; should be one of the 14 standard fonts listed above
self.pdf_support_label_height = 8 # Height in points of edge support font
self.pdf_support_as_percent = True # If True, support values will be shown as percentages (e.g. 93.1) rather than proportions (e.g. 0.931)
self.pdf_support_decimals = 1 # The number of decimal places shown in support values (e.g. to get 93.7, specify 1; to round up to 94, specify 0)
self.pdf_ladderize = 'right' # Valid values are 'right', 'left' or None
self.pdf_page_width = 8.5 # Page width in inches
self.pdf_page_height = 11.0 # Page length in inches
self.pdf_line_width = 1.0 # Width of lines representing edges in the tree
self.pdf_left_margin = 1.0 # Left margin in inches (1 inch = 72 points)
self.pdf_right_margin = 1.0 # Right margin in inches (1 inch = 72 points)
self.pdf_top_margin = 1.0 # Top margin in inches (1 inch = 72 points)
self.pdf_bottom_margin = 1.0 # Bottom margin in inches (1 inch = 72 points)
self.keep_xy_proportional = True # If True, vertical dimension of each tree in a collection will be kept proportional to its horizontal dimension
self.keep_tip_labels_proportional = True # If True, tip label height will be kept commensurate with size of tree for each tree in a printed collection (smaller trees will have smaller tip labels)
self.pdf_treefile = None # Set to tree file name if you want to make one pdf file with each tree from tree file on a separate page
self.pdf_newick = None # Set to the tree description to print if only want to save one tree to a pdf file
self.pdf_outgroup_taxon = None # Set to taxon name of tip serving as the outgroup for display rooting purposes (note: at this time outgroup can consist of just one taxon)