def makeCalculator(self, *args, **kw):
if args:
discontinued('method', "makeCalculator(aligns)", '1.6')
# and shadowing a quite different superclass method.
self.setAlignment(*args)
if getattr(self, 'used_as_calculator', False):
warnings.warn('PC used as two different calculators', stacklevel=2)
self.used_as_calculator = True
return self
else:
return super(_LF, self).makeCalculator(**kw)
def drawToPDF(self, filename, total_width=None, height=None, **kw):
# Matches, as far as possible, old ReportLab version
if total_width is not None:
kw['width'] = total_width / 72
kw2 = {}
for (k,v) in kw.items():
if k in ['wraps', 'border', 'withTrackLabelColumn']:
discontinued('argument', "%s" % k, '1.6')
else:
kw2[k] = v
kw2['format'] = 'pdf'
if height:
kw2['height'] = height / 72
return self.drawToFile(filename, **kw2)
def drawToPDF(self, filename, total_width=None, height=None, **kw):
# Matches, as far as possible, old ReportLab version
if total_width is not None:
kw['width'] = total_width / 72
kw2 = {}
for (k, v) in kw.items():
if k in ['wraps', 'border', 'withTrackLabelColumn']:
discontinued('argument', "%s" % k, '1.6')
else:
kw2[k] = v
kw2['format'] = 'pdf'
if height:
kw2['height'] = height / 72
return self.drawToFile(filename, **kw2)
def makeFigure(self, window=20, join_gaps=None, min_gap=0, **kw):
"""Drawing of a line segment based dotplot with annotated axes"""
# hard to pick min_gap without knowing pixels per base, and
# matplotlib is reasonably fast anyway, so:
if join_gaps is not None:
discontinued('argument', 'join_gaps', '1.6')
ax = comparison_display(self.seq1d, self.seq2d, **kw)
(fwd, rev) = self._calc_lines(window, None, min_gap)
for (lines, colour) in [(fwd, 'blue'), (rev, 'red')]:
vertices = []
for segment in lines:
vertices.extend(segment)
if vertices:
ops = [Path.MOVETO, Path.LINETO] * (len(vertices) // 2)
path = Path(vertices, ops)
patch = PathPatch(path, edgecolor=colour, fill=False)
ax.add_patch(patch)
return ax.get_figure()
def makeFigure(self, window=20, join_gaps=None, min_gap=0, **kw):
"""Drawing of a line segment based dotplot with annotated axes"""
# hard to pick min_gap without knowing pixels per base, and
# matplotlib is reasonably fast anyway, so:
if join_gaps is not None:
discontinued('argument', 'join_gaps', '1.6')
ax = comparison_display(self.seq1d, self.seq2d, **kw)
(fwd, rev) = self._calc_lines(window, None, min_gap)
for (lines, colour) in [(fwd, 'blue'), (rev, 'red')]:
vertices = []
for segment in lines:
vertices.extend(segment)
if vertices:
ops = [Path.MOVETO, Path.LINETO] * (len(vertices)//2)
path = Path(vertices, ops)
patch = PathPatch(path, edgecolor=colour, fill=False)
ax.add_patch(patch)
return ax.get_figure()
def getStatisticsAsDict(self,
with_parent_names=True,
with_edge_names=False):
"""Returns a dictionary containing the statistics for each edge of the
tree, and any other information provided by the substitution model. The
dictionary is keyed at the top-level by parameter name, and then by
edge.name.
Arguments:
- with_edge_names: if True, an ordered list of edge names is
included under the top-level key 'edge.names'. Default is
False.
"""
discontinued(
'method', "'getStatisticsAsDict' "
"use 'getParamValueDict(['edge'])' is nearly equivalent", '1.6')
stats_dict = self.getParamValueDict(['edge'])
if hasattr(self.model, 'scale_masks'):
for predicate in self.model.scale_masks:
stats_dict[predicate] = self.getScaledLengths(predicate)
edge_vector = [e for e in self._tree.getEdgeVector() if not e.isroot()]
# do the edge names
if with_parent_names:
parents = {}
for edge in edge_vector:
if edge.Parent.isroot():
parents[edge.Name] = "root"
else:
parents[edge.Name] = str(edge.Parent.Name)
stats_dict["edge.parent"] = parents
if with_edge_names:
stats_dict['edge.name'] = (
[e.Name for e in edge_vector if e.istip()] +
[e.Name for e in edge_vector if not e.istip()])
return stats_dict
def getStatisticsAsDict(self, with_parent_names=True,
with_edge_names=False):
"""Returns a dictionary containing the statistics for each edge of the
tree, and any other information provided by the substitution model. The
dictionary is keyed at the top-level by parameter name, and then by
edge.name.
Arguments:
- with_edge_names: if True, an ordered list of edge names is
included under the top-level key 'edge.names'. Default is
False.
"""
discontinued('method', "'getStatisticsAsDict' "
"use 'getParamValueDict(['edge'])' is nearly equivalent",
'1.6')
stats_dict = self.getParamValueDict(['edge'])
if hasattr(self.model, 'scale_masks'):
for predicate in self.model.scale_masks:
stats_dict[predicate] = self.getScaledLengths(predicate)
edge_vector = [e for e in self._tree.getEdgeVector() if not e.isroot()]
# do the edge names
if with_parent_names:
parents = {}
for edge in edge_vector:
if edge.Parent.isroot():
parents[edge.Name] = "root"
else:
parents[edge.Name] = str(edge.Parent.Name)
stats_dict["edge.parent"] = parents
if with_edge_names:
stats_dict['edge.name'] = (
[e.Name for e in edge_vector if e.istip()] +
[e.Name for e in edge_vector if not e.istip()])
return stats_dict
def asReportlabTable(header, formatted_table, total_width=476, table_style = None):
"""Returns a reportlab table instance.
Arguments:
- header: series with column headings
- formatted_table: a two dimensional structure (list/tuple) of strings
previously formatted to the same width within a column.
- total_width: table width
- table_style: reportlab compliant table style settings.
"""
discontinued('function', 'asReportlabTable', 1.5)
from reportlab.platypus import Table as reportlabTable
from reportlab.lib import colors
if not table_style:
table_style = [('GRID', (0,0), (-1,-1), 0.5, colors.grey),
('BOX', (0,0), (-1,-1), 0.5, colors.black),
('BACKGROUND', (0,0), (-1,0), colors.lightgrey),
('VALIGN', (0,0), (-1,-1), 'MIDDLE'),]
formatted_table = formatted_table[:]
header = header[:]
formatted_table.insert(0, header)
return reportlabTable(formatted_table, total_width/len(formatted_table[0]),
style = table_style)