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# Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# Revisions copyright 2008-2010 by Peter Cock.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# Contact: Leighton Pritchard, The James Hutton Institute,
# Invergowrie, Dundee, Scotland, DD2 5DA, UK
# [email protected]
################################################################################
#
# TODO: Make representation of Ymax and Ymin values at this level, so that
# calculation of graph/axis drawing is simplified
"""GraphSet module.
Provides:
- GraphSet - container for GraphData objects
For drawing capabilities, this module uses reportlab to draw and write
the diagram: http://www.reportlab.com
"""
# ReportLab imports
from reportlab.lib import colors
from ._Graph import GraphData
class GraphSet:
"""Graph Set.
Attributes:
- id Unique identifier for the set
- name String describing the set
"""
def __init__(self, name=None):
"""Initialize.
Arguments:
- name String identifying the graph set sensibly
"""
self.id = id # Unique identifier for the set
self._next_id = 0 # Holds unique ids for graphs
self._graphs = {} # Holds graphs, keyed by unique id
self.name = name # Holds description of graph
def new_graph(
self,
data,
name=None,
style="bar",
color=colors.lightgreen,
altcolor=colors.darkseagreen,
linewidth=1,
center=None,
colour=None,
altcolour=None,
centre=None,
):
"""Add a GraphData object to the diagram.
Arguments:
- data List of (position, value) int tuples
- name String, description of the graph
- style String ('bar', 'heat', 'line') describing how the graph
will be drawn
- color colors.Color describing the color to draw all or 'high'
(some styles) data (overridden by backwards compatible
argument with UK spelling, colour).
- altcolor colors.Color describing the color to draw 'low' (some
styles) data (overridden by backwards compatible argument
with UK spelling, colour).
- linewidth Float describing linewidth for graph
- center Float setting the value at which the x-axis
crosses the y-axis (overridden by backwards
compatible argument with UK spelling, centre)
Add a GraphData object to the diagram (will be stored internally).
"""
# Let the UK spelling (colour) override the USA spelling (color)
if colour is not None:
color = colour
if altcolour is not None:
altcolor = altcolour
if centre is not None:
center = centre
id = self._next_id # get id number
graph = GraphData(id, data, name, style, color, altcolor, center)
graph.linewidth = linewidth
self._graphs[id] = graph # add graph data
self._next_id += 1 # increment next id
return graph
def del_graph(self, graph_id):
"""Remove a graph from the set, indicated by its id."""
del self._graphs[graph_id]
def get_graphs(self):
"""Return list of all graphs in the graph set, sorted by id.
Sorting is to ensure reliable stacking.
"""
return [self._graphs[id] for id in sorted(self._graphs)]
def get_ids(self):
"""Return a list of all ids for the graph set."""
return list(self._graphs.keys())
def range(self):
"""Return the lowest and highest base (or mark) numbers as a tuple."""
lows, highs = [], []
for graph in self._graphs.values():
low, high = graph.range()
lows.append(low)
highs.append(high)
return (min(lows), max(highs))
def data_quartiles(self):
"""Return (minimum, lowerQ, medianQ, upperQ, maximum) values as a tuple."""
data = []
for graph in self._graphs.values():
data += list(graph.data.values())
data.sort()
datalen = len(data)
return (
data[0],
data[datalen / 4],
data[datalen / 2],
data[3 * datalen / 4],
data[-1],
)
def to_string(self, verbose=0):
"""Return a formatted string with information about the set.
Arguments:
- verbose - Flag indicating whether a short or complete account
of the set is required
"""
if not verbose:
return f"{self}"
else:
outstr = [f"\n<{self.__class__}: {self.name}>"]
outstr.append("%d graphs" % len(self._graphs))
for key in self._graphs:
outstr.append(f"{self._graphs[key]}")
return "\n".join(outstr)
def __len__(self):
"""Return the number of graphs in the set."""
return len(self._graphs)
def __getitem__(self, key):
"""Return a graph, keyed by id."""
return self._graphs[key]
def __str__(self):
"""Return a formatted string with information about the feature set."""
outstr = [f"\n<{self.__class__}: {self.name}>"]
outstr.append("%d graphs" % len(self._graphs))
outstr = "\n".join(outstr)
return outstr
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