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# Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# Revisions copyright 2008-2010 by Peter Cock.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Contact: Leighton Pritchard, Scottish Crop Research Institute,
# Invergowrie, Dundee, Scotland, DD2 5DA, UK
# L.Pritchard@scri.ac.uk
################################################################################
#
# TODO: Make representation of Ymax and Ymin values at this level, so that
# calculation of graph/axis drawing is simplified
""" GraphSet module
Provides:
o GraphSet - container for GraphData objects
For drawing capabilities, this module uses reportlab to draw and write
the diagram:
http://www.reportlab.com
For dealing with biological information, the package expects BioPython
objects:
http://www.biopython.org
"""
# ReportLab imports
from reportlab.lib import colors
from _Graph import GraphData
class GraphSet(object):
""" GraphSet
Provides:
Methods:
o __init__(self, set_id=None, name=None) Called on instantiation
o new_graph(self, data, name, style='bar', color=colors.lightgreen,
altcolor=colors.darkseagreen) Create new graph in the set
from the passed data, with the passed parameters
o del_graph(self, graph_id) Delete graph with the passed id
o get_graphs(self) Returns a list of all graphs
o get_ids(self) Returns a list of graph ids
o range(self) Returns the range covered by the graphs in the set
o to_string(self, verbose=0) Returns a string describing the set
o __len__(self) Returns the length of sequence covered by the set
o __getitem__(self, key) Returns the graph with the id of the passed key
o __str__(self) Returns a string describing the set
Attributes:
o id Unique identifier for the set
o name String describing the set
"""
def __init__(self, name=None):
""" __init__(self, name=None)
o 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):
""" new_graph(self, data, name=None, style='bar', color=colors.lightgreen,
altcolor=colors.darkseagreen)
o data List of (position, value) int tuples
o name String, description of the graph
o style String ('bar', 'heat', 'line') describing how the graph
will be drawn
o color colors.Color describing the color to draw all or 'high'
(some styles) data (overridden by backwards compatible
argument with UK spelling, colour).
o altcolor colors.Color describing the color to draw 'low' (some
styles) data (overridden by backwards compatible argument
with UK spelling, colour).
o linewidth Float describing linewidth for graph
o 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):
""" del_graph(self, graph_id)
o graph_id Identifying value of the graph
Remove a graph from the set, indicated by its id
"""
del self._graphs[graph_id]
def get_graphs(self):
""" get_graphs(self) -> [Graph, Graph, ...]
Return a list of all graphs in the graph set, sorted by id (for
reliable stacking...)
"""
ids = self._graphs.keys()
ids.sort()
return [self._graphs[id] for id in ids]
def get_ids(self):
""" get_ids(self) -> [int, int, ...]
Return a list of all ids for the graph set
"""
return self._graphs.keys()
def range(self):
""" range(self) -> (int, int)
Returns 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):
""" data_quartiles(self) -> (float, float, float, float, float)
Returns the (minimum, lowerQ, medianQ, upperQ, maximum) values as
a tuple
"""
data = []
for graph in self._graphs.values():
data += 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):
""" to_string(self, verbose=0) -> ""
o verbose Flag indicating whether a short or complete account
of the set is required
Returns a formatted string with information about the set
"""
if not verbose:
return "%s" % self
else:
outstr = ["\n<%s: %s>" % (self.__class__, self.name)]
outstr.append("%d graphs" % len(self._graphs))
for key in self._graphs:
outstr.append("%s" % self._graphs[key])
return "\n".join(outstr)
def __len__(self):
""" __len__(self) -> int
Return the number of graphs in the set
"""
return len(self._graphs)
def __getitem__(self, key):
""" __getitem__(self, key) -> Graph
Return a graph, keyed by id
"""
return self._graphs[key]
def __str__(self):
""" __str__(self) -> ""
Returns a formatted string with information about the feature set
"""
outstr = ["\n<%s: %s>" % (self.__class__, self.name)]
outstr.append("%d graphs" % len(self._graphs))
outstr = "\n".join(outstr)
return outstr
################################################################################
# RUN AS SCRIPT
################################################################################
if __name__ == '__main__':
# Test code
gdgs = GraphSet(0, 'test data')
testdata1 = [(1, 10), (5, 15), (10, 20), (20, 40)]
testdata2 = [(250, .34), (251, .7), (252, .7), (253, .54), (254, .65)]
gdgs.add_graph(testdata1, 'TestData 1')
gdgs.add_graph(testdata2, 'TestData 2')
print gdgs
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