# Copyright 2001 by Brad Chapman. All rights reserved.

#

# 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.

"""Display information distributed across a Chromosome-like object.

These classes are meant to show the distribution of some kind of information

as it changes across any kind of segment. It was designed with chromosome

distributions in mind, but could also work for chromosome regions, BAC clones

or anything similar.

Reportlab is used for producing the graphical output.

"""

# standard library

import math

# reportlab

from reportlab.lib.pagesizes import letter

from reportlab.lib.units import inch

from reportlab.lib import colors

from reportlab.graphics.shapes import Drawing, String

from reportlab.graphics.charts.barcharts import VerticalBarChart

from reportlab.graphics.charts.barcharts import BarChartProperties

from reportlab.graphics.widgetbase import TypedPropertyCollection

from Bio.Graphics import _write

class DistributionPage(object):

"""Display a grouping of distributions on a page.

This organizes Distributions, and will display them nicely

on a single page.

"""

def __init__(self, output_format="pdf"):

"""Initialize."""

self.distributions = []

# customizable attributes

self.number_of_columns = 1

self.page_size = letter

self.title_size = 20

self.output_format = output_format

def draw(self, output_file, title):

"""Draw out the distribution information.

Arguments:

- output_file - The name of the file to output the information to,

or a handle to write to.

- title - A title to display on the graphic.

"""

width, height = self.page_size

cur_drawing = Drawing(width, height)

self._draw_title(cur_drawing, title, width, height)

# calculate the x and y position changes for each distribution

cur_x_pos = inch * .5

end_x_pos = width - inch * .5

cur_y_pos = height - 1.5 * inch

end_y_pos = .5 * inch

x_pos_change = ((end_x_pos - cur_x_pos) /

float(self.number_of_columns))

num_y_rows = math.ceil(float(len(self.distributions)) /

float(self.number_of_columns))

y_pos_change = (cur_y_pos - end_y_pos) / num_y_rows

self._draw_distributions(cur_drawing, cur_x_pos, x_pos_change,

cur_y_pos, y_pos_change, num_y_rows)

self._draw_legend(cur_drawing, 2.5 * inch, width)

return _write(cur_drawing, output_file, self.output_format)

def _draw_title(self, cur_drawing, title, width, height):

"""Add the title of the figure to the drawing (PRIVATE)."""

title_string = String(width / 2, height - inch, title)

title_string.fontName = "Helvetica-Bold"

title_string.fontSize = self.title_size

title_string.textAnchor = "middle"

cur_drawing.add(title_string)

def _draw_distributions(self, cur_drawing, start_x_pos, x_pos_change,

start_y_pos, y_pos_change, num_y_drawings):

"""Draw all of the distributions on the page (PRIVATE).

Arguments:

- cur_drawing - The drawing we are working with.

- start_x_pos - The x position on the page to start drawing at.

- x_pos_change - The change in x position between each figure.

- start_y_pos - The y position on the page to start drawing at.

- y_pos_change - The change in y position between each figure.

- num_y_drawings - The number of drawings we'll have in the y

(up/down) direction.

"""

for y_drawing in range(int(num_y_drawings)):

# if we are on the last y position, we may not be able

# to fill all of the x columns

if (y_drawing + 1) * self.number_of_columns > \

len(self.distributions):

num_x_drawings = len(self.distributions) - \

y_drawing * self.number_of_columns

else:

num_x_drawings = self.number_of_columns

for x_drawing in range(num_x_drawings):

dist_num = y_drawing * self.number_of_columns + x_drawing

cur_distribution = self.distributions[dist_num]

# find the x and y boundaries of the distribution

x_pos = start_x_pos + x_drawing * x_pos_change

end_x_pos = x_pos + x_pos_change

end_y_pos = start_y_pos - y_drawing * y_pos_change

y_pos = end_y_pos - y_pos_change

# draw the distribution

cur_distribution.draw(cur_drawing, x_pos, y_pos, end_x_pos,

end_y_pos)

def _draw_legend(self, cur_drawing, start_y, width):

"""Add a legend to the figure (PRIVATE).

Subclasses can implement to provide a specialized legend.

"""

pass

class BarChartDistribution(object):

"""Display the distribution of values as a bunch of bars."""

def __init__(self, display_info=None):

"""Initialize a Bar Chart display of distribution info.

Attributes:

- display_info - the information to be displayed in the distribution.

This should be ordered as a list of lists, where each internal list

is a data set to display in the bar chart.

"""

if display_info is None:

display_info = []

self.display_info = display_info

self.x_axis_title = ""

self.y_axis_title = ""

self.chart_title = ""

self.chart_title_size = 10

self.padding_percent = 0.15

def draw(self, cur_drawing, start_x, start_y, end_x, end_y):

"""Draw a bar chart with the info in the specified range."""

bar_chart = VerticalBarChart()

if self.chart_title:

self._draw_title(cur_drawing, self.chart_title,

start_x, start_y, end_x, end_y)

# set the position of the bar chart

x_start, x_end, y_start, y_end = self._determine_position(start_x,

start_y,

end_x,

end_y)

bar_chart.x = x_start

bar_chart.y = y_start

bar_chart.width = abs(x_start - x_end)

bar_chart.height = abs(y_start - y_end)

# set the information in the bar chart

bar_chart.data = self.display_info

bar_chart.valueAxis.valueMin = min(self.display_info[0])

bar_chart.valueAxis.valueMax = max(self.display_info[0])

for data_set in self.display_info[1:]:

if min(data_set) < bar_chart.valueAxis.valueMin:

bar_chart.valueAxis.valueMin = min(data_set)

if max(data_set) > bar_chart.valueAxis.valueMax:

bar_chart.valueAxis.valueMax = max(data_set)

# set other formatting options

if len(self.display_info) == 1:

bar_chart.groupSpacing = 0

style = TypedPropertyCollection(BarChartProperties)

style.strokeWidth = 0

style.strokeColor = colors.green

style[0].fillColor = colors.green

bar_chart.bars = style

# set the labels

# XXX labels don't work yet

# bar_chart.valueAxis.title = self.x_axis_title

# bar_chart.categoryAxis.title = self.y_axis_title

cur_drawing.add(bar_chart)

def _draw_title(self, cur_drawing, title, start_x, start_y, end_x, end_y):

"""Add the title of the figure to the drawing (PRIVATE)."""

x_center = start_x + (end_x - start_x) / 2

y_pos = end_y + (self.padding_percent * (start_y - end_y)) / 2

title_string = String(x_center, y_pos, title)

title_string.fontName = "Helvetica-Bold"

title_string.fontSize = self.chart_title_size

title_string.textAnchor = "middle"

cur_drawing.add(title_string)

def _determine_position(self, start_x, start_y, end_x, end_y):

"""Calculate the position of the chart with blank space (PRIVATE).

This uses some padding around the chart, and takes into account

whether the chart has a title. It returns 4 values, which are,

in order, the x_start, x_end, y_start and y_end of the chart

itself.

"""

x_padding = self.padding_percent * (end_x - start_x)

y_padding = self.padding_percent * (start_y - end_y)

new_x_start = start_x + x_padding

new_x_end = end_x - x_padding

if self.chart_title:

new_y_start = start_y - y_padding - self.chart_title_size

else:

new_y_start = start_y - y_padding

new_y_end = end_y + y_padding

return new_x_start, new_x_end, new_y_start, new_y_end

class LineDistribution(object):

"""Display the distribution of values as connected lines.

This distribution displays the change in values across the object as

lines. This also allows multiple distributions to be displayed on a

single graph.

"""

def __init__(self):

"""Initialize."""

pass

def draw(self, cur_drawing, start_x, start_y, end_x, end_y):

"""Draw a line distribution into the current drawing."""

pass