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DisplayRepresentation.py

00001 """Represent information for graphical display.

Classes in this module are designed to hold information in a way that
makes it easy to draw graphical figures.
"""
# reportlab
from reportlab.lib import colors

# local stuff
from Bio.Graphics.BasicChromosome import ChromosomeSegment
from Bio.Graphics.BasicChromosome import TelomereSegment

# --- constants
# This is a default color scheme based on the light spectrum.
# Based on my vague recollections from biology, this is our friend ROY G. BIV
RAINBOW_COLORS = {(1, 1)  : colors.violet,
                  (2, 2)  : colors.indigo,
                  (3, 3)  : colors.blue,
                  (4, 4)  : colors.green,
                  (5, 5)  : colors.yellow,
                  (6, 6)  : colors.orange,
                  (7, 20) : colors.red}

00024 class ChromosomeCounts:
    """Represent a chromosome with count information.

    This is used to display information about counts along a chromosome.
    The segments are expected to have different count information, which
    will be displayed using a color scheme.

    I envision using this class when you think that certain regions of
    the chromosome will be especially abundant in the counts, and you
    want to pick those out.
    """
00035     def __init__(self, segment_names, color_scheme = RAINBOW_COLORS):
        """Initialize a representation of chromosome counts.

        Arguments:

        o segment_names - An ordered list of all segment names along
        the chromosome. The count and other information will be added to
        these.

        o color_scheme - A coloring scheme to use in the counts. This should
        be a dictionary mapping count ranges to colors (specified in
        reportlab.lib.colors).
        """
        self._names = segment_names
        self._count_info = {}
        self._label_info = {}
        self._scale_info = {}
        for name in self._names:
            self._count_info[name] = 0
            self._label_info[name] = None
            self._scale_info[name] = 1
        
        self._color_scheme = color_scheme

00059     def add_count(self, segment_name, count = 1):
        """Add counts to the given segment name.

        Arguments:

        o segment_name - The name of the segment we should add counts to.
        If the name is not present, a KeyError will be raised.

        o count - The counts to add the current segment. This defaults to
        a single count.
        """
        try:
            self._count_info[segment_name] += count
        except KeyError:
            raise KeyError("Segment name %s not found." % segment_name)

00075     def scale_segment_value(self, segment_name, scale_value = None):
        """Divide the counts for a segment by some kind of scale value.

        This is useful if segments aren't represented by raw counts, but
        are instead counts divided by some number.
        """
        try:
            self._count_info[segment_name] = \
              float(self._count_info[segment_name]) / float(scale_value)
        except KeyError:
            raise KeyError("Segment name %s not found." % segment_name)

00087     def add_label(self, segment_name, label):
        """Add a label to a specfic segment.

        Raises a KeyError is the specified segment name is not found.
        """
        if segment_name in self._label_info:
            self._label_info[segment_name] = label
        else:
            raise KeyError("Segment name %s not found." % segment_name)

00097     def set_scale(self, segment_name, scale):
        """Set the scale for a specific chromosome segment.

        By default all segments have the same scale -- this allows scaling
        by the size of the segment.

        Raises a KeyError is the specified segment name is not found.
        """
        if segment_name in self._label_info:
            self._scale_info[segment_name] = scale
        else:
            raise KeyError("Segment name %s not found." % segment_name)

00110     def get_segment_info(self):
        """Retrieve the color and label info about the segments.

        Returns a list consiting of two tuples specifying the counts and
        label name for each segment. The list is ordered according to the
        original listing of names. Labels are set as None if no label
        was specified.
        """
        order_info = []

        for seg_name in self._names:
            order_info.append((self._count_info[seg_name],
                               self._label_info[seg_name]))

        return order_info

00126     def fill_chromosome(self, chromosome):
        """Add the collected segment information to a chromosome for drawing.

        Arguments:

        o chromosome - A Chromosome graphics object that we can add
        chromosome segments to.

        This creates ChromosomeSegment (and TelomereSegment) objects to
        fill in the chromosome. The information is derived from the
        label and count information, with counts transformed to the
        specified color map.

        Returns the chromosome with all of the segments added.
        """
        for seg_num in range(len(self._names)):
            is_end_segment = 0
            # make the top and bottom telomeres
            if seg_num == 0:
                cur_segment = TelomereSegment()
                is_end_segment = 1
            elif seg_num == len(self._names) - 1:
                cur_segment = TelomereSegment(1)
                is_end_segment = 1
            # otherwise, they are just regular segments
            else:
                cur_segment = ChromosomeSegment()

            seg_name = self._names[seg_num]
            if self._count_info[seg_name] > 0:
                color = self._color_from_count(self._count_info[seg_name])
                cur_segment.fill_color = color
            
            if self._label_info[seg_name] is not None:
                cur_segment.label = self._label_info[seg_name]

            # give end segments extra size so they look right
            if is_end_segment:
                cur_segment.scale = 3
            else:
                cur_segment.scale = self._scale_info[seg_name]

            chromosome.add(cur_segment)

        return chromosome

00172     def _color_from_count(self, count):
        """Translate the given count into a color using the color scheme.
        """
        for count_start, count_end in self._color_scheme.keys():
            if count >= count_start and count <= count_end:
                return self._color_scheme[(count_start, count_end)]

        # if we got here we didn't find a color for the count
        raise ValueError("Count value %s was not found in the color scheme."
                         % count)
        
        
        

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