Class LinearDrawer

source code

                    object --+    
                             |    
_AbstractDrawer.AbstractDrawer --+
                                 |
                                LinearDrawer

LinearDrawer(AbstractDrawer)

Inherits from:

o AbstractDrawer

Provides:

Methods:

o __init__(self, ...) Called on instantiation

o set_page_size(self, pagesize, orientation)    Set the page size to the
                                            passed size and orientation

o set_margins(self, x, y, xl, xr, yt, yb)   Set the drawable area of the
                                            page

o set_bounds(self, start, end)  Set the bounds for the elements to be
                                drawn

o is_in_bounds(self, value)     Returns a boolean for whether the position
                                is actually to be drawn

o __len__(self)     Returns the length of sequence that will be drawn


o draw(self)    Place the drawing elements on the diagram

o init_fragments(self)  Calculate information
                        about sequence fragment locations on the drawing

o set_track_heights(self)   Calculate information about the offset of
                            each track from the fragment base

o draw_test_tracks(self)    Add lines demarcating each track to the
                            drawing

o draw_track(self, track)   Return the contents of the passed track as
                            drawing elements

o draw_scale(self, track)   Return a scale for the passed track as
                            drawing elements

o draw_tick(self, tickpos, ctr, ticklen, track, draw_label) Return a
                            tick line and possibly a label

o draw_greytrack(self, track)   Return a grey background and superposed
                                label for the passed track as drawing
                                elements

o draw_feature_set(self, set)   Return the features in the passed set as
                                drawing elements

o draw_feature(self, feature)   Return a single feature as drawing
                                elements

o get_feature_sigil(self, feature, x0, x1, fragment)    Return a single
                                feature as its sigil in drawing elements

o draw_graph_set(self, set)     Return the data in a set of graphs as
                                drawing elements

o draw_line_graph(self, graph)  Return the data in a graph as a line
                                graph in drawing elements

o draw_heat_graph(self, graph)  Return the data in a graph as a heat
                                graph in drawing elements

o draw_bar_graph(self, graph)   Return the data in a graph as a bar
                                graph in drawing elements

o canvas_location(self, base)   Return the fragment, and the offset from
                                the left margin, of a passed position
                                in the sequence, on the diagram.

Attributes:

o tracklines    Boolean for whether to draw lines dilineating tracks

o pagesize      Tuple describing the size of the page in pixels

o x0            Float X co-ord for leftmost point of drawable area

o xlim          Float X co-ord for rightmost point of drawable area

o y0            Float Y co-ord for lowest point of drawable area

o ylim          Float Y co-ord for topmost point of drawable area

o pagewidth     Float pixel width of drawable area

o pageheight    Float pixel height of drawable area

o xcenter       Float X co-ord of center of drawable area

o ycenter       Float Y co-ord of center of drawable area

o start         Int, base to start drawing from

o end           Int, base to stop drawing at

o length        Int, size of sequence to be drawn

o fragments     Int, number of fragments into which to divide the
                drawn sequence

o fragment_size Float (0->1) the proportion of the fragment height to
                draw in

o track_size    Float (0->1) the proportion of the track height to
                draw in

o drawing       Drawing canvas

o drawn_tracks  List of ints denoting which tracks are to be drawn

o current_track_level   Int denoting which track is currently being
                        drawn

o fragment_height   Float total fragment height in pixels

o fragment_bases    Int total fragment length in bases

o fragment_lines    Dictionary of top and bottom y-coords of fragment,
                    keyed by fragment number

o fragment_limits   Dictionary of start and end bases of each fragment,
                    keyed by fragment number

o track_offsets     Dictionary of number of pixels that each track top,
                    center and bottom is offset from the base of a
                    fragment, keyed by track

o cross_track_links List of tuples each with four entries (track A,
                    feature A, track B, feature B) to be linked.

([element, element,...], [element, element,...])

(element, element)

([element, element,...], [element, element,...])

([element, element,...], [element, element,...])

([element, element,...], [element, element,...])

([element, element,...], [element, element,...])

(element, element, element)

([element, element,...], [element, element,...])

[element, element,...]

[element, element,...]

[element, element,...]

(int, float)

o parent    Diagram object containing the data that the drawer
            draws

o pagesize  String describing the ISO size of the image, or a tuple
            of pixels

o orientation   String describing the required orientation of the
                final drawing ('landscape' or 'portrait')

o x         Float (0->1) describing the relative size of the X
            margins to the page

o y         Float (0->1) describing the relative size of the Y
            margins to the page

o xl        Float (0->1) describing the relative size of the left X
            margin to the page (overrides x)

o xl        Float (0->1) describing the relative size of the left X
            margin to the page (overrides x)

o xr        Float (0->1) describing the relative size of the right X
            margin to the page (overrides x)

o yt        Float (0->1) describing the relative size of the top Y
            margin to the page (overrides y)

o yb        Float (0->1) describing the relative size of the lower Y
            margin to the page (overrides y)

o start     Int, the position to begin drawing the diagram at

o end       Int, the position to stop drawing the diagram at

o tracklines    Boolean flag to show (or not) lines delineating tracks
                on the diagram

o fragments Int, the number of equal fragments into which the
            sequence should be divided for drawing

o fragment_size Float(0->1) The proportion of the available height
                for the fragment that should be taken up in drawing

o track_size    The proportion of the available track height that
                should be taken up in drawing

o cross_track_links List of tuples each with four entries (track A,
                    feature A, track B, feature B) to be linked.

Initialises useful values for calculating the positioning of
diagram elements

Since tracks may not be of identical heights, the bottom and top
offsets of each track relative to the fragment top and bottom is
stored in a dictionary - self.track_offsets, keyed by track number

o track     Track object

Returns a tuple (list of elements in the track, list of labels in
the track)

o tickpos   Int, position of the tick on the sequence

o ctr       Float, Y co-ord of the center of the track

o ticklen   How long to draw the tick

o track     Track, the track the tick is drawn on

o draw_label    Boolean, write the tick label?

Returns a drawing element that is the tick on the scale

o track     Track object

Returns a tuple of (list of elements in the scale, list of labels
in the scale)

o track     Track object

Put in a grey background to the current track in all fragments,
if track specifies that we should

o set       FeatureSet object

Returns a tuple (list of elements describing features, list of
labels for elements)

o feature           Feature containing location info

Returns tuple of (list of elements describing single feature, list
of labels for those elements)

o feature       Feature object

o x0            Start X co-ordinate on diagram

o x1            End X co-ordinate on diagram

o fragment      The fragment on which the feature appears

Returns a drawable indicator of the feature, and any required label
for it

o set       GraphSet object

Returns tuple (list of graph elements, list of graph labels)

o graph     Graph object

Returns a line graph as a list of drawable elements

o graph     Graph object

Returns a list of drawable elements for the heat graph

o graph     Graph object

Returns a list of drawable elements for a bar graph of the passed
Graph object

o base      The base number on the genome sequence

Returns the x-coordinate and fragment number of a base on the
genome sequence, in the context of the current drawing setup

Draw JAGGY sigil.

Although we may in future expose the head/tail jaggy lengths, for now
both the left and right edges are drawn jagged.