Class Diagram
source code
object --+
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Diagram
Diagram
Provides:
Attributes:
o name String, identifier for the diagram
o tracks List of Track objects comprising the diagram
o format String, format of the diagram (circular/linear)
o pagesize String, the pagesize of output
o orientation String, the page orientation (landscape/portrait)
o x Float, the proportion of the page to take up with even
X margins
o y Float, the proportion of the page to take up with even
Y margins
o xl Float, the proportion of the page to take up with the
left X margin
o xr Float, the proportion of the page to take up with the
right X margin
o yt Float, the proportion of the page to take up with the
top Y margin
o yb Float, the proportion of the page to take up with the
bottom Y margin
o start Int, the base/aa position to start the diagram at
o end Int, the base/aa position to end the diagram at
o tracklines Boolean, True if track guidelines are to be drawn
o fragments Int, for a linear diagram, the number of equal divisions
into which the sequence is divided
o fragment_size Float, the proportion of the space available to each
fragment that should be used in drawing
o track_size Float, the proportion of the space available to each
track that should be used in drawing
o circular Boolean, True if the genome/sequence to be drawn is, in
reality, circular.
Methods:
o __init__(self, name=None) Called on instantiation
o draw(self, format='circular', pagesize='A3', orientation='landscape',
x=0.05, y=0.05, xl=None, xr=None, yt=None, yb=None,
start=None, end=None, tracklines=0, fragments=10,
fragment_size=0.9, track_size=0.75) Instructs the package to draw
the diagram
o write(self, filename='test1.ps', output='PS') Writes the drawn
diagram to a specified file, in a specified format.
o add_track(self, track, track_level) Adds a Track object to the
diagram, with instructions to place it at a particular level on
the diagram
o del_track(self, track_level) Removes the track that is to be drawn
at a particular level on the diagram
o get_tracks(self) Returns the list of Track objects to be drawn
contained in the diagram
o renumber_tracks(self, low=1) Renumbers all tracks consecutively,
optionally from a passed lowest number
o get_levels(self) Returns a list of levels currently occupied by
Track objects
o get_drawn_levels(self) Returns a list of levels currently occupied
by Track objects that will be shown in the drawn diagram (i.e.
are not hidden)
o range(self) Returns the lowest- and highest-numbered positions
contained within features in all tracks on the diagram as a tuple.
o __getitem__(self, key) Returns the track contained at the level of
the passed key
o __str__(self) Returns a formatted string describing the diagram
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draw(self,
format=None,
pagesize=None,
orientation=None,
x=None,
y=None,
xl=None,
xr=None,
yt=None,
yb=None,
start=None,
end=None,
tracklines=None,
fragments=None,
fragment_size=None,
track_size=None)
Draws the diagram using the passed parameters, if any, to override
previous settings for the diagram object. |
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write(self,
filename='test1.ps',
output='PS',
dpi=72)
o filename String indicating the name of the output file,
or a handle to write to. |
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write_to_string(self,
output='PS')
o output String indicating output format, one of PS, PDF,
SVG, JPG, BMP, GIF, PNG, TIFF or TIFF (as
specified for the write method). |
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Track
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new_track(self,
track_level)
o track_level Int, the level at which the track will be drawn
(above an arbitrary baseline) |
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del_track(self,
track_level)
o track_level Int, the level of the track on the diagram to delete |
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list
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get_tracks(self)
Returns a list of the tracks contained in the diagram |
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move_track(self,
from_level,
to_level)
o from_level Int, the level at which the track to be moved is
found |
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[int, int, ...]
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get_levels(self)
Return a sorted list of levels occupied by tracks in the diagram |
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[int, int, ...]
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get_drawn_levels(self)
Return a sorted list of levels occupied by tracks that are not
explicitly hidden |
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(int, int)
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range(self)
Returns the lowest and highest base (or mark) numbers containd in
track features as a tuple |
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Track
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""
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__subclasshook__
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Inherited from object :
__class__
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o name String describing the diagram
o format String: 'circular' or 'linear', depending on the sort of
diagram required
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, for linear diagrams, the number of sections into
which to break the sequence being drawn
o fragment_size Float (0->1), for linear diagrams, describing
the proportion of space in a fragment to take
up with tracks
o track_size Float (0->1) describing the proportion of space
in a track to take up with sigils
o circular Boolean flag to indicate whether the sequence being
drawn is circular
- Overrides:
object.__init__
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o attr An attribute of the Track class
o value The value to set that attribute
Set the passed attribute of all tracks in the set to the passed
value
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write(self,
filename='test1.ps',
output='PS',
dpi=72)
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o filename String indicating the name of the output file,
or a handle to write to.
o output String indicating output format, one of PS, PDF,
SVG, or provided the ReportLab renderPM module is
installed, one of the bitmap formats JPG, BMP,
GIF, PNG, TIFF or TIFF. The format can be given
in upper or lower case.
o dpi Resolution (dots per inch) for bitmap formats.
Write the completed drawing out to a file in a prescribed format
No return value.
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o output String indicating output format, one of PS, PDF,
SVG, JPG, BMP, GIF, PNG, TIFF or TIFF (as
specified for the write method).
o dpi Resolution (dots per inch) for bitmap formats.
Return the completed drawing as a string in a prescribed format
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o track Track object to draw
o track_level Int, the level at which the track will be drawn
(above an arbitrary baseline)
Add a pre-existing Track to the diagram at a given level
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o track_level Int, the level at which the track will be drawn
(above an arbitrary baseline)
Add a new Track to the diagram at a given level and returns it for
further user manipulation.
- Returns: Track
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o track_level Int, the level of the track on the diagram to
delete
Remove the track at the passed level from the diagram
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o from_level Int, the level at which the track to be moved is
found
o to_level Int, the level to move the track to
Moves a track from one level on the diagram to another
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o low Int, the track number to start from
o step Int, the track interval for separation of tracks
Reassigns all the tracks to run consecutively from the lowest value
(low)
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o key The id of a track in the diagram
Return the Track object with the passed id
- Returns: Track
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__str__(self)
(Informal representation operator)
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Returns a formatted string with information about the diagram
- Returns: ""
- Overrides:
object.__str__
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