<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Graphics-module.html">Package Graphics</a> ::
<a href="Bio.Graphics.GenomeDiagram-module.html">Package GenomeDiagram</a> ::
<a href="Bio.Graphics.GenomeDiagram._LinearDrawer-module.html" onclick="show_private();">Module _LinearDrawer</a> ::
Class LinearDrawer
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class LinearDrawer</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html">_AbstractDrawer.AbstractDrawer</a> --+
|
<strong class="uidshort">LinearDrawer</strong>
</pre>
<hr />
<pre class="literalblock">
LinearDrawer(AbstractDrawer)
Inherits from:
o AbstractDrawer
Provides:
Methods:
o __init__(self, parent=None, 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) 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
</pre>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">AbstractDrawer</span>)</span><br />
o parent Diagram object containing the data that the drawer
draws</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.__init__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="draw"></a><span class="summary-sig-name">draw</span>(<span class="summary-sig-arg">self</span>)</span><br />
Draw a linear diagram of the data in the parent Diagram object</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="init_fragments"></a><span class="summary-sig-name">init_fragments</span>(<span class="summary-sig-arg">self</span>)</span><br />
Initialises useful values for calculating the positioning of diagram
elements</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.init_fragments">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="set_track_heights"></a><span class="summary-sig-name">set_track_heights</span>(<span class="summary-sig-arg">self</span>)</span><br />
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</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.set_track_heights">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="draw_test_tracks"></a><span class="summary-sig-name">draw_test_tracks</span>(<span class="summary-sig-arg">self</span>)</span><br />
Draw red lines indicating the top and bottom of each fragment, and
blue ones indicating tracks to be drawn.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_test_tracks">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">([element, element,...], [element, element,...])</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw_track" class="summary-sig-name">draw_track</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">track</span>)</span><br />
o track Track object</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_track">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">(element, element)</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw_tick" class="summary-sig-name">draw_tick</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">tickpos</span>,
<span class="summary-sig-arg">ctr</span>,
<span class="summary-sig-arg">ticklen</span>)</span><br />
o tickpos Int, position of the tick on the sequence</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_tick">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">([element, element,...], [element, element,...])</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw_scale" class="summary-sig-name">draw_scale</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">track</span>)</span><br />
o track Track object</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_scale">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">([element, element,...], [element, element,...])</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw_greytrack" class="summary-sig-name">draw_greytrack</a>(<span class="summary-sig-arg">self</span>)</span><br />
o track Track object</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_greytrack">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">([element, element,...], [element, element,...])</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw_feature_set" class="summary-sig-name">draw_feature_set</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">set</span>)</span><br />
o set FeatureSet object</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_feature_set">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">([element, element,...], [element, element,...])</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw_feature" class="summary-sig-name">draw_feature</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">feature</span>,
<span class="summary-sig-arg">parent_feature</span>=<span class="summary-sig-default">None</span>)</span><br />
o feature Feature containing location info</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_feature">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="draw_feature_location"></a><span class="summary-sig-name">draw_feature_location</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">feature</span>,
<span class="summary-sig-arg">locstart</span>,
<span class="summary-sig-arg">locend</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_feature_location">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">(element, element, element)</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#get_feature_sigil" class="summary-sig-name">get_feature_sigil</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">feature</span>,
<span class="summary-sig-arg">x0</span>,
<span class="summary-sig-arg">x1</span>,
<span class="summary-sig-arg">fragment</span>)</span><br />
o feature Feature object</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.get_feature_sigil">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">([element, element,...], [element, element,...])</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw_graph_set" class="summary-sig-name">draw_graph_set</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">set</span>)</span><br />
o set GraphSet object</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_graph_set">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">[element, element,...]</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw_line_graph" class="summary-sig-name">draw_line_graph</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">graph</span>)</span><br />
o graph Graph object</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_line_graph">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">[element, element,...]</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw_heat_graph" class="summary-sig-name">draw_heat_graph</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">graph</span>)</span><br />
o graph Graph object</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_heat_graph">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">[element, element,...]</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw_bar_graph" class="summary-sig-name">draw_bar_graph</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">graph</span>)</span><br />
o graph Graph object</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_bar_graph">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">(int, float)</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#canvas_location" class="summary-sig-name">canvas_location</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">base</span>)</span><br />
o base The base number on the genome sequence</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.canvas_location">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html">_AbstractDrawer.AbstractDrawer</a></code></b>:
<code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html#__len__">__len__</a></code>,
<code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html#is_in_bounds">is_in_bounds</a></code>,
<code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html#set_bounds">set_bounds</a></code>,
<code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html#set_margins">set_margins</a></code>,
<code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html#set_page_size">set_page_size</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html">_AbstractDrawer.AbstractDrawer</a></code></b> (private):
<code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html#_set_xcentre" onclick="show_private();">_set_xcentre</a></code>,
<code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html#_set_ycentre" onclick="show_private();">_set_ycentre</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html">_AbstractDrawer.AbstractDrawer</a></code></b>:
<code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html#xcentre">xcentre</a></code>,
<code><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer-class.html#ycentre">ycentre</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">AbstractDrawer</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.__init__">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
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
</pre>
<dl class="fields">
<dt>Overrides:
object.__init__
</dt>
</dl>
</td></tr></table>
</div>
<a name="draw_track"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">draw_track</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">track</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_track">source code</a></span>
</td>
</tr></table>
<p>o track Track object</p>
<p>Returns a tuple (list of elements in the track, list of labels in the
track)</p>
<dl class="fields">
<dt>Returns: ([element, element,...], [element, element,...])</dt>
</dl>
</td></tr></table>
</div>
<a name="draw_tick"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">draw_tick</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">tickpos</span>,
<span class="sig-arg">ctr</span>,
<span class="sig-arg">ticklen</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_tick">source code</a></span>
</td>
</tr></table>
<p>o tickpos Int, position of the tick on the sequence</p>
<p>o ctr Float, Y co-ord of the center of the track</p>
<p>o ticklen How long to draw the tick</p>
<p>o track Track, the track the tick is drawn on</p>
<p>o draw_label Boolean, write the tick label?</p>
<p>Returns a drawing element that is the tick on the scale</p>
<dl class="fields">
<dt>Returns: (element, element)</dt>
</dl>
</td></tr></table>
</div>
<a name="draw_scale"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">draw_scale</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">track</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_scale">source code</a></span>
</td>
</tr></table>
<p>o track Track object</p>
<p>Returns a tuple of (list of elements in the scale, list of labels in
the scale)</p>
<dl class="fields">
<dt>Returns: ([element, element,...], [element, element,...])</dt>
</dl>
</td></tr></table>
</div>
<a name="draw_greytrack"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">draw_greytrack</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_greytrack">source code</a></span>
</td>
</tr></table>
<p>o track Track object</p>
<p>Put in a grey background to the current track in all fragments, if
track specifies that we should</p>
<dl class="fields">
<dt>Returns: ([element, element,...], [element, element,...])</dt>
</dl>
</td></tr></table>
</div>
<a name="draw_feature_set"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">draw_feature_set</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">set</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_feature_set">source code</a></span>
</td>
</tr></table>
<p>o set FeatureSet object</p>
<p>Returns a tuple (list of elements describing features, list of labels
for elements)</p>
<dl class="fields">
<dt>Returns: ([element, element,...], [element, element,...])</dt>
</dl>
</td></tr></table>
</div>
<a name="draw_feature"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">draw_feature</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">feature</span>,
<span class="sig-arg">parent_feature</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_feature">source code</a></span>
</td>
</tr></table>
<p>o feature Feature containing location info</p>
<p>Returns tuple of (list of elements describing single feature, list of
labels for those elements)</p>
<dl class="fields">
<dt>Returns: ([element, element,...], [element, element,...])</dt>
</dl>
</td></tr></table>
</div>
<a name="get_feature_sigil"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">get_feature_sigil</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">feature</span>,
<span class="sig-arg">x0</span>,
<span class="sig-arg">x1</span>,
<span class="sig-arg">fragment</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.get_feature_sigil">source code</a></span>
</td>
</tr></table>
<p>o feature Feature object</p>
<p>o x0 Start X co-ordinate on diagram</p>
<p>o x1 End X co-ordinate on diagram</p>
<p>o fragment The fragment on which the feature appears</p>
<p>Returns a drawable indicator of the feature, and any required label
for it</p>
<dl class="fields">
<dt>Returns: (element, element, element)</dt>
</dl>
</td></tr></table>
</div>
<a name="draw_graph_set"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">draw_graph_set</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">set</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_graph_set">source code</a></span>
</td>
</tr></table>
<p>o set GraphSet object</p>
<p>Returns tuple (list of graph elements, list of graph labels)</p>
<dl class="fields">
<dt>Returns: ([element, element,...], [element, element,...])</dt>
</dl>
</td></tr></table>
</div>
<a name="draw_line_graph"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">draw_line_graph</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">graph</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_line_graph">source code</a></span>
</td>
</tr></table>
<p>o graph Graph object</p>
<p>Returns a line graph as a list of drawable elements</p>
<dl class="fields">
<dt>Returns: [element, element,...]</dt>
</dl>
</td></tr></table>
</div>
<a name="draw_heat_graph"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">draw_heat_graph</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">graph</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_heat_graph">source code</a></span>
</td>
</tr></table>
<p>o graph Graph object</p>
<p>Returns a list of drawable elements for the heat graph</p>
<dl class="fields">
<dt>Returns: [element, element,...]</dt>
</dl>
</td></tr></table>
</div>
<a name="draw_bar_graph"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">draw_bar_graph</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">graph</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.draw_bar_graph">source code</a></span>
</td>
</tr></table>
<p>o graph Graph object</p>
<p>Returns a list of drawable elements for a bar graph of the passed
Graph object</p>
<dl class="fields">
<dt>Returns: [element, element,...]</dt>
</dl>
</td></tr></table>
</div>
<a name="canvas_location"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">canvas_location</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">base</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-pysrc.html#LinearDrawer.canvas_location">source code</a></span>
</td>
</tr></table>
<p>o base The base number on the genome sequence</p>
<p>Returns the x-coordinate and fragment number of a base on the genome
sequence, in the context of the current drawing setup</p>
<dl class="fields">
<dt>Returns: (int, float)</dt>
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Thu Aug 18 18:19:26 2011
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
