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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqFeature-module.html">Module SeqFeature</a> ::
Class FeatureLocation
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<h1 class="epydoc">Class FeatureLocation</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#FeatureLocation">source code</a></span></p>
<p>Specify the location of a feature along a sequence.</p>
<p>This attempts to deal with fuzziness of position ends, but also make
it easy to get the start and end in the 'normal' case (no fuzziness).</p>
<p>You should access the start and end attributes with
your_location.start and your_location.end. If the start and end are
exact, this will return the positions, if not, we'll return the
approriate Fuzzy class with info about the position and fuzziness.</p>
<p>Note that the start and end location numbering follow Python's scheme,
thus a GenBank entry of 123..150 (one based counting) becomes a location
of [122:150] (zero based counting).</p>
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<td><span class="summary-sig"><a href="Bio.SeqFeature.FeatureLocation-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>)</span><br />
Specify the start and end of a sequence feature.</td>
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<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#FeatureLocation.__init__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqFeature.FeatureLocation-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns a representation of the location.</td>
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<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#FeatureLocation.__str__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqFeature.FeatureLocation-class.html#__getattr__" class="summary-sig-name">__getattr__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">attr</span>)</span><br />
Make it easy to get non-fuzzy starts and ends.</td>
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<span class="codelink"><a href="Bio.SeqFeature-pysrc.html#FeatureLocation.__getattr__">source code</a></span>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">start</span>,
<span class="sig-arg">end</span>)</span>
<br /><em class="fname">(Constructor)</em>
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<p>Specify the start and end of a sequence feature.</p>
<p>start and end arguments specify the values where the feature begins
and ends. These can either by any of the *Position objects that inherit
from AbstractPosition, or can just be integers specifying the position.
In the case of integers, the values are assumed to be exact and are
converted in ExactPosition arguments. This is meant to make it easy to
deal with non-fuzzy ends.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#FeatureLocation.__str__">source code</a></span>
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<p>Returns a representation of the location. For the simple case this
uses the python splicing syntax, [122:150] (zero based counting) which
GenBank would call 123..150 (one based counting).</p>
<dl class="fields">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__getattr__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">attr</span>)</span>
<br /><em class="fname">(Qualification operator)</em>
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</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqFeature-pysrc.html#FeatureLocation.__getattr__">source code</a></span>
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<p>Make it easy to get non-fuzzy starts and ends.</p>
<p>We override get_attribute here so that in non-fuzzy cases we can just
return the start and end position without any hassle.</p>
<p>To get fuzzy start and ends, just ask for item.start and item.end. To
get non-fuzzy attributes (ie. the position only) ask for
'item.nofuzzy_start', 'item.nofuzzy_end'. These should return the largest
range of the fuzzy position. So something like: (10.20)..(30.40) should
return 10 for start, and 40 for end.</p>
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