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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqRecord-module.html">Module SeqRecord</a> ::
Class _RestrictedDict
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class _RestrictedDict</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqRecord-pysrc.html#_RestrictedDict">source code</a></span></p>
<pre class="base-tree">
object --+
|
dict --+
|
<strong class="uidshort">_RestrictedDict</strong>
</pre>
<hr />
<p>Dict which only allows sequences of given length as values
(PRIVATE).</p>
<p>This simple subclass of the Python dictionary is used in the SeqRecord
object for holding per-letter-annotations. This class is intended to
prevent simple errors by only allowing python sequences (e.g. lists,
strings and tuples) to be stored, and only if their length matches that
expected (the length of the SeqRecord's seq object). It cannot however
prevent the entries being edited in situ (for example appending entries
to a list).</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>x = _RestrictedDict(5)
<span class="py-prompt">>>> </span>x[<span class="py-string">"test"</span>] = <span class="py-string">"hello"</span>
<span class="py-prompt">>>> </span>x
<span class="py-output">{'test': 'hello'}</span></pre>
<p>Adding entries which don't have the expected length are blocked:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>x[<span class="py-string">"test"</span>] = <span class="py-string">"hello world"</span>
<span class="py-except">Traceback (most recent call last):</span>
<span class="py-except">...</span>
<span class="py-except">TypeError: We only allow python sequences (lists, tuples or strings) of length 5.</span></pre>
<p>The expected length is stored as a private attribute,</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>x._length
<span class="py-output">5</span></pre>
<p>In order that the SeqRecord (and other objects using this class) can
be pickled, for example for use in the multiprocessing library, we need
to be able to pickle the restricted dictionary objects.</p>
<p>Using the default protocol, which is 0 on Python 2.x,</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">import</span> pickle
<span class="py-prompt">>>> </span>y = pickle.loads(pickle.dumps(x))
<span class="py-prompt">>>> </span>y
<span class="py-output">{'test': 'hello'}</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>y._length
<span class="py-output">5</span></pre>
<p>Using the highest protocol, which is 2 on Python 2.x,</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">import</span> pickle
<span class="py-prompt">>>> </span>z = pickle.loads(pickle.dumps(x, pickle.HIGHEST_PROTOCOL))
<span class="py-prompt">>>> </span>z
<span class="py-output">{'test': 'hello'}</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>z._length
<span class="py-output">5</span></pre>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"><pre class="literalblock">
new empty dictionary
</pre></span>
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<td><span class="summary-sig"><a href="Bio.SeqRecord._RestrictedDict-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">length</span>)</span><br />
Create an EMPTY restricted dictionary.</td>
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<span class="codelink"><a href="Bio.SeqRecord-pysrc.html#_RestrictedDict.__init__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.SeqRecord._RestrictedDict-class.html#__setitem__" class="summary-sig-name">__setitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>,
<span class="summary-sig-arg">value</span>)</span><br />
x[i]=y</td>
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<span class="codelink"><a href="Bio.SeqRecord-pysrc.html#_RestrictedDict.__setitem__">source code</a></span>
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<span class="summary-type">None</span>
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<td><span class="summary-sig"><a href="Bio.SeqRecord._RestrictedDict-class.html#update" class="summary-sig-name">update</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">new_dict</span>)</span><br />
Update D from dict/iterable E and F.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqRecord-pysrc.html#_RestrictedDict.update">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code>dict</code></b>:
<code>__cmp__</code>,
<code>__contains__</code>,
<code>__delitem__</code>,
<code>__eq__</code>,
<code>__ge__</code>,
<code>__getattribute__</code>,
<code>__getitem__</code>,
<code>__gt__</code>,
<code>__iter__</code>,
<code>__le__</code>,
<code>__len__</code>,
<code>__lt__</code>,
<code>__ne__</code>,
<code>__new__</code>,
<code>__repr__</code>,
<code>__sizeof__</code>,
<code>clear</code>,
<code>copy</code>,
<code>fromkeys</code>,
<code>get</code>,
<code>has_key</code>,
<code>items</code>,
<code>iteritems</code>,
<code>iterkeys</code>,
<code>itervalues</code>,
<code>keys</code>,
<code>pop</code>,
<code>popitem</code>,
<code>setdefault</code>,
<code>values</code>,
<code>viewitems</code>,
<code>viewkeys</code>,
<code>viewvalues</code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
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<p class="indent-wrapped-lines"><b>Inherited from <code>dict</code></b>:
<code>__hash__</code>
</p>
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<!-- ==================== PROPERTIES ==================== -->
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
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<a name="__init__"></a>
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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">length</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqRecord-pysrc.html#_RestrictedDict.__init__">source code</a></span>
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<p>Create an EMPTY restricted dictionary.</p>
<dl class="fields">
<dt>Returns: <pre class="literalblock">
new empty dictionary
</pre></dt>
<dt>Overrides:
object.__init__
</dt>
</dl>
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<a name="__setitem__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__setitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">key</span>,
<span class="sig-arg">value</span>)</span>
<br /><em class="fname">(Index assignment operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqRecord-pysrc.html#_RestrictedDict.__setitem__">source code</a></span>
</td>
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<p>x[i]=y</p>
<dl class="fields">
<dt>Overrides:
dict.__setitem__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">update</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">new_dict</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqRecord-pysrc.html#_RestrictedDict.update">source code</a></span>
</td>
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<p>Update D from dict/iterable E and F. If E has a .keys() method, does:
for k in E: D[k] = E[k] If E lacks .keys() method, does: for (k, v)
in E: D[k] = v In either case, this is followed by: for k in F: D[k] =
F[k]</p>
<dl class="fields">
<dt>Returns: None</dt>
<dt>Overrides:
dict.update
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
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