Automated update df707302870820e46f9d40d31101e5951f43a0aa

dev/api/Bio.Align.html

@@ -917,7 +917,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <p>An Alignment object has a <cite>.sequences</cite> attribute storing the sequences
 (Seq, MutableSeq, SeqRecord, or string objects) that were aligned, as well
 as a <cite>.coordinates</cite> attribute storing the sequence coordinates defining the
-alignment as a numpy array.</p>
+alignment as a NumPy array.</p>
 <dl class="simple">
 <dt>Other commonly used attributes (which may or may not be present) are:</dt><dd><ul class="simple">
 <li><dl class="simple">
@@ -943,7 +943,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <p>For an alignment consisting of N sequences, printed as N lines with
 the same number of columns, where gaps are represented by dashes,
 this method will calculate the sequence coordinates that define the
-alignment. The coordinates are returned as a numpy array of integers,
+alignment. The coordinates are returned as a NumPy array of integers,
 and can be used to create an Alignment object.</p>
 <p>The argument skipped columns should be None (the default) or an empty
 list. If skipped_columns is a list, then the indices of any columns in
@@ -1478,7 +1478,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dt class="sig sig-object py" id="Bio.Align.Alignment.indices">
 <em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">indices</span></span><a class="headerlink" href="#Bio.Align.Alignment.indices" title="Permalink to this definition"></a></dt>
 <dd><p>Return the sequence index of each lettter in the alignment.</p>
-<p>This property returns a 2D numpy array with the sequence index of each
+<p>This property returns a 2D NumPy array with the sequence index of each
 letter in the alignment. Gaps are indicated by -1.  The array has the
 same number of rows and columns as the alignment, as given by
 <cite>self.shape</cite>.</p>
@@ -1536,7 +1536,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dt class="sig sig-object py" id="Bio.Align.Alignment.inverse_indices">
 <em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">inverse_indices</span></span><a class="headerlink" href="#Bio.Align.Alignment.inverse_indices" title="Permalink to this definition"></a></dt>
 <dd><p>Return the alignment column index for each letter in each sequence.</p>
-<p>This property returns a list of 1D numpy arrays; the number of arrays
+<p>This property returns a list of 1D NumPy arrays; the number of arrays
 is equal to the number of aligned sequences, and the length of each
 array is equal to the length of the corresponding sequence. For each
 letter in each sequence, the array contains the corresponding column