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Merge pull request #437 from GavinHuttley/master
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Updated docs
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@GavinHuttley
GavinHuttley committed Dec 6, 2019
2 parents 6d81c17 + 814b78e commit 9e0ce5c
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2 changes: 1 addition & 1 deletion doc/app/user_function.rst
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Expand Up @@ -56,7 +56,7 @@ Renaming sequences

This time we wrap a method call on a ``SequenceCollection`` (and the alignment sub-classes) for renaming sequences. We also illustrate here that to support both aligned and unaligned data types as input/output, we have to include these in the construction of the custom function.

.. note:: The ``SERIALISABLE_TYPE`` indicates the data has the ability to converted to ``json``.
.. note:: The ``SERIALISABLE_TYPE`` indicates the data has the ability to be converted to ``json``.

.. doctest::

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2 changes: 1 addition & 1 deletion doc/cookbook/calc_genetic_distance.ipynb
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Expand Up @@ -259,7 +259,7 @@
{
"data": {
"text/plain": [
"<cogent3.evolve.fast_distance.TN93Pair at 0x1186bc518>"
"<cogent3.evolve.fast_distance.TN93Pair at 0x11eed9160>"
]
},
"execution_count": 3,
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189 changes: 171 additions & 18 deletions doc/cookbook/evo_modelling.ipynb
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20 changes: 10 additions & 10 deletions doc/cookbook/what_codes.ipynb
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Expand Up @@ -168,11 +168,11 @@
"<body>\n",
"<table>\n",
"<tr style=\"background-color:rgba(161, 195, 209, 0.5);\"><td></td><td><b>0</b></td></tr>\n",
"<tr><td class=\"label\">TombBat</td><td><span class=\"T_dna\">T</span><span class=\"G_dna\">G</span><span class=\"T_dna\">T</span><span class=\"G_dna\">G</span><span class=\"G_dna\">G</span><span class=\"C_dna\">C</span><span class=\"A_dna\">A</span><span class=\"C_dna\">C</span><span class=\"A_dna\">A</span><span class=\"A_dna\">A</span><span class=\"G_dna\">G</span><span class=\"T_dna\">T</span><span class=\"A_dna\">A</span><span class=\"C_dna\">C</span><span class=\"T_dna\">T</span><span class=\"C_dna\">C</span><span class=\"A_dna\">A</span><span class=\"T_dna\">T</span><span class=\"G_dna\">G</span><span class=\"C_dna\">C</span><span class=\"C_dna\">C</span></td></tr>\n",
"<tr><td class=\"label\">FlyingFox</td><td><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"A_dna\">.</span><span class=\"A_dna\">A</span><span class=\"T_dna\">.</span><span class=\"G_dna\">G</span><span class=\"C_dna\">.</span><span class=\"T_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"C_dna\">.</span></td></tr>\n",
"<tr><td class=\"label\">DogFaced</td><td><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"A_dna\">.</span><span class=\"A_dna\">A</span><span class=\"T_dna\">.</span><span class=\"A_dna\">.</span><span class=\"C_dna\">.</span><span class=\"T_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"C_dna\">.</span></td></tr>\n",
"<tr><td class=\"label\">FreeTaile</td><td><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"G_dna\">G</span><span class=\"A_dna\">A</span><span class=\"T_dna\">.</span><span class=\"A_dna\">.</span><span class=\"C_dna\">.</span><span class=\"T_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"C_dna\">.</span></td></tr>\n",
"<tr><td class=\"label\">LittleBro</td><td><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"G_dna\">G</span><span class=\"A_dna\">A</span><span class=\"T_dna\">.</span><span class=\"A_dna\">.</span><span class=\"C_dna\">.</span><span class=\"T_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"C_dna\">.</span></td></tr>\n",
"<tr><td class=\"label\">FlyingFox</td><td><span class=\"T_dna\">T</span><span class=\"G_dna\">G</span><span class=\"T_dna\">T</span><span class=\"G_dna\">G</span><span class=\"G_dna\">G</span><span class=\"C_dna\">C</span><span class=\"A_dna\">A</span><span class=\"C_dna\">C</span><span class=\"A_dna\">A</span><span class=\"A_dna\">A</span><span class=\"A_dna\">A</span><span class=\"T_dna\">T</span><span class=\"G_dna\">G</span><span class=\"C_dna\">C</span><span class=\"T_dna\">T</span><span class=\"C_dna\">C</span><span class=\"A_dna\">A</span><span class=\"T_dna\">T</span><span class=\"G_dna\">G</span><span class=\"C_dna\">C</span><span class=\"C_dna\">C</span></td></tr>\n",
"<tr><td class=\"label\">DogFaced</td><td><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"A_dna\">.</span><span class=\"A_dna\">.</span><span class=\"T_dna\">.</span><span class=\"A_dna\">A</span><span class=\"C_dna\">.</span><span class=\"T_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"C_dna\">.</span></td></tr>\n",
"<tr><td class=\"label\">FreeTaile</td><td><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"G_dna\">G</span><span class=\"A_dna\">.</span><span class=\"T_dna\">.</span><span class=\"A_dna\">A</span><span class=\"C_dna\">.</span><span class=\"T_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"C_dna\">.</span></td></tr>\n",
"<tr><td class=\"label\">LittleBro</td><td><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"G_dna\">G</span><span class=\"A_dna\">.</span><span class=\"T_dna\">.</span><span class=\"A_dna\">A</span><span class=\"C_dna\">.</span><span class=\"T_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"C_dna\">.</span></td></tr>\n",
"<tr><td class=\"label\">TombBat</td><td><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"A_dna\">.</span><span class=\"G_dna\">G</span><span class=\"T_dna\">.</span><span class=\"A_dna\">A</span><span class=\"C_dna\">.</span><span class=\"T_dna\">.</span><span class=\"C_dna\">.</span><span class=\"A_dna\">.</span><span class=\"T_dna\">.</span><span class=\"G_dna\">.</span><span class=\"C_dna\">.</span><span class=\"C_dna\">.</span></td></tr>\n",
"</table>\n",
"<p><i>5 x 21 dna alignment</i></p>\n",
"</body>"
Expand Down Expand Up @@ -240,11 +240,11 @@
"<body>\n",
"<table>\n",
"<tr style=\"background-color:rgba(161, 195, 209, 0.5);\"><td></td><td><b>0</b></td></tr>\n",
"<tr><td class=\"label\">TombBat</td><td><span class=\"C_protein\">C</span><span class=\"G_protein\">G</span><span class=\"T_protein\">T</span><span class=\"S_protein\">S</span><span class=\"T_protein\">T</span><span class=\"H_protein\">H</span><span class=\"A_protein\">A</span><span class=\"S_protein\">S</span><span class=\"S_protein\">S</span><span class=\"V_protein\">V</span><span class=\"Q_protein\">Q</span><span class=\"H_protein\">H</span><span class=\"E_protein\">E</span><span class=\"N_protein\">N</span><span class=\"S_protein\">S</span><span class=\"S_protein\">S</span><span class=\"L_protein\">L</span><span class=\"L_protein\">L</span><span class=\"L_protein\">L</span><span class=\"T_protein\">T</span></td></tr>\n",
"<tr><td class=\"label\">FlyingFox</td><td><span class=\"C_protein\">.</span><span class=\"G_protein\">.</span><span class=\"T_protein\">.</span><span class=\"N_protein\">N</span><span class=\"A_protein\">A</span><span class=\"H_protein\">.</span><span class=\"A_protein\">.</span><span class=\"S_protein\">.</span><span class=\"S_protein\">.</span><span class=\"L_protein\">L</span><span class=\"Q_protein\">.</span><span class=\"H_protein\">.</span><span class=\"E_protein\">.</span><span class=\"N_protein\">.</span><span class=\"ambig_protein\">-</span><span class=\"S_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">.</span><span class=\"Y_protein\">Y</span><span class=\"T_protein\">.</span></td></tr>\n",
"<tr><td class=\"label\">DogFaced</td><td><span class=\"C_protein\">.</span><span class=\"G_protein\">.</span><span class=\"T_protein\">.</span><span class=\"N_protein\">N</span><span class=\"T_protein\">.</span><span class=\"H_protein\">.</span><span class=\"A_protein\">.</span><span class=\"N_protein\">N</span><span class=\"S_protein\">.</span><span class=\"L_protein\">L</span><span class=\"Q_protein\">.</span><span class=\"H_protein\">.</span><span class=\"E_protein\">.</span><span class=\"N_protein\">.</span><span class=\"S_protein\">.</span><span class=\"S_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">.</span><span class=\"Y_protein\">Y</span><span class=\"T_protein\">.</span></td></tr>\n",
"<tr><td class=\"label\">FreeTaile</td><td><span class=\"C_protein\">.</span><span class=\"G_protein\">.</span><span class=\"T_protein\">.</span><span class=\"D_protein\">D</span><span class=\"T_protein\">.</span><span class=\"H_protein\">.</span><span class=\"A_protein\">.</span><span class=\"S_protein\">.</span><span class=\"S_protein\">.</span><span class=\"L_protein\">L</span><span class=\"Q_protein\">.</span><span class=\"H_protein\">.</span><span class=\"E_protein\">.</span><span class=\"N_protein\">.</span><span class=\"S_protein\">.</span><span class=\"S_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">.</span><span class=\"T_protein\">.</span></td></tr>\n",
"<tr><td class=\"label\">LittleBro</td><td><span class=\"C_protein\">.</span><span class=\"G_protein\">.</span><span class=\"T_protein\">.</span><span class=\"D_protein\">D</span><span class=\"T_protein\">.</span><span class=\"H_protein\">.</span><span class=\"A_protein\">.</span><span class=\"S_protein\">.</span><span class=\"S_protein\">.</span><span class=\"L_protein\">L</span><span class=\"Q_protein\">.</span><span class=\"H_protein\">.</span><span class=\"E_protein\">.</span><span class=\"N_protein\">.</span><span class=\"S_protein\">.</span><span class=\"S_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">.</span><span class=\"T_protein\">.</span></td></tr>\n",
"<tr><td class=\"label\">FlyingFox</td><td><span class=\"C_protein\">C</span><span class=\"G_protein\">G</span><span class=\"T_protein\">T</span><span class=\"N_protein\">N</span><span class=\"A_protein\">A</span><span class=\"H_protein\">H</span><span class=\"A_protein\">A</span><span class=\"S_protein\">S</span><span class=\"S_protein\">S</span><span class=\"L_protein\">L</span><span class=\"Q_protein\">Q</span><span class=\"H_protein\">H</span><span class=\"E_protein\">E</span><span class=\"N_protein\">N</span><span class=\"ambig_protein\">-</span><span class=\"S_protein\">S</span><span class=\"L_protein\">L</span><span class=\"L_protein\">L</span><span class=\"Y_protein\">Y</span><span class=\"T_protein\">T</span></td></tr>\n",
"<tr><td class=\"label\">DogFaced</td><td><span class=\"C_protein\">.</span><span class=\"G_protein\">.</span><span class=\"T_protein\">.</span><span class=\"N_protein\">.</span><span class=\"T_protein\">T</span><span class=\"H_protein\">.</span><span class=\"A_protein\">.</span><span class=\"N_protein\">N</span><span class=\"S_protein\">.</span><span class=\"L_protein\">.</span><span class=\"Q_protein\">.</span><span class=\"H_protein\">.</span><span class=\"E_protein\">.</span><span class=\"N_protein\">.</span><span class=\"S_protein\">S</span><span class=\"S_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">.</span><span class=\"Y_protein\">.</span><span class=\"T_protein\">.</span></td></tr>\n",
"<tr><td class=\"label\">FreeTaile</td><td><span class=\"C_protein\">.</span><span class=\"G_protein\">.</span><span class=\"T_protein\">.</span><span class=\"D_protein\">D</span><span class=\"T_protein\">T</span><span class=\"H_protein\">.</span><span class=\"A_protein\">.</span><span class=\"S_protein\">.</span><span class=\"S_protein\">.</span><span class=\"L_protein\">.</span><span class=\"Q_protein\">.</span><span class=\"H_protein\">.</span><span class=\"E_protein\">.</span><span class=\"N_protein\">.</span><span class=\"S_protein\">S</span><span class=\"S_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">L</span><span class=\"T_protein\">.</span></td></tr>\n",
"<tr><td class=\"label\">LittleBro</td><td><span class=\"C_protein\">.</span><span class=\"G_protein\">.</span><span class=\"T_protein\">.</span><span class=\"D_protein\">D</span><span class=\"T_protein\">T</span><span class=\"H_protein\">.</span><span class=\"A_protein\">.</span><span class=\"S_protein\">.</span><span class=\"S_protein\">.</span><span class=\"L_protein\">.</span><span class=\"Q_protein\">.</span><span class=\"H_protein\">.</span><span class=\"E_protein\">.</span><span class=\"N_protein\">.</span><span class=\"S_protein\">S</span><span class=\"S_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">L</span><span class=\"T_protein\">.</span></td></tr>\n",
"<tr><td class=\"label\">TombBat</td><td><span class=\"C_protein\">.</span><span class=\"G_protein\">.</span><span class=\"T_protein\">.</span><span class=\"S_protein\">S</span><span class=\"T_protein\">T</span><span class=\"H_protein\">.</span><span class=\"A_protein\">.</span><span class=\"S_protein\">.</span><span class=\"S_protein\">.</span><span class=\"V_protein\">V</span><span class=\"Q_protein\">.</span><span class=\"H_protein\">.</span><span class=\"E_protein\">.</span><span class=\"N_protein\">.</span><span class=\"S_protein\">S</span><span class=\"S_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">.</span><span class=\"L_protein\">L</span><span class=\"T_protein\">.</span></td></tr>\n",
"</table>\n",
"<p><i>5 x 20 protein alignment</i></p>\n",
"</body>"
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