Add Aligner and pyopal.align to the documentation

althonos · Jan 17, 2024 · ffffb94 · ffffb94
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diff --git a/docs/api/aligner.rst b/docs/api/aligner.rst
@@ -0,0 +1,9 @@
+Aligner
+=======
+
+.. currentmodule:: pyopal
+
+
+.. autoclass:: pyopal.Aligner
+   :special-members: __init__
+   :members:
diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -1,22 +1,32 @@
 API Reference
 =============
 
+.. currentmodule:: pyopal
+
+
+Functions
+---------
+
+.. autofunction:: pyopal.align
+
+
+Classes
+-------
+
 .. toctree::
    :hidden:
 
    alphabet <alphabet>
    score_matrix <score_matrix>
    database <database>
+   aligner <aligner>
    result <result>
 
 
-.. currentmodule:: pyopal
-
-
 .. only:: html
 
     Alphabet
-    --------
+    ^^^^^^^^
 
     .. autosummary::
         :nosignatures:
@@ -25,7 +35,7 @@ API Reference
 
 
     ScoreMatrix
-    -----------
+    ^^^^^^^^^^^
 
     .. autosummary::
         :nosignatures:
@@ -34,16 +44,25 @@ API Reference
 
 
     Database
-    --------
+    ^^^^^^^^
 
     .. autosummary::
         :nosignatures:
 
         pyopal.Database
 
 
+    Aligner
+    ^^^^^^^
+
+    .. autosummary::
+        :nosignatures:
+
+        pyopal.Aligner
+
+
     Results
-    -------
+    ^^^^^^^
 
     .. autosummary::
        :nosignatures:
@@ -52,3 +71,4 @@ API Reference
        pyopal.EndResult
        pyopal.FullResult
 
+
diff --git a/pyopal/__init__.py b/pyopal/__init__.py
@@ -74,8 +74,8 @@ def align(
     Arguments:
         query (`str` or byte-like object): The sequence to query the
             database with.
-        database (`~pyopal.BaseDatabase`): The database sequences
-            to align the query to.
+        database (iterable of `str` or byte-like objects): The database 
+            sequences to align the query to.
         score_matrix (`~pyopal.ScoreMatrix`): The scoring matrix
             to use for the alignment.
 
@@ -108,6 +108,13 @@ def align(
             the main threads for aligning, otherwise spawns a 
             `multiprocessing.pool.ThreadPool`.
 
+    Yields:
+        `~pyopal.ScoreResult`: Results for the alignment of the query
+        to each target sequence in the database. The actual type depends 
+        on the requested ``mode``: it will be `ScoreResult` for mode 
+        ``score``, `EndResult` for mode ``end`` and `FullResult` for 
+        mode ``full``.
+
     """
     # derive default parameters
     if threads == 0: