example commit for #176

src/pydna/common_sub_strings.py

@@ -16,7 +16,9 @@
 # from array import array as _array
 # import itertools as _itertools
 from operator import itemgetter as _itemgetter
+from typing import List as _List, Tuple as _Tuple
 
+Match = _Tuple[int, int, int]
 
 # def _kark_sort(s, SA, n, K):
 #     def radixpass(a, b, r, s, n, k):
@@ -312,16 +314,37 @@
 #     return match
 
 
-def common_sub_strings(stringx: str, stringy: str, limit=25):
+def common_sub_strings(stringx: str, stringy: str, limit=25) -> _List[Match]:
+    """
+    Finds all common substrings between stringx and stringy, and returns
+    them sorted by length.
+
+    This function is case sensitive.
+
+    Parameters
+    ----------
+    stringx : str
+    stringy : str
+    limit : int, optional
+
+    Returns
+    -------
+    list of tuple
+        [(startx1, starty1, length1),(startx2, starty2, length2), ...]
+
+        startx1 = startposition in x, where substring 1 starts
+        starty1 = position in y where substring 1 starts
+        length1 = lenght of substring
+    """
     from pydivsufsort import common_substrings
 
-    match = common_substrings(stringx, stringy, limit=limit)
-    match.sort()
-    match.sort(key=_itemgetter(2), reverse=True)
-    return match
+    matches = common_substrings(stringx, stringy, limit=limit)
+    matches.sort()
+    matches.sort(key=_itemgetter(2), reverse=True)
+    return matches
 
 
-def terminal_overlap(stringx: str, stringy: str, limit=15):
+def terminal_overlap(stringx: str, stringy: str, limit=15) -> _List[Match]:
     """Finds the the flanking common substrings between stringx and stringy
     longer than limit. This means that the results only contains substrings
     that starts or ends at the the ends of stringx and stringy.