Make all lines at most 80 chars long

cfe-lab · Sep 19, 2024 · c3802ab · c3802ab
1 parent 1e110bb
commit c3802ab
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Showing 5 changed files with 376 additions and 181 deletions.
diff --git a/src/aligntools/coordinate_mapping.py b/src/aligntools/coordinate_mapping.py
@@ -6,10 +6,13 @@
 
 class CoordinateMapping:
     """
-    Manages bidirectional mappings between reference and query coordinates, as well as operation indices.
+    Manages bidirectional mappings between reference and query
+    coordinates, as well as operation indices.
 
-    The mapping enables conversion from reference to query coordinates and vice versa. It also manages the
-    association of these coordinates with their respective operations in the alignment process.
+    The mapping enables conversion from reference to query coordinates
+    and vice versa. It also manages the association of these
+    coordinates with their respective operations in the alignment
+    process.
     """
 
     def __init__(self) -> None:
@@ -28,20 +31,25 @@ def extend(self,
         self.ref_to_op.extend(ref_index, op_index)
         self.query_to_op.extend(query_index, op_index)
 
-    def translate(self, reference_delta: int, query_delta: int) -> 'CoordinateMapping':
+    def translate(self, reference_delta: int, query_delta: int) \
+            -> 'CoordinateMapping':
         """
-        Generate a new CoordinateMapping with shifted coordinate spaces.
-
-        This method creates a new mapping where each original coordinate in
-        the reference and query sequences is shifted. This allows for adapting
-        the CoordinateMapping to account for changes or offsets in sequence positions,
-        such as when sequences are trimmed or extended.
+        Generate a new CoordinateMapping with shifted coordinate
+        spaces.
+
+        This method creates a new mapping where each original
+        coordinate in the reference and query sequences is
+        shifted. This allows for adapting the CoordinateMapping to
+        account for changes or offsets in sequence positions, such as
+        when sequences are trimmed or extended.
         """
 
         ret = CoordinateMapping()
 
-        ret.ref_to_query = self.ref_to_query.translate(reference_delta, query_delta)
-        ret.query_to_ref = self.query_to_ref.translate(query_delta, reference_delta)
+        ret.ref_to_query = self.ref_to_query.translate(
+            reference_delta, query_delta)
+        ret.query_to_ref = self.query_to_ref.translate(
+            query_delta, reference_delta)
         ret.ref_to_op = self.ref_to_op.translate(reference_delta, 0)
         ret.query_to_op = self.query_to_op.translate(query_delta, 0)
 

diff --git a/src/aligntools/int_dict.py b/src/aligntools/int_dict.py
@@ -4,12 +4,15 @@
 
 class IntDict(Mapping[int, int]):
     """
-    An extension of the basic Python dictionary designed for integer-to-integer mappings.
-
-    The IntDict maintains not just key-value pairs (as in a normal dictionary) but also
-    tracks additional sets called `domain` and `codomain`. These sets are supersets
-    of the keys and values respectively, as they include integers that might not be used
-    directly in mappings but are within the range of interest for the domain and codomain.
+    An extension of the basic Python dictionary designed for
+    integer-to-integer mappings.
+
+    The IntDict maintains not just key-value pairs (as in a normal
+    dictionary) but also tracks additional sets called `domain` and
+    `codomain`. These sets are supersets of the keys and values
+    respectively, as they include integers that might not be used
+    directly in mappings but are within the range of interest for the
+    domain and codomain.
     """
 
     def __init__(self) -> None:
@@ -35,10 +38,11 @@ def right_min(self, index: int) -> Optional[int]:
 
     def translate(self, domain_delta: int, codomain_delta: int) -> 'IntDict':
         """
-        Generates a new IntDict by shifting the entire mapping -- keys and values
-        are incremented by domain_delta and codomain_delta, respectively.
-        This shift operation preserves the inherent ordering and relative spacing within the mapping,
-        effectively repositioning the dataset within the integer space.
+        Generates a new IntDict by shifting the entire mapping -- keys
+        and values are incremented by domain_delta and codomain_delta,
+        respectively.  This shift operation preserves the inherent
+        ordering and relative spacing within the mapping, effectively
+        repositioning the dataset within the integer space.
         """
 
         ret = IntDict()