From 8283030e7fc4f954508eb8545bd13aca0b3cfae0 Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Wed, 31 Jul 2024 14:04:46 -0700
Subject: [PATCH] fixups

---
 pybedlite/bed_record.py                  |  2 +-
 pybedlite/overlap_detector.py            | 15 +++++----------
 pybedlite/tests/test_overlap_detector.py | 18 +++++++++---------
 3 files changed, 15 insertions(+), 20 deletions(-)

diff --git a/pybedlite/bed_record.py b/pybedlite/bed_record.py
index 1f685a1..37d90c3 100644
--- a/pybedlite/bed_record.py
+++ b/pybedlite/bed_record.py
@@ -188,7 +188,7 @@ def refname(self) -> str:
         return self.chrom
 
     @property
-    def is_negative(self) -> bool:
+    def negative(self) -> bool:
         """True if the interval is on the negative strand, False otherwise"""
         return self.strand is not None and self.strand == BedStrand.Positive
 
diff --git a/pybedlite/overlap_detector.py b/pybedlite/overlap_detector.py
index f19acb0..c79ead1 100644
--- a/pybedlite/overlap_detector.py
+++ b/pybedlite/overlap_detector.py
@@ -17,7 +17,7 @@
 for sorting them in :func:`~pybedlite.overlap_detector.OverlapDetector.get_overlaps` using
 the following property if it is present, otherwise assumed to be positive stranded:
 
-  * `is_negative (bool)`: Whether the feature is negative stranded or not
+  * `negative (bool)`: Whether the feature is negative stranded or not
 
 This is encapsulated in the :class:`~pybedlite.overlap_detector.StrandedGenomicSpan` protocol.
 
@@ -101,7 +101,7 @@ def end(self) -> int:
 
 class StrandedGenomicSpan(GenomicSpan, Protocol):
     @property
-    def is_negative(self) -> bool:
+    def negative(self) -> bool:
         """True if the interval is on the negative strand, False otherwise"""
 
 
@@ -135,11 +135,6 @@ def __attrs_post_init__(self) -> None:
         if self.end <= self.start:
             raise ValueError(f"end <= start: {self.end} <= {self.start}")
 
-    @property
-    def is_negative(self) -> bool:
-        """True if the interval is on the negative strand, False otherwise"""
-        return self.negative
-
     def overlap(self, other: "Interval") -> int:
         """Returns the overlap between this interval and the other, or zero if there is none.
 
@@ -297,14 +292,14 @@ def get_overlaps(self, interval: GenomicSpan) -> List[GenericGenomicsSpan]:
                 key=lambda intv: (
                     intv.start,
                     intv.end,
-                    self._is_negative(intv),
+                    self._negative(intv),
                     intv.refname,
                 ),
             )
 
     @staticmethod
-    def _is_negative(interval: GenomicSpan) -> bool:
-        return getattr(interval, "is_negative", False)
+    def _negative(interval: GenomicSpan) -> bool:
+        return getattr(interval, "negative", False)
 
     def get_enclosing_intervals(self, interval: GenomicSpan) -> List[GenericGenomicsSpan]:
         """Returns the set of intervals in this detector that wholly enclose the query interval.
diff --git a/pybedlite/tests/test_overlap_detector.py b/pybedlite/tests/test_overlap_detector.py
index c458ddc..38e3bd5 100644
--- a/pybedlite/tests/test_overlap_detector.py
+++ b/pybedlite/tests/test_overlap_detector.py
@@ -207,7 +207,7 @@ class ZeroBasedOpenEndedProtocol:
         end: int
 
         @property
-        def is_negative(self) -> bool:
+        def negative(self) -> bool:
             return False
 
     @dataclass(eq=True, frozen=True)
@@ -226,7 +226,7 @@ def start(self) -> int:
             return self.one_based_start - 1
 
         @property
-        def is_negative(self) -> bool:
+        def negative(self) -> bool:
             """True if the interval is on the negative strand, False otherwise"""
             return False
 
@@ -246,7 +246,7 @@ class ZeroBasedStranded:
         refname: str
         zero_based_start: int
         end: int
-        is_negative: bool
+        negative: bool
 
         @property
         def start(self) -> int:
@@ -258,7 +258,7 @@ def start(self) -> int:
     one_based_protocol = OneBasedProtocol(contig="chr1", one_based_start=10, end=60)
     zero_based_unstranded = ZeroBasedUnstranded(refname="chr1", zero_based_start=20, end=70)
     zero_based_stranded = ZeroBasedStranded(
-        refname="chr1", zero_based_start=30, end=80, is_negative=True
+        refname="chr1", zero_based_start=30, end=80, negative=True
     )
     # Set up an overlap detector to hold all the features we care about
     AllKinds: TypeAlias = Union[
@@ -272,10 +272,10 @@ def start(self) -> int:
     ]
     detector: OverlapDetector[AllKinds] = OverlapDetector(features)
 
-    assert OverlapDetector._is_negative(zero_based_protocol) is False
-    assert OverlapDetector._is_negative(one_based_protocol) is False
-    assert OverlapDetector._is_negative(zero_based_unstranded) is False
-    assert OverlapDetector._is_negative(zero_based_stranded) is True
+    assert OverlapDetector._negative(zero_based_protocol) is False
+    assert OverlapDetector._negative(one_based_protocol) is False
+    assert OverlapDetector._negative(zero_based_unstranded) is False
+    assert OverlapDetector._negative(zero_based_stranded) is True
 
     # Query the overlap detector with yet another type
     assert detector.get_overlaps(Interval("chr1", 0, 1)) == []
@@ -325,7 +325,7 @@ def start(self) -> int:
             return self.zero_based_start
 
         @property
-        def is_negative(self) -> bool:
+        def negative(self) -> bool:
             """True if the interval is on the negative strand, False otherwise"""
             return False