Make remove_all_gap_columns linear and fix empty-row misalignment

lib/bx/align/core.py

@@ -219,34 +219,18 @@ def remove_all_gap_columns(self) -> None:
         Remove any columns containing only gaps from alignment components,
         text of components is modified IN PLACE.
         """
-        seqs: list[list[str] | None] = []
-        for c in self.components:
-            if c.empty or c.text is None:
-                seqs.append(None)
-            else:
-                seqs.append(list(c.text))
-        i = 0
-        text_size = self.text_size
-        while i < text_size:
-            all_gap = True
-            for seq in seqs:
-                if seq is None:
-                    continue
-                if seq[i] != "-":
-                    all_gap = False
-            if all_gap:
-                for seq in seqs:
-                    if seq is None:
-                        continue
-                    del seq[i]
-                text_size -= 1
-            else:
-                i += 1
-        for component, seq in zip(self.components, seqs):
-            if seq is None:
-                continue
-            component.text = "".join(seq)
-        self.text_size = text_size
+        # A component can occur more than once; rebuild each object only once.
+        texts = list({id(c): (c, c.text) for c in self.components if not c.empty and c.text is not None}.values())
+        if any("-" not in text for _, text in texts):
+            return
+        # Decide which columns to retain before modifying any component. Deleting
+        # individual gaps from lists repeatedly shifts the remaining alignment.
+        keep = [i for i in range(self.text_size) if any(text[i] != "-" for _, text in texts)]
+        if len(keep) == self.text_size:
+            return
+        for component, text in texts:
+            component.text = "".join(text[i] for i in keep)
+        self.text_size = len(keep)
 
     def __eq__(self, other: object) -> bool:
         if other is None or not isinstance(other, type(self)):

lib/bx/align/maf_tests.py

@@ -4,6 +4,8 @@
 
 from io import StringIO
 
+import pytest
+
 from bx import align
 from bx.align import maf
 
@@ -211,7 +213,9 @@ def test_column_iter():
         assert c == expected[i]
 
 
-def test_remove_all_gap_column():
+@pytest.mark.parametrize("empty_index", [0, 1, 3])
+@pytest.mark.parametrize("repeat_component", [False, True])
+def test_remove_all_gap_column(empty_index, repeat_component):
     complex_maf_gap = align.Alignment()
     complex_maf_gap.score = "7009"
     complex_maf_gap.components.append(
@@ -231,7 +235,15 @@ def test_remove_all_gap_column():
     complex_maf_gap.components[-1].empty = True
     complex_maf_gap.components[-1].synteny_empty = maf.MAF_INSERT_STATUS
     complex_maf_gap.text_size = 11
+    empty = complex_maf_gap.components.pop()
+    complex_maf_gap.components.insert(empty_index, empty)
+    if repeat_component:
+        complex_maf_gap.add_component(next(c for c in complex_maf_gap.components if not c.empty))
     complex_maf_gap.remove_all_gap_columns()
+    if repeat_component:
+        complex_maf_gap.components.pop()
+    # Return the empty row to its fixture position for the equality check.
+    complex_maf_gap.components.append(complex_maf_gap.components.pop(empty_index))
     assert complex_maf_gap == complex_maf