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medema-group · Dec 5, 2024 · 29ea5a2 · 29ea5a2
1 parent 16b51be
commit 29ea5a2
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Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/big_scape/comparison/lcs.py b/big_scape/comparison/lcs.py
@@ -287,7 +287,9 @@ def find_domain_lcs_region(
 
         # Length
 
-        # clear the lists if it's not empty and the current match is longer
+        # clear the longest list if it's not empty and the current match is longer.
+        # also clear the central list as we do not care about a shorter LCS even if it
+        # is more central
         if len(use_longest_list) > 0 and length > use_longest_list[0][1]:
             use_longest_list.clear()
             use_central_list.clear()
@@ -524,7 +526,9 @@ def find_domain_lcs_protocluster(
 
         # Length
 
-        # clear the lists if it's not empty and the current match is longer
+        # clear the longest list if it's not empty and the current match is longer.
+        # also clear the central list as we do not care about a shorter LCS even if it
+        # is more central
         if len(use_longest_list) > 0 and length > use_longest_list[0][1]:
             use_longest_list.clear()
             use_central_list.clear()

diff --git a/big_scape/output/legacy_output.py b/big_scape/output/legacy_output.py
@@ -638,11 +638,13 @@ def write_network_file(
         .where(edge_params_table.c.weights.in_(incl_weights))
         .where(edge_params_table.c.alignment_mode == aln_mode)
         .where(edge_params_table.c.extend_strategy == ext_strat)
-        .where(distance_table.c.distance < 1)
     )
 
     if cutoff is not None:
         select_statement = select_statement.where(distance_table.c.distance < cutoff)
+    else:
+        # still do not include edges with a distance of 1
+        select_statement = select_statement.where(distance_table.c.distance < 1)
 
     edgelist = set(DB.execute(select_statement).fetchall())