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Use the BiopythonDeprecationWarning class in alignment warning.

This is an old backwards compatibility hack we need to phase out.
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1 parent f519723 commit dfb082f27bd03094e90fc49cb92ca10bc095ded0 @peterjc peterjc committed Dec 30, 2012
Showing with 2 additions and 1 deletion.
  1. +2 −1 Bio/Align/
3 Bio/Align/
@@ -146,13 +146,14 @@ def __init__(self, records, alphabet=None):
alphabet = records
records = []
import warnings
+ from Bio import BiopythonDeprecationWarning
warnings.warn("Invalid records argument: While the old "
"Bio.Align.Generic.Alignment class only "
"accepted a single argument (the alphabet), the "
"newer Bio.Align.MultipleSeqAlignment class "
"expects a list/iterator of SeqRecord objects "
"(which can be an empty list) and an optional "
- "alphabet argument")
+ "alphabet argument", BiopythonDeprecationWarning)
else :
raise ValueError("Invalid records argument")
if alphabet is not None :

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