From 6193629666c292d7cdaf10b0ccf018a4a700a84a Mon Sep 17 00:00:00 2001
From: "Jeroen F.J. Laros" <jlaros@fixedpoint.nl>
Date: Sun, 19 Apr 2015 13:59:21 +0200
Subject: [PATCH] Using composition instead of subclassing for the HGVSList
class.
---
mutalyzer/variant.py | 40 ++++++++++++++++++++++++++++++++--------
1 file changed, 32 insertions(+), 8 deletions(-)
diff --git a/mutalyzer/variant.py b/mutalyzer/variant.py
index 5b84b3dc..fc3818d3 100644
--- a/mutalyzer/variant.py
+++ b/mutalyzer/variant.py
@@ -18,21 +18,41 @@ WEIGHTS = {
}
-class HGVSList(list):
+class HGVSList(object):
"""
Container for a list of sequences or variants.
"""
+ def __init__(self, items=[]):
+ self.items = list(items)
+
+
+ def __getitem__(self, index):
+ return self.items[index]
+
+
+ def __bool__(self):
+ return bool(len(self.items) > 0)
+
+
+ def __nonzero__(self): # Python 2.x compatibility.
+ return self.__bool__()
+
+
def __unicode__(self):
- if len(self) > 1:
- return '[{}]'.format(';'.join(map(unicode, self)))
- return unicode(self[0])
+ if len(self.items) > 1:
+ return '[{}]'.format(';'.join(map(unicode, self.items)))
+ return unicode(self.items[0])
+
+
+ def append(self, item):
+ self.items.append(item)
def weight(self):
- weight = sum(map(lambda x: x.weight(), self))
+ weight = sum(map(lambda x: x.weight(), self.items))
- if len(self) > 1:
- return weight + (len(self) + 1) * extractor.WEIGHT_SEPARATOR
+ if len(self.items) > 1:
+ return weight + (len(self.items) + 1) * extractor.WEIGHT_SEPARATOR
return weight
@@ -82,10 +102,14 @@ class ISeq(object):
return '{}_{}{}'.format(self.start, self.end, inverted)
- def __nonzero__(self):
+ def __bool__(self):
return bool(self.sequence)
+ def __nonzero__(self): # Python 2.x compatibility.
+ return self.__bool__()
+
+
def weight(self):
if self.type == 'ins':
return len(self.sequence) * extractor.WEIGHT_BASE
--
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