From d377279494087358c4c6d37a0af6128d01bc4602 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Mon, 23 Jul 2018 14:28:25 -0500
Subject: [PATCH] Changed recursive strand-tracing routine into a for loop
---
segmentmodel.py | 40 ++++++++++++++++++++++++----------------
1 file changed, 24 insertions(+), 16 deletions(-)
diff --git a/segmentmodel.py b/segmentmodel.py
index 1b7300e..12f7962 100644
--- a/segmentmodel.py
+++ b/segmentmodel.py
@@ -368,6 +368,9 @@ class Segment(ConnectableElement, Group):
self.sequence = None
+ def __repr__(self):
+ return "<{} {}[{:d}]>".format( type(self), self.name, self.num_nt )
+
def _set_splines_from_ends(self):
a = np.array([self.start_position,self.end_position]).T
@@ -2101,23 +2104,28 @@ class SegmentModel(ArbdModel):
""" Build strands from connectivity of helices """
def _recursively_build_strand(strand, segment, pos, is_fwd, mycounter=0, move_at_least=0.5):
- mycounter+=1
- if mycounter > 10000:
- import pdb
- pdb.set_trace()
- s,seg = [strand, segment]
-
- #if seg.name == "22-1" and pos > 140:
- # if seg.name == "22-2":
- # import pdb
- # pdb.set_trace()
-
- end_pos, next_seg, next_pos, next_dir, move_at_least = seg.get_strand_segment(pos, is_fwd, move_at_least)
- s.add_dna(seg, pos, end_pos, is_fwd)
+ seg = segment
+ history = []
+ while True:
+ mycounter+=1
+ if mycounter > 10000:
+ import pdb
+ pdb.set_trace()
+
+ #if seg.name == "22-1" and pos > 140:
+ # if seg.name == "22-2":
+ # import pdb
+ # pdb.set_trace()
+
+ end_pos, next_seg, next_pos, next_dir, move_at_least = seg.get_strand_segment(pos, is_fwd, move_at_least)
+ strand.add_dna(seg, pos, end_pos, is_fwd)
+
+ if next_seg is None:
+ return
+ else:
+ history.append((seg,pos,is_fwd))
+ seg,pos,is_fwd = (next_seg, next_pos, next_dir)
- if next_seg is not None:
- # print(" next_dir: {}".format(next_dir))
- _recursively_build_strand(s, next_seg, next_pos, next_dir, mycounter, move_at_least)
for seg in self.segments:
locs = seg.get_5prime_locations()
--
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