From 5455d407e70a28a15ab9a8608611575dc35ec5c6 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 13 Aug 2019 17:01:35 -0500
Subject: [PATCH] Moved _connect_ends routine from 'DoubleStrandedSegment' to
parent 'Segment'
---
mrdna/segmentmodel.py | 50 ++++++++++++++++++++++---------------------
1 file changed, 26 insertions(+), 24 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 86550d1..0ffdc48 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -754,6 +754,30 @@ class Segment(ConnectableElement, Group):
on_fwd_strand = True
self.add_location(nt,"3prime",on_fwd_strand)
+ ## Real work
+ def _connect_ends(self, end1, end2, type_, force_connection=False):
+ debug = False
+ ## TODO remove self?
+ ## validate the input
+ for end in (end1, end2):
+ assert( isinstance(end, Location) )
+ assert( end.type_ in ("end3","end5") )
+ assert( end1.type_ != end2.type_ )
+
+ ## Remove other connections involving these points
+ if end1.connection is not None:
+ if debug: print("WARNING: reconnecting {}".format(end1))
+ end1.connection.delete()
+ if end2.connection is not None:
+ if debug: print("WARNING: reconnecting {}".format(end2))
+ end2.connection.delete()
+
+ ## Create and add connection
+ if end2.type_ == "end5":
+ end1.container._connect( end2.container, Connection( end1, end2, type_=type_ ), in_3prime_direction=True )
+ else:
+ end2.container._connect( end1.container, Connection( end2, end1, type_=type_ ), in_3prime_direction=True )
+
def get_3prime_locations(self):
return sorted(self.get_locations("3prime"),key=lambda x: x.address)
@@ -1126,29 +1150,6 @@ class DoubleStrandedSegment(Segment):
loc.is_3prime_side_of_connection = True
other_loc.is_3prime_side_of_connection = False
- ## Real work
- def _connect_ends(self, end1, end2, type_, force_connection):
- debug = False
- ## TODO remove self?
- ## validate the input
- for end in (end1, end2):
- assert( isinstance(end, Location) )
- assert( end.type_ in ("end3","end5") )
- assert( end1.type_ != end2.type_ )
-
- ## Remove other connections involving these points
- if end1.connection is not None:
- if debug: print("WARNING: reconnecting {}".format(end1))
- end1.connection.delete()
- if end2.connection is not None:
- if debug: print("WARNING: reconnecting {}".format(end2))
- end2.connection.delete()
-
- ## Create and add connection
- if end2.type_ == "end5":
- end1.container._connect( end2.container, Connection( end1, end2, type_=type_ ), in_3prime_direction=True )
- else:
- end2.container._connect( end1.container, Connection( end2, end1, type_=type_ ), in_3prime_direction=True )
def _get_num_beads(self, contour, max_basepairs_per_bead, max_nucleotides_per_bead):
# return int(contour*self.num_nt // max_basepairs_per_bead)
return int(contour*(self.num_nt**2/(self.num_nt+1)) // max_basepairs_per_bead)
@@ -2887,7 +2888,8 @@ class SegmentModel(ArbdModel):
history = []
if not strands_cover_segment(seg, is_fwd):
pos = nt = find_nt_not_in_strand(seg, is_fwd)
- s = Strand(is_circular = True)
+ s = Strand(segname="S{:03d}".format(len(strands)),
+ is_circular = True)
history = _recursively_build_strand(s, seg, pos, is_fwd)
strands.append(s)
return history
--
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