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# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_updater_main.py - enforce rules on newly changed DNA-related model objects,
including DnaGroups, AxisChunks, PAM atoms, etc.
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from dna.updater.dna_updater_globals import get_changes_and_clear
from dna.updater.dna_updater_globals import ignore_new_changes
from dna.updater.dna_updater_globals import clear_updater_run_globals
from dna.updater.dna_updater_globals import _f_invalid_dna_ladders
from dna.updater.dna_updater_globals import restore_dnaladder_inval_policy
from dna.updater.dna_updater_globals import DNALADDER_INVAL_IS_OK
from utilities import debug_flags
from dna.updater.dna_updater_utils import remove_killed_atoms
from dna.updater.dna_updater_utils import remove_closed_or_disabled_assy_atoms
from dna.updater.dna_updater_atoms import update_PAM_atoms_and_bonds
from dna.updater.dna_updater_chunks import update_PAM_chunks
from dna.updater.dna_updater_groups import update_DNA_groups
from dna.updater.dna_updater_debug import debug_prints_as_dna_updater_starts
from dna.updater.dna_updater_debug import debug_prints_as_dna_updater_ends
from dna.model.DnaMarker import _f_are_there_any_homeless_dna_markers
from dna.model.DnaMarker import _f_get_homeless_dna_markers
# ==
_runcount = 0 # for debugging [bruce 080227]
def full_dna_update():
"""
[meant to be called from _master_model_updater]
Enforce rules on all newly changed DNA-related model objects,
including DnaGroups, AxisChunks, PAM atoms, etc.
@warning: external calls to any smaller parts of the dna updater
would probably have bugs, due to the lack of beginning
and ending calls to clear_updater_run_globals, and possibly
for many other reasons. In fact, external calls to this function
rather than to update_parts (which calls it) are risky, since it's
not reviewed how much this function depends on things that
update_parts has normally done by the time it calls this.
@note: The newly changed objects are not necessarily
all in the same assy (class assembly).
E.g. there might be some from an open mmp file
and some from a just-opened part library part.
@return: None
"""
global _runcount
_runcount += 1
clear_updater_run_globals()
try:
_full_dna_update_0( _runcount) # includes debug_prints_as_dna_updater_starts
finally:
debug_prints_as_dna_updater_ends( _runcount)
clear_updater_run_globals()
return
def _full_dna_update_0( _runcount):
"""
[private helper for full_dna_update -- do all the work]
"""
# TODO: process _f_baseatom_wants_pam: (or maybe a bit later, after delete bare, and error finding?)
# - extend to well-structured basepairs; drop structure error atoms (as whole basepairs)
# - these and their baseatom neighbors in our changed atoms, maybe even real .changed_structure
changed_atoms = get_changes_and_clear()
debug_prints_as_dna_updater_starts( _runcount, changed_atoms)
# note: this function should not modify changed_atoms.
# note: the corresponding _ends call is in our caller.
if not changed_atoms and not _f_are_there_any_homeless_dna_markers():
# maybe: also check _f_baseatom_wants_pam, invalid ladders, here and elsewhere
# (or it might be more efficient to officially require _changed_structure on representative atoms,
# which we're already doing now as a kluge workaround for the lack of testing those here)
# [bruce 080413 comment]
#
# note: adding marker check (2 places) fixed bug 2673 [bruce 080317]
return # optimization (might not be redundant with caller)
# print debug info about the set of changed_atoms (and markers needing update)
if debug_flags.DEBUG_DNA_UPDATER_MINIMAL:
print "\ndna updater: %d changed atoms to scan%s" % \
( len(changed_atoms),
_f_are_there_any_homeless_dna_markers() and " (and some DnaMarkers)" or ""
)
if debug_flags.DEBUG_DNA_UPDATER and changed_atoms:
# someday: should be _VERBOSE, but has been useful enough to keep seeing for awhile
items = changed_atoms.items()
items.sort()
atoms = [item[1] for item in items]
NUMBER_TO_PRINT = 10
if debug_flags.DEBUG_DNA_UPDATER_VERBOSE or len(atoms) <= NUMBER_TO_PRINT:
print " they are: %r" % atoms
else:
print " the first %d of them are: %r ..." % \
(NUMBER_TO_PRINT, atoms[:NUMBER_TO_PRINT])
if changed_atoms:
remove_killed_atoms( changed_atoms) # only affects this dict, not the atoms
if changed_atoms:
remove_closed_or_disabled_assy_atoms( changed_atoms)
# This should remove all remaining atoms from closed files.
# Note: only allowed when no killed atoms are present in changed_atoms;
# raises exceptions otherwise.
if changed_atoms:
update_PAM_atoms_and_bonds( changed_atoms)
# this can invalidate DnaLadders as it changes various things
# which call atom._changed_structure -- that's necessary to allow,
# so we don't change dnaladder_inval_policy until below,
# inside update_PAM_chunks [bruce 080413 comment]
# (REVIEW: atom._changed_structure does not directly invalidate
# dna ladders, so I'm not sure if this comment is just wrong,
# or if it meant something not exactly what it said, like,
# this can cause more ladders to be invalidated than otherwise
# in an upcoming step -- though if it meant that, it seems
# wrong too, since the existence of that upcoming step
# might be enough reason to not be able to change the policy yet.
# [bruce 080529 addendum/Q])
if not changed_atoms and not _f_are_there_any_homeless_dna_markers() and not _f_invalid_dna_ladders:
return # optimization
homeless_markers = _f_get_homeless_dna_markers() #e rename, homeless is an obs misleading term ####
# this includes markers whose atoms got killed (which calls marker.remove_atom)
# or got changed in structure (which calls marker.changed_structure)
# so it should not be necessary to also add to this all markers noticed
# on changed_atoms, even though that might include more markers than
# we have so far (especially after we add atoms from invalid ladders below).
#
# NOTE: it can include fewer markers than are noticed by _f_are_there_any_homeless_dna_markers
# since that does not check whether they are truly homeless.
assert not _f_are_there_any_homeless_dna_markers() # since getting them cleared them
new_chunks, new_wholechains = update_PAM_chunks( changed_atoms, homeless_markers)
# note: at the right time during this or a subroutine, it sets
# dnaladder_inval_policy to DNALADDER_INVAL_IS_ERROR
# review: if not new_chunks, return? wait and see if there are also new_markers, etc...
update_DNA_groups( new_chunks, new_wholechains)
# review:
# args? a list of nodes, old and new, whose parents should be ok? or just find them all, scanning MT?
# the underlying nodes we need to place are just chunks and jigs. we can ignore old ones...
# so we need a list of new or moved ones... chunks got made in update_PAM_chunks; jigs, in update_PAM_atoms_and_bonds...
# maybe pass some dicts into these for them to add things to?
ignore_new_changes("as full_dna_update returns", changes_ok = False )
if debug_flags.DEBUG_DNA_UPDATER_MINIMAL:
if _f_are_there_any_homeless_dna_markers():
print "dna updater fyi: as updater returns, some DnaMarkers await processing by next run"
# might be normal...don't know. find out, by printing it even
# in minimal debug output. [bruce 080317]
if _f_invalid_dna_ladders: #bruce 080413
print "\n*** likely bug: some invalid ladders are recorded, as dna updater returns:", _f_invalid_dna_ladders
# but don't clear them, in case this was sometimes routine and we were
# working around bugs (unknowingly) by invalidating them next time around
restore_dnaladder_inval_policy( DNALADDER_INVAL_IS_OK)
return # from _full_dna_update_0
# end
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