move rail_end_atom_to_ladder from DnaLadder to dna_updater_globals

author: Bruce Smith <bruce@nanorex.com> 2008-05-11 06:13:55 +0000
committer: Bruce Smith <bruce@nanorex.com> 2008-05-11 06:13:55 +0000
commit: 3c84ccd50247d3c7ba263f1b63664718ff441ac1 (patch)
tree: 12228876668a62cfc5f1be30f9f28a2e0a7a78e9
parent: 3fc603e1fa80e53ba163dabfec251ed970709cb5 (diff)
download: nanoengineer-theirix-3c84ccd50247d3c7ba263f1b63664718ff441ac1.tar.gz
nanoengineer-theirix-3c84ccd50247d3c7ba263f1b63664718ff441ac1.zip
5 files changed, 57 insertions, 81 deletions
diff --git a/cad/src/dna/model/DnaLadder.py b/cad/src/dna/model/DnaLadder.py
index e82381d25..88e8c424c 100644
--- a/cad/src/dna/model/DnaLadder.py
+++ b/cad/src/dna/model/DnaLadder.py
@@ -104,6 +104,8 @@ from dna.updater.dna_updater_globals import DNALADDER_INVAL_IS_OK
 from dna.updater.dna_updater_globals import DNALADDER_INVAL_IS_ERROR
 from dna.updater.dna_updater_globals import DNALADDER_INVAL_IS_NOOP_BUT_OK
 
+from dna.updater.dna_updater_globals import rail_end_atom_to_ladder
+
 # ==
 
 ### REVIEW: should a DnaLadder contain any undoable state?
@@ -420,7 +422,7 @@ class DnaLadder(object, DnaLadder_pam_conversion_methods):
             self.valid = val
             if val:
                 # tell the rail end atoms their ladder;
-                # see _rail_end_atom_to_ladder for how this hint is interpreted
+                # see rail_end_atom_to_ladder for how this hint is interpreted
                 for atom in self.rail_end_baseatoms():
                     # (could debug-warn if already set to a valid ladder)
                     if atom._DnaLadder__ladder is not None and atom._DnaLadder__ladder.valid:
@@ -730,7 +732,7 @@ class DnaLadder(object, DnaLadder_pam_conversion_methods):
                (strand1.bond_direction, self)
         end_atom = strand1.end_baseatoms()[end]
         assert not end_atom._dna_updater__error # otherwise we should not get this far with it
-        assert self is _rail_end_atom_to_ladder(end_atom) # sanity check
+        assert self is rail_end_atom_to_ladder(end_atom) # sanity check
         bond_direction_to_other = LADDER_BOND_DIRECTION_TO_OTHER_AT_END_OF_STRAND1[end]
         next_atom = end_atom.strand_next_baseatom(bond_direction = bond_direction_to_other)
             # (note: strand_next_baseatom returns None if end_atom or the atom it
@@ -741,11 +743,11 @@ class DnaLadder(object, DnaLadder_pam_conversion_methods):
             # (report error in that case??)
             return None
         assert not next_atom._dna_updater__error
-        other = _rail_end_atom_to_ladder(next_atom)
+        other = rail_end_atom_to_ladder(next_atom)
             # other ladder (might be self in case of ring)
         if other.error:
             return None
-        # other.valid was checked in _rail_end_atom_to_ladder
+        # other.valid was checked in rail_end_atom_to_ladder
         if other is self:
             return None
         if len(self) + len(other) > MAX_LADDER_LENGTH:
@@ -1371,7 +1373,7 @@ class DnaLadder(object, DnaLadder_pam_conversion_methods):
             # (note: strand_next_baseatom returns None if end_atom or the atom it
             #  might return has ._dna_updater__error set, or if it reaches a non-Ss atom.)
         if next_atom is not None:            
-            return _rail_end_atom_to_ladder(next_atom)
+            return rail_end_atom_to_ladder(next_atom)
         return None
         
     pass # end of class DnaLadder
@@ -1465,31 +1467,6 @@ class DnaSingleStrandDomain(DnaLadder):
 
 # ==
 
-def _rail_end_atom_to_ladder(atom): # FIX: not really private, and part of an import cycle (used here and in DnaLadderRailChunk).
-    """
-    Atom is believed to be the end-atom of a rail in a valid DnaLadder.
-    Return that ladder. If anything looks wrong, either console print an error message
-    and return None (which is likely to cause exceptions in the caller),
-    or raise some kind of exception (which is what we do now, since easiest).
-    """
-    # various exceptions are possible from the following; all are errors
-    try:
-        ladder = atom._DnaLadder__ladder
-        assert isinstance(ladder, DnaLadder)
-        assert ladder.valid, "%r not valid" % ladder
-            # note: changes in _ladder_set_valid mean this will become common for bugs, attrerror will be rare [080413]
-            # or: if not, print "likely bug: invalid ladder %r found on %r during merging" % (ladder, atom) #k
-            # REVIEW: it might be better to return an invalid ladder than no ladder or raise an exception,
-            # so we might change this to return one, provided the atom is in the end_baseatoms. ####
-        assert atom in ladder.rail_end_baseatoms()
-        return ladder
-    except:
-        error = atom._dna_updater__error and ("[%s]" % atom._dna_updater__error) or ""
-        print "\nfollowing exception is an error in _rail_end_atom_to_ladder(%r%s): " % \
-              (atom, error)
-        raise
-    pass
-
 def _end_to_end_bonded( atom1, atom2, strandQ):
     """
     Are the expected end-to-end bonds present between end atoms
diff --git a/cad/src/dna/model/DnaLadderRailChunk.py b/cad/src/dna/model/DnaLadderRailChunk.py
index 2218f3f92..f5dacfa69 100644
--- a/cad/src/dna/model/DnaLadderRailChunk.py
+++ b/cad/src/dna/model/DnaLadderRailChunk.py
@@ -15,6 +15,8 @@ from model.chunk import Chunk
 from model.elements import Singlet
 from model.elements import Pl5
 
+from files.mmp.files_mmp_writing import writemmp_mapping
+
 from utilities.constants import gensym
 from utilities.constants import black
 from utilities.constants import ave_colors
@@ -35,9 +37,7 @@ from PyQt4.Qt import QFont, QString # for debug code
 
 from utilities.debug_prefs import debug_pref, Choice_boolean_False
 
-# see also:
-## from dna_model.DnaLadder import _rail_end_atom_to_ladder
-# (below, perhaps in a cycle)
+from dna.updater.dna_updater_globals import rail_end_atom_to_ladder
 
 # ==
 
@@ -242,12 +242,7 @@ class DnaLadderRailChunk(Chunk):
                 # should print the missing atoms if we can, but for now print the present atoms:
                 print " present atoms are", self.atoms.values()
         
-        # following import is a KLUGE to avoid recursive import
-        # (still has import cycle, ought to ### FIX -- should refile that func somehow)
-        from dna.model.DnaLadder import _rail_end_atom_to_ladder
-            # todo: make not private... or get by without it here (another init arg??)
-            # review: make this import toplevel? right now it's probably in a cycle.
-        self.ladder = _rail_end_atom_to_ladder( chain.baseatoms[0] )
+        self.ladder = rail_end_atom_to_ladder( chain.baseatoms[0] )
         self._set_properties_from_grab_atom_info( use_disp, use_picked,
                                                   use_display_as_pam, use_save_as_pam)
             # uses args and self attrs to set self.display and self.hidden
@@ -266,8 +261,7 @@ class DnaLadderRailChunk(Chunk):
             self.ladder.ladder_invalidate_and_assert_permitted()
         self.ladder = ladder
         # can't do this, no self.chain; could do it if passed the chain:
-        ## from dna_model.DnaLadder import _rail_end_atom_to_ladder
-        ## assert self.ladder == _rail_end_atom_to_ladder( self.chain.baseatoms[0] )
+        ## assert self.ladder == rail_end_atom_to_ladder( self.chain.baseatoms[0] )
         return
 
     _counted_chunks = () # kluge, so len is always legal,
@@ -751,8 +745,6 @@ class DnaLadderRailChunk(Chunk):
             # since (if this happens to be a PAM5 chunk) we use the memo
             # to interleave the Pl atoms into the best order for writing
             # (one that permits an upcoming mmp format optimization).
-            from files.mmp.files_mmp_writing import writemmp_mapping
-                # might be import cycle, might be a problem if done at toplevel
             mapping = writemmp_mapping(self.assy)
         
         initial_atoms = self.indexed_atoms_in_order(mapping = mapping)
diff --git a/cad/src/dna/model/outtakes/BaseIterator.py b/cad/src/dna/model/outtakes/BaseIterator.py
index b61c35441..21805b615 100644
--- a/cad/src/dna/model/outtakes/BaseIterator.py
+++ b/cad/src/dna/model/outtakes/BaseIterator.py
@@ -96,10 +96,10 @@ class BaseIterator(object):
         assert next_atom != -1 # if this fails, prior dna updater run didn't do enough of its job
         # todo: handle exceptions in the following
 ##        next_chunk = next_atom.molecule ### BUG: invalid during updater, chunks get broken. ##### BIG LOGIC BUG, uhoh @@@@@@
-##            # can we use _rail_end_atom_to_ladder? i guess so, it got set by last updater run... ladder is still valid... ###DOIT
+##            # can we use rail_end_atom_to_ladder? i guess so, it got set by last updater run... ladder is still valid... ###DOIT
 ##        assert next_chunk
 ##        next_ladder = next_chunk.ladder
-##        next_ladder = _rail_end_atom_to_ladder(next_atom) # IMPORT - nevermind, see below
+##        next_ladder = rail_end_atom_to_ladder(next_atom) # IMPORT - nevermind, see below
 ##        assert next_ladder #k redundant?
         # now scan through whichrail and whichend until we find next_atom... what about len==1 case??
         # ah, in that case use new rail's neighbor_baseatoms to find our own... or can we use wholechain for all this? ###DECIDE
diff --git a/cad/src/dna/model/pam3plus5_ops.py b/cad/src/dna/model/pam3plus5_ops.py
index 63b77c42d..8675c8d26 100644
--- a/cad/src/dna/model/pam3plus5_ops.py
+++ b/cad/src/dna/model/pam3plus5_ops.py
@@ -23,14 +23,22 @@ from utilities.constants import Pl_STICKY_BOND_DIRECTION
 from model.elements import Pl5, Singlet
 
 from utilities import debug_flags
-##from utilities.constants import MODEL_PAM5
-
-##from dna.updater.dna_updater_prefs import pref_dna_updater_convert_to_PAM3plus5
 
 import foundation.env as env
 from utilities.Log import redmsg, graymsg
 
 from model.bond_constants import find_bond, find_Pl_bonds
+from model.bond_constants import V_SINGLE
+
+from model.bonds import bond_atoms_faster
+
+from dna.updater.dna_updater_globals import DNALADDER_INVAL_IS_NOOP_BUT_OK
+from dna.updater.dna_updater_globals import DNALADDER_INVAL_IS_OK
+from dna.updater.dna_updater_globals import temporarily_set_dnaladder_inval_policy
+from dna.updater.dna_updater_globals import restore_dnaladder_inval_policy
+
+from dna.updater.dna_updater_globals import _f_atom_to_ladder_location_dict
+from dna.updater.dna_updater_globals import rail_end_atom_to_ladder
 
 # ==
 
@@ -117,14 +125,6 @@ def kill_Pl_and_rebond_neighbors(atom):
     
     # could also assert no dna updater error
 
-    if 1:
-        # kluge: do these at runtime to avoid import recursion issues.
-        # clean this up asap after the release.
-        from dna.updater.dna_updater_globals import DNALADDER_INVAL_IS_NOOP_BUT_OK
-        from dna.updater.dna_updater_globals import DNALADDER_INVAL_IS_OK
-        from dna.updater.dna_updater_globals import temporarily_set_dnaladder_inval_policy
-        from dna.updater.dna_updater_globals import restore_dnaladder_inval_policy
-
     _old = temporarily_set_dnaladder_inval_policy( DNALADDER_INVAL_IS_NOOP_BUT_OK)
         # REVIEW: can this ever be called outside dna updater?
         # If so, we might not want to change the policy then
@@ -312,14 +312,6 @@ def insert_Pl_between(s1, s2): #bruce 080409/080410
     @return: the Pl5 atom we made. (Never returns None. Errors are either
              not detected or cause exceptions.)
     """
-    if 1:
-        # kluge: do these at runtime to avoid import recursion issues.
-        # clean this up asap after the release.
-        from dna.updater.dna_updater_globals import DNALADDER_INVAL_IS_NOOP_BUT_OK
-        from dna.updater.dna_updater_globals import DNALADDER_INVAL_IS_OK
-        from dna.updater.dna_updater_globals import temporarily_set_dnaladder_inval_policy
-        from dna.updater.dna_updater_globals import restore_dnaladder_inval_policy
-
     _old = temporarily_set_dnaladder_inval_policy( DNALADDER_INVAL_IS_NOOP_BUT_OK)
         # REVIEW: can this ever be called outside dna updater?
         # If so, we might not want to change the policy then
@@ -377,9 +369,6 @@ def _insert_Pl_between_0(s1, s2):
         # tell caller it needs to, and is allowed to, correct pos
 
     # bond it to s1 and s2
-    from model.bonds import bond_atoms_faster
-    from model.bond_constants import V_SINGLE
-        # runtime imports, since we're imported indirectly by chem.py
     b1 = bond_atoms_faster(Pl, s1, V_SINGLE)
     b2 = bond_atoms_faster(Pl, s2, V_SINGLE)
 
@@ -478,24 +467,12 @@ def _f_find_new_ladder_location_of_baseatom(self):
     # that atom.molecule.ladder can find fresh ladders
     # that didn't yet remake their chunks
     
-##    # buggy version (the assert ladder.valid below will typically always fail)
-##    ladder = self.molecule.ladder
-##    assert ladder
-##    assert ladder.valid # routinely fails (for a known reason)...
-##    whichrail, index = ladder.whichrail_and_index_of_baseatom(self)
-##        # TODO: pass index hint to optimize?
-    
-    # keep these as runtime imports for now, see comment at top of module;
-    # WARNING: these will freak out the import cycle graph; no trivial fix at the moment
-    from dna.updater.dna_updater_globals import _f_atom_to_ladder_location_dict
-    from dna.model.DnaLadder import _rail_end_atom_to_ladder # refile this sometime soon!
-    
     locator = _f_atom_to_ladder_location_dict
     data = locator.get(self.key)
     if data:
         return data # (ladder, whichrail, index)
     # otherwise it must be an end atom on a non-fresh ladder
-    ladder = _rail_end_atom_to_ladder(self)
+    ladder = rail_end_atom_to_ladder(self)
     whichrail, index = ladder.whichrail_and_index_of_baseatom(self)
         # by search in ladder, optimized to try the ends first
     return ladder, whichrail, index
diff --git a/cad/src/dna/updater/dna_updater_globals.py b/cad/src/dna/updater/dna_updater_globals.py
index 5be6b75fb..646c0e511 100644
--- a/cad/src/dna/updater/dna_updater_globals.py
+++ b/cad/src/dna/updater/dna_updater_globals.py
@@ -173,7 +173,7 @@ _f_atom_to_ladder_location_dict = {}
     #bruce 080411, to permit finding ladder/rail/index of atoms in freshly
     # made ladders which didn't yet remake their chunks
     # (needn't store all end atoms, since those can be found using
-    #  _rail_end_atom_to_ladder -- important for bridging Pls
+    #  rail_end_atom_to_ladder -- important for bridging Pls
     #  between fresh and old-untouched ladders)
 
 DNALADDER_INVAL_IS_OK = 0
@@ -220,4 +220,34 @@ def restore_dnaladder_inval_policy(old): # bruce 080413
     dnaladder_inval_policy = old
     return
 
+# ==
+
+def rail_end_atom_to_ladder(atom):
+    """
+    Atom is believed to be the end-atom of a rail in a valid DnaLadder.
+    Return that ladder. If anything looks wrong, either console print an error message
+    and return None (which is likely to cause exceptions in the caller),
+    or raise some kind of exception (which is what we do now, since easiest).
+    """
+    #bruce 080510 moved this from DnaLadder.py to avoid import cycles
+    # various exceptions are possible from the following; all are errors
+    try:
+        ladder = atom._DnaLadder__ladder
+            # note: this attribute name is hardcoded in several files
+        ## assert isinstance(ladder, DnaLadder)
+            # (not worth the trouble, since we don't want the DnaLadder import)
+        assert ladder.valid, "%r not valid" % ladder
+            # note: changes in _ladder_set_valid mean this will become common for bugs, attrerror will be rare [080413]
+            # or: if not, print "likely bug: invalid ladder %r found on %r during merging" % (ladder, atom) #k
+            # REVIEW: it might be better to return an invalid ladder than no ladder or raise an exception,
+            # so we might change this to return one, provided the atom is in the end_baseatoms. ####
+        assert atom in ladder.rail_end_baseatoms()
+        return ladder
+    except:
+        error = atom._dna_updater__error and ("[%s]" % atom._dna_updater__error) or ""
+        print "\nfollowing exception is an error in rail_end_atom_to_ladder(%r%s): " % \
+              (atom, error)
+        raise
+    pass
+
 # end
author	Bruce Smith <bruce@nanorex.com>	2008-05-11 06:13:55 +0000
committer	Bruce Smith <bruce@nanorex.com>	2008-05-11 06:13:55 +0000
commit	3c84ccd50247d3c7ba263f1b63664718ff441ac1 (patch)
tree	12228876668a62cfc5f1be30f9f28a2e0a7a78e9
parent	3fc603e1fa80e53ba163dabfec251ed970709cb5 (diff)
download	nanoengineer-theirix-3c84ccd50247d3c7ba263f1b63664718ff441ac1.tar.gz nanoengineer-theirix-3c84ccd50247d3c7ba263f1b63664718ff441ac1.zip