path: root/cad/src/dna/updater/dna_updater_prefs.py

# Copyright 2007-2008 Nanorex, Inc.  See LICENSE file for details.
"""
dna_updater_prefs.py - access to preferences settings affecting the dna updater

@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc.  See LICENSE file for details.

History:

bruce 080317 revised many debug_pref menu texts, prefs_keys, non_debug settings
"""

from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
from utilities.debug_prefs import Choice

import foundation.env as env

from utilities.Log import orangemsg
from utilities.GlobalPreferences import dna_updater_is_enabled

from utilities import debug_flags

# ==

def initialize_prefs():
    """
    """

    # make debug prefs appear in debug menu
    pref_fix_deprecated_PAM3_atoms()
    pref_fix_deprecated_PAM5_atoms()

    pref_fix_bare_PAM3_atoms()
    pref_fix_bare_PAM5_atoms()

    pref_permit_bare_axis_atoms()

    pref_print_bond_direction_errors()
    pref_per_ladder_colors()
    pref_draw_internal_markers()

    pref_dna_updater_convert_to_PAM3plus5()
    pref_mmp_save_convert_to_PAM5()
    pref_renderers_convert_to_PAM5()
    pref_minimizers_convert_to_PAM5()

    pref_fix_after_readmmp_before_updaters()
    pref_fix_after_readmmp_after_updaters()

    _update_our_debug_flags('arbitrary value')
        # makes them appear in the menu,
        # and also sets their debug flags
        # to the current pref values

    return

# ==

def pref_fix_deprecated_PAM3_atoms():
    res = debug_pref("DNA: fix deprecated PAM3 atoms?",
                     Choice_boolean_True,
                     ## non_debug = True, # disabled, bruce 080317
                     prefs_key = "A10/DNA: fix deprecated PAM3 atoms?", # changed, bruce 080317
                     call_with_new_value = _changed_dna_updater_behavior_pref )
    return res

def pref_fix_deprecated_PAM5_atoms():
    res = debug_pref("DNA: fix deprecated PAM5 atoms?",
                     Choice_boolean_True, # False -> True, 080201
                     ## non_debug = True, # disabled, bruce 080317
                     prefs_key = "A10/DNA: fix deprecated PAM5 atoms?", # changed, bruce 080317
                     call_with_new_value = _changed_dna_updater_behavior_pref )
    return res

def pref_fix_bare_PAM3_atoms():
    res = debug_pref("DNA: fix bare PAM3 atoms?",
                     Choice_boolean_True,
                     ## non_debug = True, # disabled, bruce 080317
                     prefs_key = "A10/DNA: fix bare PAM3 atoms?", # changed, bruce 080317
                     call_with_new_value = _changed_dna_updater_behavior_pref )
    return res

def pref_fix_bare_PAM5_atoms():
    res = debug_pref("DNA: fix bare PAM5 atoms?",
                     Choice_boolean_True, # False -> True, 080201
                     ## non_debug = True, # disabled, bruce 080317
                     prefs_key = "A10/DNA: fix bare PAM5 atoms?", # changed, bruce 080317
                     call_with_new_value = _changed_dna_updater_behavior_pref )
    return res

def dna_updater_warn_when_transmuting_deprecated_elements(): #bruce 080416 (not in .rc2)
    res = debug_pref("DNA: warn when transmuting deprecated PAM elements?",
                     Choice_boolean_False, # warning is not useful for a released version,
                         # and is distracting since it always happens during Insert DNA
                     ## non_debug = True,
                     prefs_key = "A10/DNA: warn when transmuting deprecated PAM elements?",
                    )
    return res

def pref_permit_bare_axis_atoms():
    #bruce 080407; seems to work, so I hope we can make it the default soon,
    # but would require adaptations in strand edit props, to delete them manually
    # and to tolerate their existence when extending one strand.
    # warning: like all updater behavior prefs, changing it at runtime and then
    # undoing to before that point might cause undo bugs,
    # so it requires atom_debug to see it.
    res = debug_pref("DNA: permit bare axis atoms? ",
                      Choice_boolean_False,
                      ## non_debug = True,
                      prefs_key = True,
                      call_with_new_value = _changed_dna_updater_behavior_pref )
    return res

def legal_numbers_of_strand_neighbors_on_axis(): #bruce 080407
    if pref_permit_bare_axis_atoms():
        return (0, 1, 2)
    else:
        return (1, 2)
    pass

# ==

def pref_print_bond_direction_errors():
    # really this means "print verbose details of them" -- they're always summarized, even when this is off
    res = debug_pref( "DNA: debug: print bond direction errors?", #bruce 080317 revised text
                      Choice_boolean_False,
                      ## non_debug = True, # disabled, bruce 080317
                      prefs_key = "A10/DNA updater: print bond direction errors?", # changed, bruce 080317
                     )
    return res

def pref_per_ladder_colors():
    res = debug_pref("DNA: debug: per-ladder colors?",
                      Choice_boolean_False,
                      non_debug = True,
                      prefs_key = "A10/DNA: debug: per-ladder colors?" )
    return res

def pref_draw_internal_markers():
    res = debug_pref("DNA: draw internal DnaMarkers?", #bruce 080317 revised text
                     Choice_boolean_False,
                     non_debug = True,
                     prefs_key = "A10/DNA: draw internal markers?", # changed, bruce 080317
                     call_with_new_value = (lambda val: env.mainwindow().glpane.gl_update()) )
    return res

# ==

# PAM3+5 prefs.  [bruce 080312]

# (These will either turn into User Prefs or per-assy settings (perhaps saved in mmp file),
#  or perhaps become finer-grained that that (applicable to portions of the model,
#  e.g. specific base pairs.)

# Note: each minimizer may need a separate pref, since support for each one differs,
# in how it works and how NE1 gets feedback from it that refers to specific atoms and bonds.

# Note: the DNA Generator model choice may also need to change somehow, for this.

# WARNING: as of 080416, these are mostly not yet implemented, and setting them
# may cause bugs. The names don't reflect this. So I am hiding them (removing
# non_debug = True). Unfortunately this didn't make it into .rc2 (since I forgot
# about it) so it may not make it into the release. [bruce 080416]
#update: these are still not implemented fully, and setting them will
# still cause bugs (e.g. some aspects of bug 2842). This won't change for v1.1
# release. [bruce 080523]

def pref_dna_updater_convert_to_PAM3plus5():
    res = debug_pref("DNA: edit as PAM3+5? ",
                      Choice_boolean_False, # when True, I'll remove the ending space
                      ## non_debug = True,
                      prefs_key = True,
                      call_with_new_value = _changed_dna_updater_behavior_pref )
    return res

def pref_mmp_save_convert_to_PAM5(): # has one use, in save_mmp_file [as of 080519]
    res = debug_pref("DNA: save as PAM5? ",
                      Choice_boolean_False, # when True, I'll remove the ending space
                      ## non_debug = True,
                      prefs_key = True )
    return res

def pref_renderers_convert_to_PAM5(): # never yet used [as of 080519]
    res = debug_pref("DNA: render externally as PAM5?", # e.g. QuteMol, POV-Ray
                      Choice_boolean_False,
                      ## non_debug = True,
                      prefs_key = True )
    return res

def pref_minimizers_convert_to_PAM5(): # never yet used [as of 080519]
    res = debug_pref("DNA: minimize in PAM5? ", # i.e. for ND-1 (GROMACS or not)
                      Choice_boolean_False, # when True, I'll remove the ending space
                      ## non_debug = True,
                      prefs_key = True )
    return res

# ==

def pref_fix_after_readmmp_before_updaters():
    res = debug_pref("DNA: do fix_after_readmmp_before_updaters? ",
                      Choice_boolean_True, # might change to False for release -- risky, maybe slow, and no huge need
                         # update, bruce 080408: for now, leave it on, just remove debug prints and non_debug = True
                         # for both related prefs; decide later whether it's slow based on profiles
                      ## non_debug = True,
                      prefs_key = True )
    return res

def pref_fix_after_readmmp_after_updaters():
    # temporary kluge (since probably not enough to protect this
    #  from making updater exceptions much worse in effect):
    # disable when dna updater is off, to work around bug in that case
    # (described in checkin mail today)
    # (only needed in "after" version) [bruce 080319]
    if not dna_updater_is_enabled():
        print "bug: the permanent version of this fix is not working, noticed in pref_fix_after_readmmp_after_updaters"
    res = debug_pref("DNA: do fix_after_readmmp_after_updaters? ",
                      Choice_boolean_True, # same comment as for before_updaters version
                      ## non_debug = True,
                      prefs_key = True )
    return res and dna_updater_is_enabled() # only ok to do this if dna updater is on

# ==

def pref_debug_dna_updater(): # 080228; note: accessed using flags matching debug_flags.DEBUG_DNA_UPDATER*
    res = debug_pref("DNA: updater debug prints",
                     Choice(["off", "minimal", "on", "verbose"],
                            ## defaultValue = "on", # todo: revise defaultValue after debugging
                            # defaultValue left "on" for now, though a bit verbose, bruce 080317
                            defaultValue = "off" #bruce 080702 revised this, and the prefs key
                           ),
                     non_debug = True,
                     prefs_key = "v111/DNA updater: debug prints", # changed, bruce 080317, 080702
                     call_with_new_value = _update_our_debug_flags )
    return res

def pref_dna_updater_slow_asserts(): # 080228; note: accessed using debug_flags.DNA_UPDATER_SLOW_ASSERTS
    res = debug_pref("DNA: updater slow asserts?",
                     ## Choice_boolean_True, # todo: test speed effect; revise before release if too slow
                     Choice_boolean_False, #bruce 080702 revised this, and the prefs key
                     non_debug = True,
                     prefs_key = "v111/DNA updater: slow asserts?", # changed, bruce 080317, 080702
                     call_with_new_value = _update_our_debug_flags )
    return res

# ==

def _changed_dna_updater_behavior_pref(val):
    if val:
        msg = "Note: to apply new DNA prefs value to existing atoms, " \
              "run \"DNA: rescan all atoms\" in debug->other menu."
        env.history.message(orangemsg(msg))
    return

def _changed_dna_updater_behavior_pref_2(val): # rename! but, not currently used.
    _changed_dna_updater_behavior_pref( True) # always print the message

def _update_our_debug_flags(val):
    del val
    # make sure the flags we control are defined in debug_flags
    # (i.e. that we got the right module here, and spelled them correctly)
    # (if not, this will fail the first time it runs)
    debug_flags.DEBUG_DNA_UPDATER
    debug_flags.DEBUG_DNA_UPDATER_VERBOSE
    debug_flags.DNA_UPDATER_SLOW_ASSERTS
    debug_flags.DEBUG_DNA_UPDATER_MINIMAL

    # update them all from the debug prefs

    debug_option = pref_debug_dna_updater() # "off", "minimal", "on", or "verbose"

    debug_flags.DEBUG_DNA_UPDATER_MINIMAL = (debug_option in ("minimal", "on", "verbose",))
    debug_flags.DEBUG_DNA_UPDATER         = (debug_option in            ("on", "verbose",))
    debug_flags.DEBUG_DNA_UPDATER_VERBOSE = (debug_option in                  ("verbose",))

    debug_flags.DNA_UPDATER_SLOW_ASSERTS = pref_dna_updater_slow_asserts()

    return

# end