class test_polyline_drag(State_preMixin, ExampleCommand):
# class constants needed by mode API for example commands
commandName = 'test_polyline_drag-commandName'
default_mode_status_text = "test_polyline_drag"
featurename = "Prototype: Example Polyline Drag Command"
## PM_class = test_polyline_drag_PM
# tracked state
rubberBand_enabled = State(
bool, False, doc="whether we're rubberbanding a new segment now")
# TODO:
### grab a polyline object from an example file in exprs ### (the one that has a closed boolean and can draw in 3d)
### have a list of them, we're rubberbanding last segment of last one...
lastSegmentStart = ORIGIN + 6 * DY # stub
lastSegmentEnd = State(
Point,
doc="endpoint of last segment; only meaningful when rubberBand_enabled"
)
# note: these might be redundant with some points in a polyline object;
# should they be aliases into one?
rubberBandDrawable = If_expr(
rubberBand_enabled,
Line(lastSegmentStart, lastSegmentEnd, red, thickness=4), NullDrawable)
whatWeDraw = Instance(rubberBandDrawable)
# init methods
def __init__(self, glpane):
# not sure why this method is needed, see comment in test_connectWithState.__init__
super(test_polyline_drag, self).__init__(glpane)
ExampleCommand.__init__(self, glpane)
return
def Draw(self):
super(test_polyline_drag, self).Draw() #k
self.whatWeDraw.draw()
return
def leftDown(self, event):
print "leftDown"
# TODO:
# get the point (mouseray in plane)
# make a real point there (or mark it as real, if we have a point object for it already)
# (so it has a blue dot of its own)
# update self.rubberBand_enabled
# STUB:
self.rubberBand_enabled = True
self.lastSegmentEnd = self.lastSegmentStart + 3 * DX
ExampleCommand.leftDown(self, event)
### will this prevent this error in mouse release:
## AttributeError: 'test_polyline_drag' object has no attribute 'LMB_press_event'
## [GLPane.py:1805] [selectAtomsMode.py:899]
return
pass
class StatefulRect(DelegatingInstanceOrExpr): ###UNFINISHED but works for now
# args
rect = ArgOrOption(Movable(Rect),
Rect(1, 1, yellow),
doc="copy state from a snapshot of this guy's state")
###k not sure of Movable; for now, we ignore it and just grab out the state attrs we happen to know about as Rect attrs
# state (maybe stateargs?)
width = State(Width, rect.width)
height = State(Width, rect.height)
color = State(Color, rect.color)
# appearance ###k missing the Movable -- does that belong in here, anyway??
delegate = Rect(width, height, color)
pass
def StateArrayRefs(type_expr, dfltval_expr, **kws): #e refile?
"""An array (expandable, arbitrarily indexed -- really a dictionary) of individually tracked/resettable state variables --
accessed as individual StateRefs to the variables.
Usage: in a class definition that uses ExprsMeta,
attr = StateArrayRefs( type_expr, dfltval_expr )
creates an attribute in each Instance which is effectively a dictionary of individually change/usage-tracked values,
each coerced to type_expr [nim] (which can't yet depend on the dictionary index ###FIX),
and each set to the value of dfltval_expr if it is accessed before it's first set.
Note: dfltval_expr is evaluated without usage tracking; it is not yet decided whether it's evaluated only once
(and if so when) or each time it's needed (the latter is more useful, but less efficient in many cases).
There is not yet any way for dfltval_expr to depend on the dictionary index. ###FIX
###e There is not yet a way to control the possible or actual dictionary indices, or to provide an initial default value
for the array as a whole (it's always {}). See also _CK_ and _CV_ rules, which provide read-only versions of those abilities.
A combo of a _CK_/_CV_ interface to a StateArray could, for now, do much of what a _CK_-like feature in StateArray should do,
though much more clumsily. In my first use of this I said "i want an arg for the index set... maybe even the initial set,
or total set, so i can iter over it..."
[NOTE: at least one dictlike class has that feature - review the ones in py_utils, see what _CK_ uses]
###e there may not yet be a way to delete an element (effectively resetting it to the value of dfltval_expr, computed somewhen).
###e there is not yet an unambiguous record of which elements are present or not in the array.
###e There is not yet a way to subscribe to updates of the set of defined array element indices,
nor to updates of all changes to the entire set of values,
let alone the same features for specific subsets, defined by index preds or sets.
###e There is not yet an efficient way to invalidate a range of indices at once
(letting smart-enoguh subscribers receive just one summary inval).
###e There is not yet a way for some of the array to be set to a virtual array (e.g. a view of part of another array or set).
See also: MapListToExpr, ArgList [nim], InstanceDict [nim], StateArg [nim].
"""
#e should change to descriptor class... [why is that not easier than it is?]
#e implem of type_expr coercion: depending on type & options, wrap with glue code when set, or coerce in simple way when set
#e options: doc, debug_name
#e somehow the State finds out its argname -- i think (does it really?) -- we might want that in debug_name
return State(StateArrayRefs_type,
call_Expr(_make_StateArrayRefs, type_expr, dfltval_expr,
_E_ATTR, _self, **kws)) #k this use of **kws
class Vertex_new(
ModelObject
): #070105 ###e maybe it also needs an official type or typename for use in rules and files?
pos0 = Arg(Position)
pos = State(Position, pos0)
color = Option(Color, black)
pass
class ModelTreeNode_trivial_glue(DelegatingInstanceOrExpr): #070206, 070207
# args
delegate = Arg(ModelObject)
# default formulae for ModelTreeNodeInterface -- including one which supplies new state
mt_name = State(str, getattr_Expr(getattr_Expr(delegate, '__class__'), '__name__')) ###k
#e type - grab it from object, or related to role in parent...
mt_kids = ()
mt_openable = False
###e something for mt_node_id
pass
class ChoiceRow_class(InstanceMacro): # stub, nim
nchoices = Arg(int)
dflt = Arg(int, 0)
kws = OptionsDict() ###IMPLEM #e see if name is correct re other proposals, eg Options not Option?
#e renamekws tosay what they are for -- the ChoiceButton --- note that we could ditch the OptionsDict and ask for
# an explicit dict of them, but then they would not be indivly customizable. Should a new sub-option cust scheme be made? #e
var = State(int, _self.dflt) ###k does _self.dflt work? Is this equiv to the above? NO, it's an lval not a stateref!
_value = SimpleRow(
0 ###stub -- the next hard thing is to apply this to a variable number of exprs or insts created by map over range(nchoices)
)
pass
class whatever(DelegatingInstanceOrExpr): ###e rename
# simulates the env that demo_ui will provide (stub version, evolving to be more like it)
ui_and_world = Instance(World()) #####
###e following needs to permit cmd_DrawOnSurface to vary
# (at least let it also be cmd_MakeRect; use a menu of options? or use one ActionButton per command, since more like a toolbar?)
# -- but with Instance inside the variation, I think --
# ie it should be a map from the desired cmd expr to the cmd instance -- or, make a new one each time, so it's a cmdrun...
# maybe see how demo_ui/toolbar was planning to do it... ###e
toolbar = SimpleColumn(
ActionButton(
_self.do_cmd_DrawOnSurface, "button: cmd_DrawOnSurface"
), #e make the text from the command #e the running one should look pressed
ActionButton(_self.do_cmd_MakeRect, "button: cmd_MakeRect"),
) ###e show it where? above PM for now?
current_cmdrun = State(
Anything, None
) # what is actually in here? an Instance of a "command run", [btw is None needed??]
# or of a command obj that handles multiple runs (ie a command_runner?)... up to it to not get messed up if that happens
# (and for now, unfortunately, not remaking it is probably a significant speed optim)
# (so should we let an outer command handler have the PM and get reused, but an inner CommandRun get remade? why bother?)
def do_cmd_DrawOnSurface(
self
): #e which name is better: do_cmd or set_cmd? depends on type of command!
self._do_cmd(cmd_DrawOnSurface)
def do_cmd_MakeRect(self):
self._do_cmd(cmd_MakeRect)
def _do_cmd(self, cmd):
"set self.current_cmdrun, etc..."
# do we make a new one if button pressed when one already running?? yes for now.
self.current_cmdrun = self.Instance(
cmd(world=self.ui_and_world),
id(cmd)) #e cache that expr? index ok? why cache instance?
#old cmt: #e args? world? new object? does its super handle some? Command vs CommandRun?
pm = current_cmdrun.property_manager
corner_stuff = SimpleColumn(toolbar, pm)
delegate = Overlay(
current_cmdrun,
DrawInCorner(corner_stuff, corner=PM_CORNER),
)
def _init_instance(self):
super(whatever, self)._init_instance()
self.do_cmd_MakeRect(
) # or at least set some command, preferably a "null" or "default" one
# note that this resets the current tool state on reload -- not really desirable;
# how was demo_ui planning to handle that? ###k
pass
class MainCommandToolButton(DelegatingInstanceOrExpr): #e rename?
"Toolbutton for one of the main tools like Features, Build, Sketch -- class hierarchy subject to revision"
# args
toolbar = Arg(Toolbar) # our parent - #e rename parent_toolbar? to distinguish from our flyout_toolbar.
toolname = Arg(str) #e.g. "Build"
command = Arg(Command, doc = "the command invoked by pressing this toolbutton (might be transient or long lasting)") ###k type ok?
subtools = Arg(list_Expr) # list of subtools (for cmenu or flyout), with None as a separator -- or as an ignored missing elt??
# like menu_spec items?
# Q: can they contain their own conditions, or just let the list be made using Ifs or filters?
# A: subtools can contain their own conditions, for being shown, enabled, etc. they are ui elements, not just operations.
#e also one for its toolbar, esp if it's a mutually exclusive pressed choice -- and ways to cause related cmd/propmgr to be entered
# state
pressed = State(bool, False, doc = "whether this button should appear pressed right now")
# formulae
plain_bordercolor = If(pressed, gray, white)
highlighted_bordercolor = If(pressed, gray, blue)
pressed_in_bordercolor = If(pressed, gray, green) # green = going to do something on_release_in
pressed_out_bordercolor = If(pressed, gray, white) # white = not going to do anything on_release_out
# appearance
delegate = Highlightable(
plain = Boxed(TextRect(toolname), bordercolor = plain_bordercolor),
highlighted = Boxed(TextRect(toolname), bordercolor = highlighted_bordercolor), #e submenu is nim
pressed_in = Boxed(TextRect(toolname), bordercolor = pressed_in_bordercolor),
pressed_out = Boxed(TextRect(toolname), bordercolor = pressed_out_bordercolor),
sbar_text = format_Expr( "%s (click for flyout [nim]; submenu is nim)", toolname ),
on_release_in = _self.on_release_in,
cmenu_obj = _self ###IMPLEM cmenu_obj option alias or renaming; or call it cmenu_maker??
)
# repr? with self.toolname. Need to recall how best to fit in -- repr_info? ##e
# actions
def on_release_in(self):
if not self.pressed:
print "on_release_in %s" % self.toolname
self.pressed = True #e for now -- later we might let main toolbar decide if this is ok
#e incremental redraw to look pressed right away? or let toolbar decide?
self.toolbar._advise_got_pressed(self)
else:
#### WRONG but not yet another way to unpress:
self.pressed = False
print "unpressed -- not normal in real life!"###
return #e stub
def cmenu_spec(self, highlightable): ###IMPLEM this simpler cmenu API (if it still seems good)
return map( self.menuitem_for_subtool, self.subtools ) ###e how can that func tell us to leave out one, or incl a sequence?
def menuitem_for_subtool(self, subtool):
# stub, assume not None etc
return ( subtool.name, subtool.cmd_invoke )
pass
class TextEditField(DelegatingInstanceOrExpr):
text = State(
str, "(empty)"
) #e dflt should be an arg, or more to the point, the text should come from a stateref ###DOIT
label = Option(str, "(field label)")
dialog_title = Option(str, "(title)")
dflt_dialog_label = "enter some text; use @@@ for \\n" # a public class attr (for clients to use in longer labels)
dialog_label = Option(str, dflt_dialog_label)
delegate = Highlightable(
SimpleRow(
Top(TextRect(label)), Top(TextRect(text))
), #e long enough? too long? nlines ok? # Top is for when >1 line in text
#e highlight form with blue border?
on_doubleclick=_self.
on_doubleclick, # on_press -> on_doubleclick -- probably better
sbar_text="double-click to edit textfield",
#e cmenu binding too?
)
def on_doubleclick(self):
ok, text = grab_text_using_dialog(default=self.text,
title=self.dialog_title,
label=self.dialog_label)
if ok:
#e unicode?? (see cad/src MT Node renaming code, or Node.name mmp code, or the Comment Node,
# for example code that can handle it)
#e filter through a func about what's acceptable?
# if it fails, repeat dialog with more specific label?
# strip whitespace? etc
# eventually customize all that, for now just do what's most useful right here
text = text.strip()
self.text = text # changes state
else:
print "cancelled text edit, old text remains: %r" % (
self.text, ) #e some other place to put a message in the UI?
return
pass
class DnaStrand_ResizeHandle(DraggableHandle_AlongLine):
"""
Provides a resize handle for editing the length of an existing Dna Strand.
"""
#Handle color will be changed depending on whether the handle is grabbed
# [bruce 080409 revised some details of this to fix bug 2747]
handleColor = Option(Color, purple) # formula from caller
# (in current usage, a state variable in caller)
handleIsGrabbed = State(Boolean, False)
# Note: this might not be needed if we passed more args to
# Highlightable (namely, the appearance when pressed);
# that would also be more reliable, since as it is, any failure for
# on_release to be called would leave the handle stuck in the
# grabbed state; client code would be wise to sometimes reset
# this state. Also, it seems rare to ever see this selection color
# since the handle is usually highlighted and yellow while dragging it.
# [Depending on the highlight and selection drawing mode. Russ 080530]
# So this state could probably just be removed, with all uses of
# _currentHandleColor changes to uses of handleColor.
# [bruce 080409]
_currentHandleColor = If_expr( handleIsGrabbed,
env.prefs[selectionColor_prefs_key],
_self.handleColor)
#The caller-specified formula that determines the radius (of the sphere) of this handle.
#See DnaStrand_EditCommand._determine_resize_handle_radius() for more
#details
sphereRadius = Option(Width, 1.5)
#Appearance of the handle. (note that it uses all the code from exprs module
# and needs more documentation there).
#See exprs.Rect.Sphere for definition of a drawable 'Sphere' object.
appearance = Overlay(
Sphere(_self.sphereRadius,
_self._currentHandleColor,
center = ORIGIN + _self.direction * 3.0 * _self.sphereRadius),
Cylinder((ORIGIN,
ORIGIN + _self.direction * 2.2 * _self.sphereRadius),
0.6 * _self.sphereRadius,
_self._currentHandleColor))
#Handle appearance when highlighted
# [this probably doesn't need to be an Option, since the client never
# passes it [bruce 080409 comment]]
HHColor = env.prefs[hoverHighlightingColor_prefs_key]
appearance_highlighted = Option(
Drawable,
Overlay(
Sphere(_self.sphereRadius,
HHColor,
center = ORIGIN + _self.direction * 3.0 * _self.sphereRadius),
Cylinder((ORIGIN,
ORIGIN + _self.direction * 2.2 * _self.sphereRadius),
0.6* _self.sphereRadius ,
HHColor)),
doc = "handle appearance when highlighted")
#Stateusbar text. Variable needs to be renamed in superclass.
sbar_text = Option(str,
"Drag the handle to resize the strand",
doc = "Statusbar text on mouseover")
#Command object specified as an 'Option' during instantiation of the class
#see DnaSegment_EditCommand class definition.
command = Option(Action,
doc = 'The Command which instantiates this handle')
#Current position of the handle. i.e. it is the position of the handle
#under the mouse. (its differert than the 'orifinal position)
#This variable is used in self.command.graphicsMode to draw a rubberband
#line and also to specify the endPoint2 of the structure while modifying
#it. See DnaSegment_EditCommand.modifyStructure for details.
if _self.origin is not None:
currentPosition = _self.origin + _self.direction * _self.height_ref.value
else:
currentPosition = ORIGIN
#Fixed end of the structure (self.command.struct) ..meaning that end won't
#move while user grabbs and draggs this handle (attached to a the other
#'moving endPoint) . This variable is used to specify endPoint1 of the
#structure while modifyin it. See DnaSegment_EditCommand.modifyStructure
#and self.on_release for details.
fixedEndOfStructure = Option(Point,
V(0, 0, 0))
#If this is false, the 'highlightable' object i.e. this handle
#won't be drawn. See DraggableHandle.py for the declararion of
#the delegate(that defines a Highlightable) We define a If_Exprs to check
#whether to draw the highlightable object.
should_draw = State(bool, True)
def ORIG_NOT_USED_hasValidParamsForDrawing(self):
"""
NOT USED AS OF 2008-04-02
Returns True if the handles origin and direction are not 'None'.
@see: DnaStrand_GraphicsMode._draw_handles() where the caller
uses this to decide whether this handle can be drawn without
a problem.
"""
#NOTE: Better to do it in the drawing code of this class?
#But it uses a delegate to draw stuff (see class Highlightable)
#May be we should pass this method to that delegate as an optional
#argument -- Ninad 2008-04-02
if self.origin is None or self.direction is None:
return False
return True
def hasValidParamsForDrawing(self):
"""
Returns True if the handles origin and direction are not 'None'.
@see: DnaStrand_GraphicsMode._draw_handles() where the caller
uses this to decide whether this handle can be drawn without
a problem.
"""
#NOTE: Better to do it in the drawing code of this class?
#But it uses a delegate to draw stuff (see class Highlightable)
#May be we should pass this method to that delegate as an optional
#argument -- Ninad 2008-04-02
#@Bug: Create a duplex; Enter Dna strand edit command,
# then shorten it such that it removes some bases of the strand from the
#original duplex. Hit undo; click on the right handle, and shorten it again
#sometimes it gives a traceback. in drawing the highlightable
#this could be because self.should_draw flag is not getting updated.
#NOTES: If this method is used, you will also need to define the
#delegate in class DraggableHandle as --
#delegate = If_Exprs(_self.should_draw, Highlightable(....))
if self.origin is None or self.direction is None:
self.should_draw = False
else:
self.should_draw = True
return self.should_draw
def on_press(self):
"""
Actions when handle is pressed (grabbed, during leftDown event)
@see: B{SelectChunks.GraphicsMode.leftDown}
@see: B{DnaStrand_EditCommand.grabbedHandle}
@see: B{DnaStrand_GraphicsMode.Draw} (which uses some attributes of
the current grabbed handle of the command.
@see: B{DragHandle_API}
"""
#Change the handle color when handle is grabbed. See declaration of
#self.handleColor in the class definition.
## self._currentHandleColor = env.prefs[selectionColor_prefs_key]
self.handleIsGrabbed = True
#assign 'self' as the curent grabbed handle of the command.
self.command.grabbedHandle = self
def on_drag(self):
"""
Method called while dragging this handle .
@see: B{DragHandle_API}
"""
pass
#The following call is disabled. Instead updating this spinbox
#is done by the command.getCursorText method . See that method for
#details
##self.command.update_numberOfBases()
def on_release(self):
"""
This method gets called during leftUp (when the handle is released)
@see: B{DnaStrand_EditCommand.modifyStructure}
@see: self.on_press
@see: B{SelectChunks.GraphicsMode.leftUp}
@see: B{DragHandle_API}
"""
## self._currentHandleColor = self.handleColor
self.handleIsGrabbed = False
if self.command and hasattr(self.command, 'modifyStructure'):
self.command.modifyStructure()
#Clear the grabbed handle attribute (the handle is no longer
#grabbed)
self.command.grabbedHandle = None
class DnaStrand_EditCommand(State_preMixin, EditCommand):
"""
Command to edit a DnaStrand (chunk object as of 2008-02-14)
To edit a Strand, first enter BuildDna_EditCommand (accessed using
Build> Dna) then, select a strand chunk of an existing DnaSegment within the
DnaGroup you are editing. When you select the strand chunk, it enters
DnaStrand_Editcommand, shows its property manager and also shows the
resize handles if any.
"""
cmd = 'Dna Strand'
sponsor_keyword = 'DNA'
prefix = 'Strand ' # used for gensym
cmdname = "DNA_STRAND"
commandName = 'DNA_STRAND'
featurename = 'Edit_Dna_Strand'
command_should_resume_prevMode = True
command_has_its_own_gui = True
command_can_be_suspended = False
# Generators for DNA, nanotubes and graphene have their MT name
# generated (in GeneratorBaseClass) from the prefix.
create_name_from_prefix = True
call_makeMenus_for_each_event = True
#Graphics Mode
GraphicsMode_class = DnaStrand_GraphicsMode
#@see: self.updateHandlePositions for details on how these variables are
#used in computation.
#@see: DnaStrand_ResizeHandle and handle declaration in this class
#definition
handlePoint1 = State( Point, ORIGIN)
handlePoint2 = State( Point, ORIGIN)
handleDirection1 = State(Vector, ORIGIN)
handleDirection2 = State(Vector, ORIGIN)
#See self._update_resizeHandle_radius where this gets changed.
#also see DnaSegment_ResizeHandle to see how its implemented.
handleSphereRadius1 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
handleSphereRadius2 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
#handleColors
handleColor1 = State(Color, purple)
handleColor2 = State(Color, purple)
#TODO: 'cylinderWidth attr used for resize handles -- needs to be renamed
#along with 'height_ref attr in exprs.DraggableHandle_AlongLine
cylinderWidth = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
cylinderWidth2 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
#Resize Handles for Strand. See self.updateHandlePositions()
leftHandle = Instance(
DnaStrand_ResizeHandle(
command = _self,
height_ref = call_Expr( ObjAttr_StateRef, _self, 'cylinderWidth'),
origin = handlePoint1,
fixedEndOfStructure = handlePoint2,
direction = handleDirection1,
sphereRadius = handleSphereRadius1,
handleColor = handleColor1
))
rightHandle = Instance(
DnaStrand_ResizeHandle(
command = _self,
height_ref = call_Expr( ObjAttr_StateRef, _self, 'cylinderWidth2'),
origin = handlePoint2,
fixedEndOfStructure = handlePoint1,
direction = handleDirection2,
sphereRadius = handleSphereRadius2,
handleColor = handleColor2
))
def __init__(self, commandSequencer, struct = None):
"""
Constructor for DnaDuplex_EditCommand
"""
glpane = commandSequencer
State_preMixin.__init__(self, glpane)
EditCommand.__init__(self, commandSequencer)
self.struct = struct
#DnaSegment object to which this strand belongs
self._parentDnaSegment = None
#It uses BuildDna_EditCommand.flyoutToolbar ( in other words, that
#toolbar is still accessible and not changes while in this command)
flyoutToolbar = None
#Graphics handles for editing the structure .
self.handles = []
self.grabbedHandle = None
#This is used for comarison purpose in model_changed method to decide
#whether to update the sequence.
self._previousNumberOfBases = None
def init_gui(self):
"""
Initialize gui.
"""
#@see DnaSegment_EditCommand.init_gui() for a detailed note.
#This command implements similar thing
self.create_and_or_show_PM_if_wanted(showPropMgr = False)
def model_changed(self):
#This MAY HAVE BUG. WHEN --
#debug pref 'call model_changed only when needed' is ON
#See related bug 2729 for details.
#The following code that updates te handle positions and the strand
#sequence fixes bugs like 2745 and updating the handle positions
#updating handle positions in model_changed instead of in
#self.graphicsMode._draw_handles() is also a minor optimization
#This can be further optimized by debug pref
#'call model_changed only when needed' but its NOT done because of an
# issue menitoned in bug 2729 - Ninad 2008-04-07
EditCommand.model_changed(self) #This also calls the
#propMgr.model_changed
if self.grabbedHandle is not None:
return
#For Rattlesnake, PAM5 segment resizing is not supported.
#@see: self.hasResizableStructure()
if self.hasValidStructure():
isStructResizable, why_not = self.hasResizableStructure()
if not isStructResizable:
self.handles = []
return
elif len(self.handles) == 0:
self._updateHandleList()
self.updateHandlePositions()
#NOTE: The following also updates self._previousParams
self._updateStrandSequence_if_needed()
def keep_empty_group(self, group):
"""
Returns True if the empty group should not be automatically deleted.
otherwise returns False. The default implementation always returns
False. Subclasses should override this method if it needs to keep the
empty group for some reasons. Note that this method will only get called
when a group has a class constant autdelete_when_empty set to True.
(and as of 2008-03-06, it is proposed that dna_updater calls this method
when needed.
@see: Command.keep_empty_group() which is overridden here.
"""
bool_keep = EditCommand.keep_empty_group(self, group)
if not bool_keep:
if self.hasValidStructure():
if group is self.struct:
bool_keep = True
elif group is self.struct.parent_node_of_class(self.assy.DnaGroup):
bool_keep = True
return bool_keep
def _createPropMgrObject(self):
"""
Creates a property manager object (that defines UI things) for this
editCommand.
"""
assert not self.propMgr
propMgr = self.win.createDnaStrandPropMgr_if_needed(self)
return propMgr
def _gatherParameters(self):
"""
Return the parameters from the property manager UI.
@return: All the parameters (get those from the property manager):
- numberOfBases
- dnaForm
- basesPerTurn
- endPoint1
- endPoint2
@rtype: tuple
"""
return self.propMgr.getParameters()
def _createStructure(self):
"""
Creates and returns the structure -- TO BE IMPLEMENTED ONCE
DNA_MODEL IS READY FOR USE.
@return : DnaStrand.
@rtype: L{Group}
@note: This needs to return a DNA object once that model is implemented
"""
pass
def _modifyStructure(self, params):
"""
Modify the structure based on the parameters specified.
Overrides EditCommand._modifystructure. This method removes the old
structure and creates a new one using self._createStructure. This
was needed for the structures like this (Dna, Nanotube etc) . .
See more comments in the method.
"""
assert self.struct
# parameters have changed, update existing structure
self._revertNumber()
# self.name needed for done message
if self.create_name_from_prefix:
# create a new name
name = self.name = gensym(self.prefix, self.assy) # (in _build_struct)
self._gensym_data_for_reusing_name = (self.prefix, name)
else:
# use externally created name
self._gensym_data_for_reusing_name = None
# (can't reuse name in this case -- not sure what prefix it was
# made with)
name = self.name
self.dna = B_Dna_PAM3_SingleStrand()
numberOfBases, \
dnaForm, \
dnaModel, \
basesPerTurn, \
duplexRise, \
color_junk = params
#see a note about color_junk in DnaSegment_EditCommand._modifyStructure()
numberOfBasesToAddOrRemove = self._determine_numberOfBases_to_change()
if numberOfBasesToAddOrRemove != 0:
resizeEndStrandAtom, resizeEndAxisAtom = \
self.get_strand_and_axis_endAtoms_at_resize_end()
if resizeEndAxisAtom:
dnaSegment = resizeEndAxisAtom.molecule.parent_node_of_class(
self.assy.DnaSegment)
resizeEnd_final_position = self._get_resizeEnd_final_position(
resizeEndAxisAtom,
abs(numberOfBasesToAddOrRemove),
duplexRise )
self.dna.modify(dnaSegment,
resizeEndAxisAtom,
numberOfBasesToAddOrRemove,
basesPerTurn,
duplexRise,
resizeEndAxisAtom.posn(),
resizeEnd_final_position,
resizeEndStrandAtom = resizeEndStrandAtom
)
return
def _finalizeStructure(self):
"""
Overrides EditCommand._finalizeStructure.
@see: EditCommand.preview_or_finalize_structure
"""
if self.struct is not None:
#@TODO 2008-03-19:Should we always do this even when strand sequence
#is not changed?? Should it waste time in comparing the current
#sequence with a previous one? Assigning sequence while leaving the
#command will be slow for large files.Need to be optimized if
#problematic.
#What if a flag is set in self.propMgr.updateSequence() when it
#updates the seq for the second time and we check that here.
#Thats not good if the method gets called multiple times for some
#reason other than the user entered sequence. So not doing here.
#Better fix would be to check if sequence gets changed (textChanged)
#in DnaSequence editor class .... Need to be revised
EditCommand._finalizeStructure(self)
self._updateStrandSequence_if_needed()
self.assignStrandSequence()
def _previewStructure(self):
EditCommand._previewStructure(self)
self.updateHandlePositions()
self._updateStrandSequence_if_needed()
def _updateStrandSequence_if_needed(self):
if self.hasValidStructure():
new_numberOfBases = self.struct.getNumberOfBases()
#@TODO Update self._previousParams again?
#This NEEDS TO BE REVISED. BUG MENTIONED BELOW----
#we already update this in EditCommand class. But, it doesn't work for
#the following bug -- 1. create a duplex with 5 basepairs, 2. resize
#red strand to 2 bases. 3. Undo 4. Redo 5. Try to resize it again to
#2 bases -- it doesn't work because self.previousParams stil stores
#bases as 2 and thinks nothing got changed! Can we declare
#self._previewStructure as a undiable state? Or better self._previousParams
#should store self.struct and should check method return value
#like self.struct.getNumberOfBases()--Ninad 2008-04-07
if self.previousParams is not None:
if new_numberOfBases != self.previousParams[0]:
self.propMgr.numberOfBasesSpinBox.setValue(new_numberOfBases)
self.previousParams = self._gatherParameters()
if not same_vals(new_numberOfBases, self._previousNumberOfBases):
self.propMgr.updateSequence()
self._previousNumberOfBases = new_numberOfBases
def _get_resizeEnd_final_position(self,
resizeEndAxisAtom,
numberOfBases,
duplexRise):
final_position = None
if self.grabbedHandle:
final_position = self.grabbedHandle.currentPosition
else:
dnaSegment = resizeEndAxisAtom.molecule.parent_node_of_class(self.assy.DnaSegment)
other_axisEndAtom = dnaSegment.getOtherAxisEndAtom(resizeEndAxisAtom)
axis_vector = resizeEndAxisAtom.posn() - other_axisEndAtom.posn()
segment_length_to_add = getDuplexLength('B-DNA',
numberOfBases,
duplexRise = duplexRise)
final_position = resizeEndAxisAtom.posn() + norm(axis_vector)*segment_length_to_add
return final_position
def getStructureName(self):
"""
Returns the name string of self.struct if there is a valid structure.
Otherwise returns None. This information is used by the name edit field
of this command's PM when we call self.propMgr.show()
@see: DnaStrand_PropertyManager.show()
@see: self.setStructureName
"""
if self.hasValidStructure():
return self.struct.name
else:
return None
def setStructureName(self, name):
"""
Sets the name of self.struct to param <name> (if there is a valid
structure.
The PM of this command callss this method while closing itself
@param name: name of the structure to be set.
@type name: string
@see: DnaStrand_PropertyManager.close()
@see: self.getStructureName()
@see: DnaSegment_GraphicsMode.leftUp ,
DnaSegment_editCommand.setStructureName for comments about some
issues.
"""
if self.hasValidStructure():
self.struct.name = name
def assignStrandSequence(self):
"""
Assigns the sequence typed in the sequence editor text field to
the selected strand chunk. The method it invokes also assigns
a complimentary sequence to the mate strand.
@see: Chunk.setStrandSequence
"""
sequenceString = self.propMgr.sequenceEditor.getPlainSequence()
sequenceString = str(sequenceString)
#assign strand sequence only if it not the same as the current sequence
seq = self.struct.getStrandSequence()
if seq != sequenceString:
self.struct.setStrandSequence(sequenceString)
def editStructure(self, struct = None):
"""
Edit the structure
@param struct: structure to be edited (in this case its a strand chunk)
@type struct: chunk or None (this will change post dna data model)
"""
EditCommand.editStructure(self, struct)
if self.hasValidStructure():
self._updatePropMgrParams()
#TO BE REVISED post dna data model - 2008-02-14
if isinstance(self.struct.dad , self.assy.DnaSegment):
self._parentDnaSegment = self.struct.dad
#For Rattlesnake, we do not support resizing of PAM5 model.
#So don't append the exprs handles to the handle list (and thus
#don't draw those handles. See self.model_changed()
isStructResizable, why_not = self.hasResizableStructure()
if not isStructResizable:
self.handles = []
else:
self._updateHandleList()
self.updateHandlePositions()
def _updatePropMgrParams(self):
"""
Subclasses may override this method.
Update some property manager parameters with the parameters of
self.struct (which is being edited)
@see: self.editStructure()
"""
#Format in which params need to be provided to the Property manager
#numberOfBases,
#dnaForm,
#dnaModel,
#basesPerTurn,
#duplexRise,
#color
self._previousNumberOfBases = self.struct.getNumberOfBases()
numberOfBases = self._previousNumberOfBases
color = self.struct.getColor()
params_for_propMgr = ( numberOfBases,
None,
None,
None,
None,
color )
#TODO 2008-03-25: better to get all parameters from self.struct and
#set it in propMgr? This will mostly work except that reverse is
#not true. i.e. we can not specify same set of params for
#self.struct.setProps ...because endPoint1 and endPoint2 are derived.
#by the structure when needed. Commenting out following line of code
#UPDATE 2008-05-06 Fixes a bug due to which the parameters in propMGr
#of DnaSegment_EditCommand are not same as the original structure
#(e.g. bases per turn and duplexrise)
self.propMgr.setParameters(params_for_propMgr)
def _getStructureType(self):
"""
Subclasses override this method to define their own structure type.
Returns the type of the structure this editCommand supports.
This is used in isinstance test.
@see: EditCommand._getStructureType() (overridden here)
"""
return self.win.assy.DnaStrand
def updateSequence(self):
"""
Public method provided for convenience. If any callers outside of this
command need to update the sequence in the sequence editor, they can simply
do currentCommand.updateSequence() rather than
currentCommand.propMgr.updateSequence()
@see: DnaStrand_ProprtyManager.updateSequence() which does the actual
job of updating the sequence string in the sequence editor.
"""
if self.propMgr is not None:
self.propMgr.updateSequence()
def hasResizableStructure(self):
"""
For Rattlesnake release, we dont support strand resizing for PAM5
models. If the structure is not resizable, the handles won't be drawn
@see:self.model_changed()
@see:DnaStrand_PropertyManager.model_changed()
@see: self.editStructure()
@see: DnaSegment.is_PAM3_DnaStrand()
"""
#Note: This method fixes bugs similar to (and including) bug 2812 but
#the changes didn't made it to Rattlesnake rc2 -- Ninad 2008-04-16
isResizable = True
why_not = ''
if not self.hasValidStructure():
isResizable = False
why_not = 'It is invalid.'
return isResizable, why_not
isResizable = self.struct.is_PAM3_DnaStrand()
if not isResizable:
why_not = 'It needs to be converted to PAM3 model.'
return isResizable, why_not
#The following fixes bug 2812
strandEndBaseAtom1, strandEndBaseAtom2 = self.struct.get_strand_end_base_atoms()
if strandEndBaseAtom1 is strandEndBaseAtom2:
isResizable = False
why_not = "It is probably a \'closed loop\'."
return isResizable, why_not
return True, ''
def _updateHandleList(self):
"""
Updates the list of handles (self.handles)
@see: self.editStructure
@see: DnaSegment_GraphicsMode._drawHandles()
"""
# note: if handlePoint1 and/or handlePoint2 can change more often than
# this runs, we'll need to rerun the two assignments above whenever they
# change and before the handle is drawn. An easy way would be to rerun
# these assignments in the draw method of our GM. [bruce 080128]
self.handles = [] # guess, but seems like a good idea [bruce 080128]
self.handles.append(self.leftHandle)
self.handles.append(self.rightHandle)
def updateHandlePositions(self):
"""
Update handle positions
"""
if len(self.handles) == 0:
#No handles are appended to self.handles list.
#@See self.model_changed() and self._updateHandleList()
return
self.cylinderWidth = CYLINDER_WIDTH_DEFAULT_VALUE
self.cylinderWidth2 = CYLINDER_WIDTH_DEFAULT_VALUE
axisAtom1 = None
axisAtom2 = None
strandEndBaseAtom1 = None
strandEndBaseAtom2 = None
#It could happen (baecause of bugs) that standEndBaseAtom1 and
#strandEndBaseAtom2 are one and the same! i.e strand end atom is
#not bonded. If this happens, we should throw a traceback bug
#exit gracefully. The possible cause of this bug may be ---
#(just an example): For some reason, the modify code is unable to
#determine the correct bond direction of the resized structure
#and therefore, while fusing the original strand with the new one created
#by DnaDuplex.modify, it is unable to find bondable pairs!
# [- Ninad 2008-03-31]
strandEndBaseAtom1, strandEndBaseAtom2 = self.struct.get_strand_end_base_atoms()
if strandEndBaseAtom1 is strandEndBaseAtom2:
print_compact_stack("bug in updating handle positions, some resized DnaStrand " \
"has only one atom")
return
if strandEndBaseAtom1:
axisAtom1 = strandEndBaseAtom1.axis_neighbor()
if axisAtom1:
self.handleDirection1 = self._get_handle_direction(axisAtom1,
strandEndBaseAtom1)
self.handlePoint1 = axisAtom1.posn()
if strandEndBaseAtom2:
axisAtom2 = strandEndBaseAtom2.axis_neighbor()
if axisAtom2:
self.handleDirection2 = self._get_handle_direction(axisAtom2,
strandEndBaseAtom2)
self.handlePoint2 = axisAtom2.posn()
# UPDATE 2008-04-15:
# Before 2008-04-15 the state attrs for exprs handles were always reset to None
#at the beginning of the method. But it is calling model_changed signal
#recursively. (se also bug 2729) So, reset thos state attrs only when
#needed -- Ninad [ this fix was not in RattleSnake rc1]
# Set handlePoints (i.e. their origins) and the handle directions to
# None if the atoms used to compute these state attrs are missing.
# The GraphicsMode checks if the handles have valid placement
# attributes set before drawing it.
if strandEndBaseAtom1 is None and strandEndBaseAtom2 is None:
#probably a ring
self.handles = []
if strandEndBaseAtom1 is None or axisAtom1 is None:
self.handleDirection1 = None
self.handlePoint1 = None
if strandEndBaseAtom2 is None or axisAtom2 is None:
self.handleDirection2 = None
self.handlePoint2 = None
#update the radius of resize handle
self._update_resizeHandle_radius(axisAtom1, axisAtom2)
#update the display color of the handles
self._update_resizeHandle_color(strandEndBaseAtom1, strandEndBaseAtom2)
def _update_resizeHandle_radius(self, axisAtom1, axisAtom2):
"""
Finds out the sphere radius to use for the resize handles, based on
atom /chunk or glpane display (whichever decides the display of the end
atoms. The default value is 1.2.
@see: self.updateHandlePositions()
@see: B{Atom.drawing_radius()}
"""
if axisAtom1 is not None:
self.handleSphereRadius1 = max(1.005*axisAtom1.drawing_radius(),
1.005*HANDLE_RADIUS_DEFAULT_VALUE)
if axisAtom2 is not None:
self.handleSphereRadius2 = max(1.005*axisAtom2.drawing_radius(),
1.005*HANDLE_RADIUS_DEFAULT_VALUE)
def _update_resizeHandle_color(self,
strandEndBaseAtom1,
strandEndBaseAtom2):
"""
Update the color of resize handles using the current color
of the *chunk* of the corresponding strand end atoms.
@Note: If no specific color is set to the chunk, it uses 'purple' as
the default color (and doesn't use the atom.element.color) . This
can be changed if needed.
"""
if strandEndBaseAtom1 is not None:
color = strandEndBaseAtom1.molecule.color
if color:
self.handleColor1 = color
if strandEndBaseAtom2 is not None:
color = strandEndBaseAtom2.molecule.color
if color:
self.handleColor2 = color
def _get_handle_direction(self, axisAtom, strandAtom):
"""
Get the handle direction.
"""
handle_direction = None
strand_rail = strandAtom.molecule.get_ladder_rail()
for bond_direction in (1, -1):
next_strand_atom = strandAtom.strand_next_baseatom(bond_direction)
if next_strand_atom:
break
if next_strand_atom:
next_axis_atom = next_strand_atom.axis_neighbor()
if next_axis_atom:
handle_direction = norm(axisAtom.posn() - next_axis_atom.posn())
return handle_direction
def getDnaRibbonParams(self):
"""
Returns parameters for drawing the dna ribbon.
If the dna rubberband line should NOT be drawn (example when you are
removing bases from the strand or if its unable to get dnaSegment) ,
it retuns None. So the caller should check if the method return value
is not None.
@see: DnaStrand_GraphicsMode._draw_handles()
"""
if self.grabbedHandle is None:
return None
if self.grabbedHandle.origin is None:
return None
direction_of_drag = norm(self.grabbedHandle.currentPosition - \
self.grabbedHandle.origin)
#If the strand bases are being removed (determined by checking the
#direction of drag) , no need to draw the rubberband line.
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
return None
strandEndAtom, axisEndAtom = self.get_strand_and_axis_endAtoms_at_resize_end()
#DnaStrand.get_DnaSegment_with_content_atom saely handles the case where
#strandEndAtom is None.
dnaSegment = self.struct.get_DnaSegment_with_content_atom(strandEndAtom)
ribbon1_direction = None
if dnaSegment:
basesPerTurn = dnaSegment.getBasesPerTurn()
duplexRise = dnaSegment.getDuplexRise()
ribbon1_start_point = strandEndAtom.posn()
if strandEndAtom:
ribbon1_start_point = strandEndAtom.posn()
for bond_direction, neighbor in strandEndAtom.bond_directions_to_neighbors():
if neighbor and neighbor.is_singlet():
ribbon1_direction = bond_direction
break
ribbon1Color = strandEndAtom.molecule.color
if not ribbon1Color:
ribbon1Color = strandEndAtom.element.color
return (self.grabbedHandle.origin,
self.grabbedHandle.currentPosition,
basesPerTurn,
duplexRise,
ribbon1_start_point,
ribbon1_direction,
ribbon1Color
)
return None
def get_strand_and_axis_endAtoms_at_resize_end(self):
resizeEndStrandAtom = None
resizeEndAxisAtom = None
strandEndAtom1, strandEndAtom2 = self.struct.get_strand_end_base_atoms()
if self.grabbedHandle is not None:
for atm in (strandEndAtom1, strandEndAtom2):
axisEndAtom = atm.axis_neighbor()
if axisEndAtom:
if same_vals(axisEndAtom.posn(), self.grabbedHandle.origin):
resizeEndStrandAtom = atm
resizeEndAxisAtom = axisEndAtom
return (resizeEndStrandAtom, resizeEndAxisAtom)
def getCursorText(self):
"""
Used by DnaStrand_GraphicsMode._draw_handles()
@TODO: It also updates the number of bases
"""
if self.grabbedHandle is None:
return
#@TODO: This updates the PM as the cursor moves.
#Need to rename this method so that you that it also does more things
#than just to return a textString. Even better if its called in
#self.model_changed but at the moment there is a bug thats why we
#are doing this update by calling getCursorText in the
#GraphicscMode._draw_handles-- Ninad 2008-04-05
self.update_numberOfBases()
if not env.prefs[dnaStrandEditCommand_showCursorTextCheckBox_prefs_key]:
return '', black
#Note: for Rattlesnake rc2, the text color is green when bases are added
#, red when subtracted black when no change. But this implementation is
#changed based on Mark's user experience. The text is now always shown
#in black color. -- Ninad 2008-04-17
textColor = black
text = ""
numberOfBases = self.propMgr.numberOfBasesSpinBox.value()
numberOfBasesString = self._getCursorText_numberOfBases(
numberOfBases)
changedBases = self._getCursorText_changedBases(
numberOfBases)
text = numberOfBasesString
if text and changedBases:
text += " " # Removed comma. Mark 2008-07-03
text += changedBases
return (text , textColor)
def _getCursorText_numberOfBases(self, numberOfBases):
"""
Return the cursor textstring that gives information about the number
of bases if the corresponding prefs_key returns True.
"""
numberOfBasesString = ''
if env.prefs[
dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key]:
numberOfBasesString = "%db"%numberOfBases
return numberOfBasesString
def _getCursorText_changedBases(self, numberOfBases):
"""
@see: self.getCursorText()
"""
changedBasesString = ''
if env.prefs[
dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key]:
original_numberOfBases = self.struct.getNumberOfBases()
changed_bases = numberOfBases - original_numberOfBases
if changed_bases > 0:
changedBasesString = "(" + "+" + str(changed_bases) + ")"
else:
changedBasesString = "(" + str(changed_bases) + ")"
return changedBasesString
def modifyStructure(self):
"""
Called when a resize handle is dragged to change the length of the
segment. (Called upon leftUp) . This method assigns the new parameters
for the segment after it is resized and calls
preview_or_finalize_structure which does the rest of the job.
Note that Client should call this public method and should never call
the private method self._modifyStructure. self._modifyStructure is
called only by self.preview_or_finalize_structure
@see: B{DnaStrand_ResizeHandle.on_release} (the caller)
@see: B{SelectChunks_GraphicsMode.leftUp} (which calls the
the relevent method in DragHandler API. )
@see: B{exprs.DraggableHandle_AlongLine}, B{exprs.DragBehavior}
@see: B{self.preview_or_finalize_structure }
@see: B{self._modifyStructure}
"""
#TODO: need to cleanup this and may be use use something like
#self.previousParams = params in the end -- 2008-03-24 (midnight)
if self.grabbedHandle is None:
return
#TODO: Important note: How does NE1 know that structure is modified?
#Because number of base pairs parameter in the PropMgr changes as you
#drag the handle . This is done in self.getCursorText() ... not the
#right place to do it. OR that method needs to be renamed to reflect
#this as suggested in that method -- Ninad 2008-03-25
self.preview_or_finalize_structure(previewing = True)
self.glpane.gl_update()
def update_numberOfBases(self):
"""
Updates the numberOfBases in the PM while a resize handle is being
dragged.
@see: self.getCursorText() where it is called.
"""
#@Note: originally (before 2008-04-05, it was called in
#DnaStrand_ResizeHandle.on_drag() but that 'may' have some bugs
#(not verified) also see self.getCursorText() to know why it is
#called there (basically a workaround for bug 2729
if self.grabbedHandle is None:
return
currentPosition = self.grabbedHandle.currentPosition
resize_end = self.grabbedHandle.origin
new_duplexLength = vlen( currentPosition - resize_end )
numberOfBasePairs_to_change = getNumberOfBasePairsFromDuplexLength('B-DNA',
new_duplexLength)
original_numberOfBases = self.struct.getNumberOfBases()
#If the dot product of handle direction and the direction in which it
#is dragged is negative, this means we need to subtract bases
direction_of_drag = norm(currentPosition - resize_end)
if dot(self.grabbedHandle.direction, direction_of_drag ) < 0:
total_number_of_bases = original_numberOfBases - numberOfBasePairs_to_change
self.propMgr.numberOfBasesSpinBox.setValue(total_number_of_bases)
else:
total_number_of_bases = original_numberOfBases + numberOfBasePairs_to_change
self.propMgr.numberOfBasesSpinBox.setValue(total_number_of_bases - 1)
def _determine_numberOfBases_to_change(self):
"""
"""
#The Property manager will be showing the current number
#of base pairs (w. May be we can use that number directly here?
#The following is safer to do so lets just recompute the
#number of base pairs. (if it turns out to be slow, we will consider
#using the already computed calue from the property manager
original_numberOfBases = self.struct.getNumberOfBases()
numberOfBasesToAddOrRemove = self.propMgr.numberOfBasesSpinBox.value()\
- original_numberOfBases
if numberOfBasesToAddOrRemove > 0:
#dna.modify will remove the first base pair it creates
#(that basepair will only be used for proper alignment of the
#duplex with the existing structure) So we need to compensate for
#this basepair by adding 1 to the new number of base pairs.
numberOfBasesToAddOrRemove += 1
return numberOfBasesToAddOrRemove
def makeMenus(self):
"""
Create context menu for this command. (Build Dna mode)
"""
if not hasattr(self, 'graphicsMode'):
return
selobj = self.glpane.selobj
if selobj is None:
return
self.Menu_spec = []
highlightedChunk = None
if isinstance(selobj, Chunk):
highlightedChunk = selobj
if isinstance(selobj, Atom):
highlightedChunk = selobj.molecule
elif isinstance(selobj, Bond):
chunk1 = selobj.atom1.molecule
chunk2 = selobj.atom2.molecule
if chunk1 is chunk2 and chunk1 is not None:
highlightedChunk = chunk1
if highlightedChunk is None:
return
if self.hasValidStructure():
if (self.struct is highlightedChunk) or \
(self.struct is highlightedChunk.parent_node_of_class(
self.assy.DnaStrand)):
item = (("Currently editing %r"%self.struct.name),
noop, 'disabled')
self.Menu_spec.append(item)
return
#following should be self.struct.getDnaGroup or self.struct.getDnaGroup
#need to formalize method name and then make change.
dnaGroup = self.struct.parent_node_of_class(self.assy.DnaGroup)
if dnaGroup is None:
return
if not dnaGroup is highlightedChunk.parent_node_of_class(self.assy.DnaGroup):
item = ("Edit unavailable: Member of a different DnaGroup",
noop, 'disabled')
self.Menu_spec.append(item)
return
highlightedChunk.make_glpane_context_menu_items(self.Menu_spec,
command = self)
class DraggablyBoxed(
Boxed
): # 070316; works 070317 [testexpr_36] before ww,hh State or resizable, and again (_36b) after them
# inherit args, options, formulae from Boxed
thing = _self.thing ###k WONT WORK unless we kluge ExprsMeta to remove this assignment from the namespace -- which we did.
###e not sure this is best syntax though. attr = _super.attr implies it'd work inside larger formulae, but it can't;
# attr = Boxed.attr might be ok, whether it can work is not reviewed; it too might imply what _super does, falsely I think.
extra1 = _self.extra1
borderthickness = _self.borderthickness
rectframe = _self.rectframe # a pure expr
# new options
resizable = Option(bool,
False,
doc="whether to make it resizable at lower right")
# works 070317 10pm (testexpr_36b) except for a few ###BUGS [updated info 070318 7pm]:
# + [fixed] the wrong corner resizes (top right) (logic bug)
# + [fixed] resizer doesn't move (understood -- wrong expr for its posn; commented below)
# - negative sizes allowed (missing feature - limit the drag - need new DragBehavior feature)
# - no clipping to interior of rectframe (missing feature - draw something clipped)
# - perspective view ought to work, but entirely ###UNTESTED.
# also, cosmetic bugs:
# - resizer doesn't follow mouse in rotated coordsys, even in ortho view (though it's still useable).
# (This is not surprising -- we're using the wrong kind of DragBehavior as a simple kluge.)
# - the resizer is ugly, in shape & color.
clipped = Option(
bool, False,
doc="###doc") #070322 new feature ### make True default after testing?
# state
# WARNING: due to ipath persistence, if you revise dflt_expr you apparently need to restart ne1 to see the change.
## ww = State(Width, thing.width + 2 * extra1) # replaces non-state formula in superclass -- seems to work
## hh = State(Width, thing.height + 2 * extra1)
## # now we just need a way to get a stateref to, effectively, the 3-tuple (ww,hh,set-value-discarder) ... instead, use whj:
whj = State(Vector,
V_expr(thing.width + 2 * extra1, -thing.height - 2 * extra1,
0)) #e not sure this is sound in rotated coordsys
translation = State(Vector, ORIGIN)
# override super formulae
ww = whj[0] # seems to work
hh = neg_Expr(
whj[1]
) # negative is needed since drag down (negative Y direction) needs to increase height
# (guess: neg_Expr wouldn't be needed if we used an appropriate new DragBehavior in resizer,
# rather than our current klugy use of SimpleDragBehavior)
# appearance
rectframe_h = Instance(
Highlightable(
## rectframe(bordercolor=green),####### cust is just to see if it works -- it doesn't, i guess i sort of know why
##bug: __call__ of <getattr_Expr#8243: (S._self, <constant_Expr#8242: 'rectframe'>)> with: () {'bordercolor': (0.0, 1.0, 0.0)}
##AssertionError: getattr exprs are not callable
TopLeft(rectframe),
#e different colored hover-highlighted version?? for now, just use sbar_text to know you're there.
sbar_text=
"draggable box frame", # this disappears on press -- is that intended? ###k
behavior=SimpleDragBehavior(
# arg1: the highlightable
_self.rectframe_h,
# arg2: a write-capable reference to _self.translation
## fails - evalled at compile time, not an expr: LvalueFromObjAndAttr( _self, 'translation'),
###BUG: why didn't anything complain when that bug caused the state value to be an add_Expr, not a number-array?
call_Expr(LvalueFromObjAndAttr, _self, 'translation'),
#e alternate forms for this that we might want to make work:
# - getattr_StateRef(_self, 'translation') # simple def of the above
# - StateRef_for( _self.translation ) # turns any lvalue into a stateref! Name is not good enough, though.
)))
resizer = Instance(
Highlightable(
Center(Rect(extra1, extra1)), #e also try BottomRight
highlighted=Center(Rect(extra1, extra1, white)),
pressed=_my.highlighted,
sbar_text="resize the box frame",
behavior=SimpleDragBehavior(
_self.resizer, call_Expr(LvalueFromObjAndAttr, _self, 'whj'))))
###BUG: in Boxed, rectframe comes first, so lbox attrs are delegated to it. We should do that too --
# but right now we draw it later in order to obscure the thing if they overlap. With clipping we won't need that --
# but without clipping we will. If the latter still matters, we need a version of Overlay with delegation != drawing order,
# or, to delegate appearance and layout to different instances ourselves. (Or just to define new formulae for lbox -- easiest.) #e
drawme = Instance(
Overlay(
If(
clipped,
Clipped(
thing,
planes=[
call_Expr(clip_to_right_of_x0, -thing.bleft - extra1 +
ww - borderthickness),
# note: the (- borderthickness) term makes the clipping reach exactly
# to the inner rectframe edge. Without it, clipping would reach to the outer edge,
# which for 3d objects inside the frame can cause them to obscure it.
# (Other interesting values are (- extra1) and (- borderthickness/2.0),
# but they both look worse, IMHO.)
call_Expr(clip_below_y0,
thing.btop + extra1 - hh + borderthickness)
]),
thing,
),
Translate(rectframe_h,
V_expr(-thing.bleft - extra1, thing.btop + extra1)),
If(
resizable,
## Translate( resizer, V_expr( thing.bright + extra1, - thing.bbottom - extra1))
###WRONG - this posn is fixed by thing's lbox dims, not affected by ww, hh;
# will the fix be clearer if we use a TopLeft alignment expr?
# It'd be hard to use it while maintaining thing's origin for use by external alignment --
# but maybe there's no point in doing that.
Translate(
resizer,
V_expr(-thing.bleft - extra1 + ww,
thing.btop + extra1 - hh)))))
_value = Translate(
drawme, ## DisplayListChunk( drawme), ###k this DisplayListChunk might break the Highlightable in rectframe_h #####
translation)
pass # end of class DraggablyBoxed
class DraggableObject(DelegatingInstanceOrExpr):
"""DraggableObject(obj) is a wrapper which makes any model object draggable (###doc the details),
and also helps provides a context menu specific to obj.
[##e It may be extended to make obj click-selectable or even region-selectable, at the proper times, too.]
WARNING: Experimental -- API/organization will surely change,
integrating not only rotation, but click to select, etc.
The resulting wrapper will typically be applied by model->view macros.
In fact, it's more complicated than that: the selection-click controller will wrap single objects,
but the draggability wrapper is more likely to be organized something like this,
where the named localvars refer to sets whose membership depends on selection:
visibles = DisplayListChunk(fixed_stuff) + distortedly_moving_stuff +
DraggableObject(DisplayListChunk(dragging_as_a_unit_stuff)).
The distortedly_moving_stuff includes things like external bonds between fixed and being-dragged atoms,
which have to stretch in individual ways during the drag.
"""
# args
obj = Arg(ModelObject)
# options
#e selectable = Option(bool, True, doc = "whether to let this object be click-selectable in the standard way") [see selected]
rotatable = Option(
bool,
True,
doc=
"whether to let this object rotate about its center using MMB/Alt/Option drags"
)
# This is intended to implement an initial subset of the "New motion UI" [070225 new feature]
# [###e default will change to False after testing]
# WARNING: as an optim, we might require that this be True initially, or even always (i.e. be a constant),
# if it will ever be True during the Instance's lifetime -- not sure. If so, this requirement must at least be documented,
# and preferably error-detected. ###FIX (if we do require that)
# experimental kluge 070314
_kluge_drag_handler = Option(
Anything,
_self,
doc=
"object to receive our on_press/on_drag/on_release events, in place of _self"
)
# state
selected = State(bool,
False) ###KLUGE test stub, only set when debug070209
translation = Option(
Vector,
V(0, 0, 0), #070404
doc=
"initial translation [WARNING: might merge with misnamed self.motion (a State attr) to make a StateOption]"
)
motion = State(
Vector, _self.translation
) # publicly visible and settable (but only with =, not +=).
##e rename to translation? (by making it a StateOption)
##e (or deprecate the concept of StateOption but make any State settable initially by a special option not just with same name?
## eg either initial_attr or initial_data = [something with dict or attr access to the data] ??)
##e NOTE [070404]: I miscoded translation as Arg rather than Option, and said StateArg rather than StateOption in docstring,
# though intending only named uses of it -- is this evidence that Arg / Option / Parameter should be the same,
# that Option should be the default meaning, and positional arglists should be handled differently and as an extra thing
# (eg like the old _args feature -- which leads to clearer code when subclassing)?? Guess: quite possibly, but needs more thought.
# WARNING: use of += has two distinct bugs, neither error directly detectable:
# - changes due to += (or the like) would not be change tracked.
# (But all changes to this need to be tracked, so our drawing effects are invalidated when it changes.)
# - value might be a shared Numeric array -- right now use of = to set this doesn't copy the array to make us own it.
rotation = State(Quat,
Q(1, 0, 0,
0)) #070225 new feature -- applied around object center
# experiment 070312: works (see test_StateArrayRefs_2) ###doc ##e clean up ##k is it making the usual case slow in a significant way??
delta_stateref = Option(StateRef,
call_Expr(LvalueFromObjAndAttr, _self, 'motion'),
doc="#doc")
use_motion = delta_stateref.value
# geometric attrs should delegate to obj, but be translated by motion as appropriate.
##e Someday we need to say that in two ways:
# - the attrs in the "geometric object interface" delegate as a group (rather than listing each one of them here)
# - but when they do, they get passed through a change-of-coords boundary, and they know their own coordsystems,
# so the right thing happens.
# But for now we have no way to say either thing, so we'll add specific formulas for specific attrs as needed. [070208]
##e Note that before the obj types know how to translate due to type, the interface (which knows the attrs indivly)
# could know it. So, delegation of all attrs in an interface can be done by special glue code which also knows
# how to transform them in useful ways, by knowing about those attrs and what transforms are useful.
# This is useful enough to keep, even once its default transforms can come from declared attr types &
# values knowing their coordsys. It adds value to that since interfaces can always know special cases about specific attrs.
if 0:
# update 070209 late: try doing this in Translate below, with the other involved exprs delegating as usual... ####k
center = obj.center + motion
# following comments are from when the above was 'if 1' a day or two ago -- still relevant since general [##e refile??]:
# Problem: won't work for objs with no center! Solution for now: don't try to eval the self attr then.
# Not perfect, since what ought to be AttributeError will turn into some other exception.
##e One better solution would involve declared interfaces for obj, and delegation of all attrs in interfaces
# of a certain kind (geometric), so if obj met more interfaces and had more attrs, those would be included,
# but if not, we would not have them either.
##e Or alternatively, we could provide an easy way to modify the above formula
# to specify a condition under which center should seem to exist here, with that cond being whether it exists on obj.
### A potential problem with both solutions: misleasing AttributeError messages, referring to self rather than obj,
# would hurt debugging. So we probably want to reraise the original AttributeError in cases like that, whatever
# the way in which we ask for that behavior. That means one construct for "passing along attr missingness",
# but *not* a composition of one construct for saying when this attr is there, and one for asking whether another is.
# Note: can't we delegate center (& other geometry) through the display delegate below, if Highlightable passes it through
# and Translate does the coordinate transformation? ###e
# appearance
obj_name = call_Expr(node_name, obj) #070216
# Note: node_name is used in MT_try2; it's better than using _e_model_type_you_make (for our use in sbar_text, below).
# BTW, node_name is a helper function associated with ModelTreeNodeInterface (informal so far).
#
# If you want to wrap an object with extra info which specifies its node_name, use ... what? ###k hmm, I forget if there
# is a way partway through being implemented...
# maybe WithAttributes( Center(Rect(0.4, 0.4, green)), mt_name = "green rect #n" )... i guess yes, ### TRY IT
# should clean this situation up, use Adaptor term for that pattern
# of interface conversion, etc... [070404 updated comment]
# (Note [070216]: I had a bug when I had a comma after the above def. This made obj_name, included directly in another expr,
# turn into a singleton tuple of the call_Expr value, but when included as _self.obj_name (normally equivalent to obj_name),
# turn into something else (since eval of a tuple must not descend inside it -- guess, might have been a tuple_Expr).
# I'm not sure how to detect this error except to stop permitting tuple(expr) to be allowed as abbrev for a tuple_Expr --
# which seems too inconvenient -- or to figure out a way for the formula scanner to detect it (and make it illegal as the
# rhs of an assignment into a class namespace -- probably ok to make illegal). ##DOIT sometime)
obj_drawn = If(
selected,
Overlay(obj, Rect(
1, 1,
blue)), ##### WRONG LOOK for selected, but should work [070209]
#BUG: Rect(1,lightblue) is gray, not light blue -- oh, it's that failure to use type to guess which arg it is!
obj)
sbar_text_for_maybe_selected = If(selected, " (selected)", "")
delegate = Highlightable(
# Note 070317: since Highlightable is outside of RotateTranslate, its coordsys doesn't change during a drag,
# thus avoiding, here in DraggableObject, the bug that came up in the first implem of DraggablyBoxed,
# whose highlightable rectframe was moving during the drag, but was also being used to supply the coordsys
# for the drag events. This bug is actually in SimpleDragBehavior above, and the fix will be confined to that class.
#
# plain appearance
RotateTranslate(obj_drawn, rotation, use_motion),
# hover-highlighted appearance (also used when dragging, below)
highlighted=RotateTranslate(
DisplayListChunk(
# This inner DisplayListChunk, in theory, might help make up for current implem of disabling them inside WarpColors...
# in my tests, it didn't make a noticeable difference (probably since obj is fast to draw). [070216 2pm]
#
# Note: if obj has its own DisplayListChunk, does that notice the value of whatever dynenv var is altered by WarpColors??
# We'll have to make it do so somehow -- perhaps by altering the displist name by that, or turning off displists due to it.
# For this initial implem [070215 4pm], we did the latter.
## WarpColors( obj_drawn, lambda color: ave_colors( 0.3, white, color ) ), # whiten the color -- ugly
## WarpColors( obj_drawn, lambda color: yellow ), # "ignore color, use yellow" -- even uglier
## WarpColors( obj_drawn, lambda color: ave_colors( 0.2, white, color ) ), # whiten, but not as much -- less ugly
WarpColors(
obj_drawn, lambda color: ave_colors(0.1, white, color)
), # whiten, even less -- even less ugly [best so far]
## WarpColors( obj_drawn, lambda color: ave_colors( 0.2, gray, color ) ), # gray-end instead of whiten -- not quite as good
## WarpColors( obj_drawn, lambda color: (color[1],color[2],color[0]) ), # permute the hues...
),
rotation,
use_motion),
pressed=_my.highlighted, # pressed_in and pressed_out appearance
###BUG (when we gave pressed_in and pressed_out separately -- ###UNTESTED since then):
# this pressed_out appearance seems to work for DNA cyls but not for draggable PalletteWell items! [070215 4pm]
## sbar_text = format_Expr( "Draggable %r", obj ),
##e should use %s on obj.name or obj.name_for_sbar, and add those attrs to ModelObject interface
# (they would delegate through viewing wrappers on obj, if any, and get to the MT-visible name of the model object itself)
##e [Can we implem something like try_Expr( try1, try2, try3) which evals to the first one evalling without an exception??
# But that doesn't seem safe unless you have to list the permissible exceptions (like in Python try/except).
# The use of this here (temporary) would be to look for obj.name, then try a different format_Expr if that fails.
# getattr(obj, 'name', dflt) would get us by, but would not as easily permit alternate format_Exprs in the two cases.]
## # older highlighted or pressed_in appearance (not sure which it was before I inserted the args above this) -- zapping it 070216 late
## If( eval_Expr(constant_Expr(constant_Expr(debug070209))),
## ###e need option or variant of If to turn off warning that cond is a constant: warn_if_constant = False??
## # also make the printed warning give a clue who we are -- even if we have to pass an option with the text of the clue??
## Translate( Boxed(obj), motion),
## #######070209 TEST THIS KLUGE -- note it does not include selected appearance
## # (but HL might incl it anyway? sometimes yes sometimes no, not sure why that would be -- ah, it depends on whether
## # mouse is over the moved object (which is silly but i recall it as happening in regular ne1 too -- ###BUG)
## #e not good highlight form
## ####BUG: the layout attrs (lbox attrs, eg bleft) are apparently not delegated, so the box is small and mostly obscured
## Translate( obj, motion)
## ),
## _obj_name = call_Expr(node_name, obj), #070216
# that can't work yet -- it tries to define a new attr in an object (this Highlightable) from outside,
# accessible in other option formulae as _this(Highlightable)._obj_name...
# instead, I moved this def into _self (far above) for now.
sbar_text=format_Expr("%s%s (can be dragged)", obj_name,
sbar_text_for_maybe_selected), # revised 070216
# This adds some info to sbar_text about what we can do with obj (drag, select, etc)...
#e someday, maybe the dynenv wants to control how info of several kinds turns into actual sbar_text.
## on_press = _self.on_press,
## on_drag = _self.on_drag,
## on_release = _self.on_release,
on_press=_kluge_drag_handler.on_press,
on_drag=_kluge_drag_handler.on_drag,
on_release=_kluge_drag_handler.on_release,
cmenu_maker=
obj ###e 070204 experimental, API very likely to be revised; makes Highlightable look for obj.make_selobj_cmenu_items
)
### DESIGN Q: do we also include the actual event binding (on_press and on_drag) -- for now, we do --
# or just supply the Draggable interface for moving self.obj
# and let the caller supply the binding to our internal "cmd" drag_from_to?? ###e
# has Draggable interface (see demo_polygon.py for explan) for changing self.motion
def _cmd_drag_from_to(
self, p1,
p2): #e rename drag_hitpoint_from_to? (in the Draggable Interface)
"""[part of the Draggable Interface; but this interface
is not general enough if it only has this method -- some objects need more info eg a moving mouseray, screenrect, etc.
Either this gets passed more info (eg a dragevent obj),
or we keep the kluge of separate self dynenv queries (like for mousepoint and screenrect),
or we provide glue code to look for this method but use more general ones if it's not there. ###e
BTW, that interface is a myth at present; all actual dragging so far is done using on_press/on_drag/on_release,
with this method at best used internally on some objs, like this one. [as of 070313]]
"""
if self._delegate.altkey:
assert 0, "should no longer be called"
## ###KLUGE, just a hack for testing Highlightable.altkey [070224]; later, do rotation instead (per "New motion UI")
## # (Is it also a ###KLUGE to detect altkey within this method, rather than caller detecting it and passing a flag
## # or calling a different method? YES.)
## ## self.motion = self.motion + (p2 - p1) * -1
## # change self.rotation... by a quat which depends on p2 - p1 projected onto the screen... or the similar mouse x,y delta...
## ###KLUGE: assume DZ is toward screen and scale is standard....
## # wait, ###BUG, we don't even have enough info to do this right, or not simply, starting from p1, rather than startpoint...
## dx,dy,dz = p2 - p1
## rotby = Q(p1,p2) ###WRONG but ought to be legal and visible and might even pretend to be a trackball in some cases and ways
## self.rotation = self.rotation + rotby
## # print "%r motion = %r rotation = %r" % (self, self.motion, self.rotation)
else:
## self.motion = self.motion + (p2 - p1)
self.delta_stateref.value = self.delta_stateref.value + (p2 - p1)
return
##e something to start & end the drag? that could include flush if desired...
# can push changes into the object
def flush(self, newmotion=V(0, 0, 0)):
self.delegate.move(
self.use_motion + newmotion
) ###k ASSUMES ModelObject always supports move (even if it's a noop) ###IMPLEM
# note, nothing wrong with modelobjects usually having one coordsys state which this affects
# and storing the rest of their data relative to that, if they want to -- but only some do.
## self.motion = V(0,0,0)
self.delta_stateref.value = V(0, 0, 0)
# if told to move, flush at the same time
def move(self, motion):
self.flush(motion)
return
# on_press etc methods are modified from demo_polygon.py class typical_DragCommand
#e note: it may happen that we add an option to pass something other than self to supply these methods.
# then these methods would be just the default for when that was not passed
# (or we might move them into a helper class, one of which can be made to delegate to self and be the default obj). [070313]
def on_press(self):
point = self.current_event_mousepoint(
) # the touched point on the visible object (hitpoint)
# (this method is defined in the Highlightable which is self.delegate)
self.oldpoint = self.startpoint = point
# decide type of drag now, so it's clearly constant during drag, and so decision code is only in one place.
# (but note that some modkey meanings might require that changes to them during the same drag are detected [nim].)
if self._delegate.altkey:
self._this_drag = 'free x-y rotate'
#e more options later, and/or more flags like this (maybe some should be booleans)
###e or better, set up a function or object which turns later points into their effects... hmm, a DragCommand instance!
##e or should that be renamed DragOperation??
self._screenrect = (ll, lr, ur,
ul) = self.screenrect(self.startpoint)
# these points should be valid in our delegate's coords == self's coords
self._dx = _dx = norm(lr - ll)
self._dy = _dy = norm(ur - lr)
self._dz = cross(
_dx, _dy
) # towards the eye (if view is ortho) (but alg is correct whether or not it is, i think)
###k check cross direction sign
self._scale = min(vlen(lr - ll), vlen(ur - lr)) * 0.4
# New motion UI suggests that 40% of that distance means 180 degrees of rotation.
# We'll draw an axis whose length is chosen so that dragging on a sphere of that size
# would have the same effect. (Maybe.)
self._objcenter = self._delegate.center
self.startrot = +self.rotation
else:
self._this_drag = 'free x-y translate'
if debug070209:
self.ndrags = 0
return
def on_drag(self):
# Note: we can assume this is a "real drag", since the caller (ultimately a selectMode method in testmode, as of 070209)
# is tracking mouse motion and not calling this until it becomes large enough, as the debug070209 prints show.
oldpoint = self.oldpoint # was saved by prior on_drag or by on_press
point = self.current_event_mousepoint(plane=self.startpoint)
if debug070209:
self.ndrags += 1
## if (self.ndrags == 1) or 1:
## print "drag event %d, model distance = %r, pixel dist not computed" % (self.ndrags, vlen(oldpoint - point),)
if self._this_drag == 'free x-y rotate':
# rotate using New motion UI
# [probably works for this specific kind of rotation, one of 4 that UI proposes;
# doesn't yet have fancy cursors or during-rotation graphics; add those only after it's a DragCommand]
# two implem choices:
# 1. know the eye direction and the screen dims in plane of startpoint, in model coords; compute in model coords
# 2. get the mouse positions (startpoint and point) and screen dims in window x,y coords, compute rotation in eye coords,
# but remember to reorient it to correspond with model if model coords are rotated already.
# Not sure which one is better.
# In general, placing user into model coords (or more precisely, into object local coords) seems more general --
# for example, what if there were several interacting users, each visible to the others?
# We'd want each user's eye & screen to be visible! (Maybe even an image of their face & screen, properly scaled and aligned?)
# And we'd want their posns to be used in the computations here, all in model coords.
# (Even if zoom had occurred, which means, even the user's *size* is quite variable!)
# I need "user in model coords" for other reasons too, so ok, I'll do it that way.
#
# [Hey, I might as well fix the bug in current_event_mousepoint which fakes the center of view, at the same time.
# (I can't remember its details right now, but I think it assumed the local origin was the cov, which is obviously wrong.)
# (But I didn't look at that code or fix that bug now.)]
vec = point - self.startpoint
uvec = norm(vec) #k needed??
axisvec = cross(
self._dz, uvec
) # unit length (suitable for glRotate -- but we need to use it to make a quat!)
axisvec = norm(
axisvec) # just to be sure (or to reduce numerical errors)
scale = self._scale
draw_axisvec = axisvec * scale #e times some other length constant too?
center = self._objcenter
self.axisends = (center - axisvec, center + axisvec
) # draw a rotation axis here ###e
self.degrees = degrees = vlen(
vec
) / scale * 180.0 # draw a textual indicator with degrees (and axisvec angle too) ###e
###e or print that info into sbar? or somewhere fixed in glpane? or in glpane near mouse?
# now set self.rotation to a quat made from axisvec and degrees
theta = degrees / 360.0 * 2 * pi
# print "axisvec %r, degrees %r, theta %r" % (axisvec ,degrees,theta)
rot = Q(axisvec, theta)
self.rotation = self.startrot + rot # note use of self.startrot rather than self.rotation on rhs
# avoid += to make sure it gets changed-tracked -- and since it would be the wrong op!
elif self._this_drag == 'free x-y translate':
self._cmd_drag_from_to(
oldpoint, point) # use Draggable interface cmd on self
else:
assert 0
self.oldpoint = point
return
def on_release(self):
#e here is where we'd decide if this was really just a "click", and if so, do something like select the object,
# if we are generalized to become the wrapper which handles that too.
if debug070209:
if not self.ndrags:
# print "release (no drags)" # ie a click
self.selected = not self.selected ###KLUGE test stub
else:
pass # print "release after %d drags" % self.ndrags
self.ndrags = 0
pass
pass # end of class DraggableObject
class DnaSegment_EditCommand(State_preMixin, EditCommand):
"""
Command to edit a DnaSegment object.
To edit a segment, first enter BuildDna_EditCommand (accessed using Build> Dna)
then, select an axis chunk of an existing DnaSegment within the DnaGroup you
are editing. When you select the axis chunk, it enters DnaSegment_Editcommand
and shows the property manager with its widgets showing the properties of
selected segment.
"""
cmd = 'Dna Segment'
sponsor_keyword = 'DNA'
prefix = 'Segment ' # used for gensym
cmdname = "DNA_SEGMENT"
commandName = 'DNA_SEGMENT'
featurename = 'Edit Dna Segment'
command_should_resume_prevMode = True
command_has_its_own_gui = True
command_can_be_suspended = False
# Generators for DNA, nanotubes and graphene have their MT name
# generated (in GeneratorBaseClass) from the prefix.
create_name_from_prefix = True
call_makeMenus_for_each_event = True
#Graphics Mode
GraphicsMode_class = DnaSegment_GraphicsMode
#This is set to BuildDna_EditCommand.flyoutToolbar (as of 2008-01-14,
#it only uses
flyoutToolbar = None
handlePoint1 = State(Point, ORIGIN)
handlePoint2 = State(Point, ORIGIN)
#The minimum 'stopper'length used for resize handles
#@see: self._update_resizeHandle_stopper_length for details.
_resizeHandle_stopper_length = State(Width, -100000)
rotationHandleBasePoint1 = State(Point, ORIGIN)
rotationHandleBasePoint2 = State(Point, ORIGIN)
#See self._update_resizeHandle_radius where this gets changed.
#also see DnaSegment_ResizeHandle to see how its implemented.
handleSphereRadius1 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
handleSphereRadius2 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
cylinderWidth = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
cylinderWidth2 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
#@TODO: modify the 'State params for rotation_distance
rotation_distance1 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
rotation_distance2 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
duplexRise = getDuplexRise('B-DNA')
leftHandle = Instance(
DnaSegment_ResizeHandle(
command=_self,
height_ref=call_Expr(ObjAttr_StateRef, _self, 'cylinderWidth'),
origin=handlePoint1,
fixedEndOfStructure=handlePoint2,
direction=norm_Expr(handlePoint1 - handlePoint2),
sphereRadius=handleSphereRadius1,
discRadius=env.prefs[dnaSegmentResizeHandle_discRadius_prefs_key],
discThickness=env.
prefs[dnaSegmentResizeHandle_discThickness_prefs_key],
range=(_resizeHandle_stopper_length, 10000)))
rightHandle = Instance(
DnaSegment_ResizeHandle(
command=_self,
height_ref=call_Expr(ObjAttr_StateRef, _self, 'cylinderWidth2'),
origin=handlePoint2,
fixedEndOfStructure=handlePoint1,
direction=norm_Expr(handlePoint2 - handlePoint1),
sphereRadius=handleSphereRadius2,
discRadius=env.prefs[dnaSegmentResizeHandle_discRadius_prefs_key],
discThickness=env.
prefs[dnaSegmentResizeHandle_discThickness_prefs_key],
range=(_resizeHandle_stopper_length, 10000)))
rotationHandle1 = Instance(
RotationHandle(command=_self,
rotationDistanceRef=call_Expr(ObjAttr_StateRef, _self,
'rotation_distance1'),
center=handlePoint1,
axis=norm_Expr(handlePoint1 - handlePoint2),
origin=rotationHandleBasePoint1,
radiusVector=norm_Expr(rotationHandleBasePoint1 -
handlePoint1)))
rotationHandle2 = Instance(
RotationHandle(command=_self,
rotationDistanceRef=call_Expr(ObjAttr_StateRef, _self,
'rotation_distance2'),
center=handlePoint2,
axis=norm_Expr(handlePoint2 - handlePoint1),
origin=rotationHandleBasePoint2,
radiusVector=norm_Expr(rotationHandleBasePoint2 -
handlePoint2)))
def __init__(self, commandSequencer, struct=None):
"""
Constructor for DnaDuplex_EditCommand
"""
glpane = commandSequencer
State_preMixin.__init__(self, glpane)
EditCommand.__init__(self, commandSequencer)
self.struct = struct
#Graphics handles for editing the structure .
self.handles = []
self.grabbedHandle = None
def init_gui(self):
"""
Initialize gui.
"""
#Note that DnaSegment_EditCommand only act as an edit command for an
#existing structure. The call to self.propMgr.show() is done only during
#the call to self.editStructure ..i .e. only after self.struct is
#updated. This is done because of the following reason:
# - self.init_gui is called immediately after entering the command.
# - self.init_gui in turn, initialized propMgr object and may also
# show the property manager. The self.propMgr.show routine calls
# an update widget method just before the show. This update method
# updates the widgets based on the parameters from the existing
# structure of the command (self.editCommand.struct)
# Although, it checks whether this structure exists, the editCommand
# could still have a self.struct attr from a previous run. (Note that
# EditCommand API was written before the command sequencer API and
# it has some loose ends like this. ) -- Ninad 2008-01-22
self.create_and_or_show_PM_if_wanted(showPropMgr=False)
def model_changed(self):
#This MAY HAVE BUG. WHEN --
#debug pref 'call model_changed only when needed' is ON
#See related bug 2729 for details.
#The following code that updates te handle positions and the strand
#sequence fixes bugs like 2745 and updating the handle positions
#updating handle positions in model_changed instead of in
#self.graphicsMode._draw_handles() is also a minor optimization
#This can be further optimized by debug pref
#'call model_changed only when needed' but its NOT done because of an
# issue menitoned in bug 2729 - Ninad 2008-04-07
EditCommand.model_changed(self) #This also calls the
#propMgr.model_changed
if self.grabbedHandle is not None:
return
#For Rattlesnake, PAM5 segment resizing is not supported.
#@see: self.hasResizableStructure()
if self.hasValidStructure():
isStructResizable, why_not = self.hasResizableStructure()
if not isStructResizable:
self.handles = []
return
elif len(self.handles) == 0:
self._updateHandleList()
self.updateHandlePositions()
self._update_previousParams_in_model_changed()
def _update_previousParams_in_model_changed(self):
#The following fixes bug 2802. The bug comment has details of what
#it does. Copying some portion of it below--
#We have fixed similar problem for strand resizing, by updating the
#self.previousParams attr in model_changed method (and also updating
#the numberOfBasePairs spinbox in the PM. But here, user can even
#change the number of basepairs from the PM. When he does that,
#the model_changed is called and it resets the number of basepairs
#spinbox value with the ones currently on the structure! Thereby
#making it impossible to upate structure using spinbox. To fix this
#we introduce a new parameter in propMgr.getParameters() which
#reports the actual number of bases on the structure.
#-- Ninad 2008-04-12
if self.previousParams is not None:
new_numberOfBasePairs = self.struct.getNumberOfBasePairs()
if new_numberOfBasePairs != self.previousParams[0]:
self.propMgr.numberOfBasePairsSpinBox.setValue(
new_numberOfBasePairs)
self.previousParams = self.propMgr.getParameters()
def editStructure(self, struct=None):
EditCommand.editStructure(self, struct)
if self.hasValidStructure():
self._updatePropMgrParams()
#Store the previous parameters. Important to set it after you
#set duplexRise and basesPerTurn attrs in the propMgr.
#self.previousParams is used in self._previewStructure and
#self._finalizeStructure to check if self.struct changed.
self.previousParams = self._gatherParameters()
#For Rattlesnake, we do not support resizing of PAM5 model.
#So don't append the exprs handles to the handle list (and thus
#don't draw those handles. See self.model_changed()
isStructResizable, why_not = self.hasResizableStructure()
if not isStructResizable:
self.handles = []
else:
self._updateHandleList()
self.updateHandlePositions()
def _updatePropMgrParams(self):
"""
Subclasses may override this method.
Update some property manager parameters with the parameters of
self.struct (which is being edited)
@see: self.editStructure()
"""
#Format in which params need to be provided to the Property manager
#(i.e. in propMgr.setParameters():
#numberOfBasePairs,
#dnaForm,
#dnaModel,
#basesPerTurn,
#duplexRise,
#endPoint1,
#endPoint2
basesPerTurn, duplexRise = self.struct.getProps()
endPoint1, endPoint2 = self.struct.getAxisEndPoints()
numberOfBasePairs = self.struct.getNumberOfBasePairs()
color = self.struct.getColor()
params_for_propMgr = (numberOfBasePairs, None, None, basesPerTurn,
duplexRise, endPoint1, endPoint2, color)
#TODO 2008-03-25: better to get all parameters from self.struct and
#set it in propMgr? This will mostly work except that reverse is
#not true. i.e. we can not specify same set of params for
#self.struct.setProps ...because endPoint1 and endPoint2 are derived.
#by the structure when needed. Commenting out following line of code
#UPDATE 2008-05-06 Fixes a bug due to which the parameters in propMGr
#of DnaSegment_EditCommand are not same as the original structure
#(e.g. bases per turn and duplexrise)
self.propMgr.setParameters(params_for_propMgr)
def keep_empty_group(self, group):
"""
Returns True if the empty group should not be automatically deleted.
otherwise returns False. The default implementation always returns
False. Subclasses should override this method if it needs to keep the
empty group for some reasons. Note that this method will only get called
when a group has a class constant autdelete_when_empty set to True.
(and as of 2008-03-06, it is proposed that dna_updater calls this method
when needed.
@see: Command.keep_empty_group() which is overridden here.
@see: BreakStrands_Command.keep_empty_group
@see: Group.autodelete_when_empty.. a class constant used by the
dna_updater (the dna updater then decides whether to call this
method to see which empty groups need to be deleted)
"""
bool_keep = EditCommand.keep_empty_group(self, group)
if not bool_keep:
if self.hasValidStructure():
if group is self.struct:
bool_keep = True
elif group is self.struct.parent_node_of_class(
self.assy.DnaGroup):
bool_keep = True
#If this command doesn't have a valid structure, as a fall back,
#lets instruct it to keep ALL the DnaGroup objects even when empty
#Reason? ..see explanation in BreakStrands_Command.keep_empty_group
elif isinstance(group, self.assy.DnaGroup):
bool_keep = True
return bool_keep
def hasResizableStructure(self):
"""
For Rattlesnake release, we dont support segment resizing for PAM5
models. If the structure is not resizable, the handles won't be drawn
@see:self.model_changed()
@see:DnaSegment_PropertyManager.model_changed()
@see: self.editStructure()
@see: DnaSegment.is_PAM3_DnaSegment()
"""
#Note: This method fixes bugs similar to bug 2812 but the changes
#didn't made it to Rattlesnake rc2 -- Ninad 2008-04-16
isResizable = True
why_not = ''
if not self.hasValidStructure():
isResizable = False
why_not = 'It is invalid.'
return isResizable, why_not
isResizable = self.struct.is_PAM3_DnaSegment()
if not isResizable:
why_not = 'It needs to be converted to PAM3 model'
return isResizable, why_not
endAtom1, endAtom2 = self.struct.getAxisEndAtoms()
if endAtom1 is None or endAtom2 is None:
isResizable = False
why_not = "Unable to determine one or both end atoms of the segment"
return isResizable, why_not
if endAtom1 is endAtom2:
isResizable = False
why_not = "Resizing a segment with single atom is unsupported"
return isResizable, why_not
return isResizable, why_not
def hasValidStructure(self):
"""
Tells the caller if this edit command has a valid structure.
Overrides EditCommand.hasValidStructure()
"""
#(By Bruce 2008-02-13)
isValid = EditCommand.hasValidStructure(self)
if not isValid:
return isValid
# would like to check here whether it's empty of axis chunks;
# instead, this will do for now (probably too slow, though):
p1, p2 = self.struct.getAxisEndPoints()
return (p1 is not None)
def _getStructureType(self):
"""
Subclasses override this method to define their own structure type.
Returns the type of the structure this editCommand supports.
This is used in isinstance test.
@see: EditCommand._getStructureType() (overridden here)
"""
return self.win.assy.DnaSegment
def _updateHandleList(self):
"""
Updates the list of handles (self.handles)
@see: self.editStructure
@see: DnaSegment_GraphicsMode._drawHandles()
"""
# note: if handlePoint1 and/or handlePoint2 can change more often than this
# runs, we'll need to rerun the two assignments above whenever they
# change and before the handle is drawn. An easy way would be to rerun
# these assignments in the draw method of our GM. [bruce 080128]
self.handles = [] # guess, but seems like a good idea [bruce 080128]
self.handles.append(self.leftHandle)
self.handles.append(self.rightHandle)
if DEBUG_ROTATION_HANDLES:
self.handles.append(self.rotationHandle1)
self.handles.append(self.rotationHandle2)
def updateHandlePositions(self):
"""
Update handle positions and also update the resize handle radii and
their 'stopper' lengths.
@see: self._update_resizeHandle_radius()
@see: self._update_resizeHandle_stopper_length()
@see: DnaSegment_GraphicsMode._drawHandles()
"""
if len(self.handles) == 0:
#No handles are appended to self.handles list.
#@See self.model_changed() and self._updateHandleList()
return
#TODO: Call this method less often by implementing model_changed
#see bug 2729 for a planned optimization
self.cylinderWidth = CYLINDER_WIDTH_DEFAULT_VALUE
self.cylinderWidth2 = CYLINDER_WIDTH_DEFAULT_VALUE
self._update_resizeHandle_radius()
handlePoint1, handlePoint2 = self.struct.getAxisEndPoints()
if handlePoint1 is not None and handlePoint2 is not None:
# (that condition is bugfix for deleted axis segment, bruce 080213)
self.handlePoint1, self.handlePoint2 = handlePoint1, handlePoint2
#Update the 'stopper' length where the resize handle being dragged
#should stop. See self._update_resizeHandle_stopper_length()
#for more details
self._update_resizeHandle_stopper_length()
if DEBUG_ROTATION_HANDLES:
self.rotation_distance1 = CYLINDER_WIDTH_DEFAULT_VALUE
self.rotation_distance2 = CYLINDER_WIDTH_DEFAULT_VALUE
#Following computes the base points for rotation handles.
#to be revised -- Ninad 2008-02-13
unitVectorAlongAxis = norm(self.handlePoint1 -
self.handlePoint2)
v = cross(self.glpane.lineOfSight, unitVectorAlongAxis)
self.rotationHandleBasePoint1 = self.handlePoint1 + norm(
v) * 4.0
self.rotationHandleBasePoint2 = self.handlePoint2 + norm(
v) * 4.0
def _update_resizeHandle_radius(self):
"""
Finds out the sphere radius to use for the resize handles, based on
atom /chunk or glpane display (whichever decides the display of the end
atoms.
@see: self.updateHandlePositions()
@see: B{Atom.drawing_radius()}
"""
atm1, atm2 = self.struct.getAxisEndAtoms()
if atm1 is not None:
self.handleSphereRadius1 = max(1.25 * atm1.drawing_radius(),
1.25 * HANDLE_RADIUS_DEFAULT_VALUE)
if atm2 is not None:
self.handleSphereRadius2 = max(1.25 * atm2.drawing_radius(),
1.25 * HANDLE_RADIUS_DEFAULT_VALUE)
def _update_resizeHandle_stopper_length(self):
"""
Update the limiting length at which the resize handle being dragged
should 'stop' without proceeding further in the drag direction.
The segment resize handle stops when you are dragging it towards the
other resizeend and the distance between the two ends reaches two
duplexes.
The self._resizeHandle_stopper_length computed in this method is
used as a lower limit of the 'range' option provided in declaration
of resize handle objects (see class definition for the details)
@see: self.updateHandlePositions()
"""
total_length = vlen(self.handlePoint1 - self.handlePoint2)
duplexRise = self.struct.getDuplexRise()
#Length of the duplex for 2 base pairs
two_bases_length = getDuplexLength('B-DNA', 2, duplexRise=duplexRise)
self._resizeHandle_stopper_length = -total_length + two_bases_length
def _createPropMgrObject(self):
"""
Creates a property manager object (that defines UI things) for this
editCommand.
"""
assert not self.propMgr
propMgr = self.win.createDnaSegmentPropMgr_if_needed(self)
return propMgr
def _gatherParameters(self):
"""
Return the parameters from the property manager UI.
@return: All the parameters (get those from the property manager):
- numberOfBases
- dnaForm
- basesPerTurn
- endPoint1
- endPoint2
@rtype: tuple
"""
return self.propMgr.getParameters()
def _createStructure(self):
"""
Creates and returns the structure (in this case a L{Group} object that
contains the DNA strand and axis chunks.
@return : group containing that contains the DNA strand and axis chunks.
@rtype: L{Group}
@note: This needs to return a DNA object once that model is implemented
"""
params = self._gatherParameters()
# No error checking in build_struct, do all your error
# checking in gather_parameters
number_of_basePairs_from_struct,\
numberOfBases, \
dnaForm, \
dnaModel, \
basesPerTurn, \
duplexRise, \
endPoint1, \
endPoint2, \
color_junk = params
#Note: color_junk is not used. Ideally it should do struct.setColor(color)
#but the color combobox in the PM directly sets the color of the
#structure to the specified one when the current index in the combobx
#changes
#If user enters the number of basepairs and hits preview i.e. endPoint1
#and endPoint2 are not entered by the user and thus have default value
#of V(0, 0, 0), then enter the endPoint1 as V(0, 0, 0) and compute
#endPoint2 using the duplex length.
#Do not use '==' equality check on vectors! its a bug. Use same_vals
# or Veq instead.
if Veq(endPoint1, endPoint2) and Veq(endPoint1, V(0, 0, 0)):
endPoint2 = endPoint1 + \
self.win.glpane.right*getDuplexLength('B-DNA',
numberOfBases)
if numberOfBases < 1:
msg = redmsg("Cannot preview/insert a DNA duplex with 0 bases.")
self.propMgr.updateMessage(msg)
self.dna = None # Fixes bug 2530. Mark 2007-09-02
return None
if dnaForm == 'B-DNA':
if dnaModel == 'PAM3':
dna = B_Dna_PAM3()
elif dnaModel == 'PAM5':
dna = B_Dna_PAM5()
else:
print "bug: unknown dnaModel type: ", dnaModel
else:
raise PluginBug("Unsupported DNA Form: " + dnaForm)
self.dna = dna # needed for done msg
# self.name needed for done message
if self.create_name_from_prefix:
# create a new name
name = self.name = gensym(self.prefix,
self.win.assy) # (in _build_struct)
self._gensym_data_for_reusing_name = (self.prefix, name)
else:
# use externally created name
self._gensym_data_for_reusing_name = None
# (can't reuse name in this case -- not sure what prefix it was
# made with)
name = self.name
# Create the model tree group node.
# Make sure that the 'topnode' of this part is a Group (under which the
# DNa group will be placed), if the topnode is not a group, make it a
# a 'Group' (applicable to Clipboard parts).See part.py
# --Part.ensure_toplevel_group method. This is an important line
# and it fixes bug 2585
self.win.assy.part.ensure_toplevel_group()
dnaSegment = DnaSegment(self.name,
self.win.assy,
self.win.assy.part.topnode,
editCommand=self)
try:
# Make the DNA duplex. <dnaGroup> will contain three chunks:
# - Strand1
# - Strand2
# - Axis
dna.make(dnaSegment, numberOfBases, basesPerTurn, duplexRise,
endPoint1, endPoint2)
#set some properties such as duplexRise and number of bases per turn
#This information will be stored on the DnaSegment object so that
#it can be retrieved while editing this object.
#This works with or without dna_updater. Now the question is
#should these props be assigned to the DnaSegment in
#dnaDuplex.make() itself ? This needs to be answered while modifying
#make() method to fit in the dna data model. --Ninad 2008-03-05
#WARNING 2008-03-05: Since self._modifyStructure calls
#self._createStructure()
#If in the near future, we actually permit modifying a
#structure (such as dna) without actually recreating the whole
#structre, then the following properties must be set in
#self._modifyStructure as well. Needs more thought.
props = (duplexRise, basesPerTurn)
dnaSegment.setProps(props)
return dnaSegment
except (PluginBug, UserError):
# Why do we need UserError here? Mark 2007-08-28
dnaSegment.kill()
raise PluginBug(
"Internal error while trying to create DNA duplex.")
def _modifyStructure(self, params):
"""
Modify the structure based on the parameters specified.
Overrides EditCommand._modifystructure. This method removes the old
structure and creates a new one using self._createStructure. This
was needed for the structures like this (Dna, Nanotube etc) . .
See more comments in the method.
"""
assert self.struct
self.dna = B_Dna_PAM3()
number_of_basePairs_from_struct,\
numberOfBases, \
dnaForm, \
dnaModel, \
basesPerTurn, \
duplexRise, \
endPoint1, \
endPoint2 , \
color = params
#Delete unused parameters.
del endPoint1
del endPoint2
del number_of_basePairs_from_struct
numberOfBasePairsToAddOrRemove = self._determine_numberOfBasePairs_to_change(
)
ladderEndAxisAtom = self.get_axisEndAtom_at_resize_end()
if numberOfBasePairsToAddOrRemove != 0:
resizeEnd_final_position = self._get_resizeEnd_final_position(
ladderEndAxisAtom, abs(numberOfBasePairsToAddOrRemove),
duplexRise)
self.dna.modify(self.struct, ladderEndAxisAtom,
numberOfBasePairsToAddOrRemove, basesPerTurn,
duplexRise, ladderEndAxisAtom.posn(),
resizeEnd_final_position)
#Find new end points of structure parameters after modification
#and set these values in the propMgr.
new_end1, new_end2 = self.struct.getAxisEndPoints()
params_to_set_in_propMgr = (numberOfBases, dnaForm, dnaModel,
basesPerTurn, duplexRise, new_end1,
new_end2, color)
#TODO: Need to set these params in the PM
#and then self.previousParams = params_to_set_in_propMgr
self.previousParams = params
return
def _get_resizeEnd_final_position(self, ladderEndAxisAtom, numberOfBases,
duplexRise):
final_position = None
if self.grabbedHandle:
final_position = self.grabbedHandle.currentPosition
else:
other_axisEndAtom = self.struct.getOtherAxisEndAtom(
ladderEndAxisAtom)
axis_vector = ladderEndAxisAtom.posn() - other_axisEndAtom.posn()
segment_length_to_add = getDuplexLength('B-DNA',
numberOfBases,
duplexRise=duplexRise)
final_position = ladderEndAxisAtom.posn(
) + norm(axis_vector) * segment_length_to_add
return final_position
def getStructureName(self):
"""
Returns the name string of self.struct if there is a valid structure.
Otherwise returns None. This information is used by the name edit field
of this command's PM when we call self.propMgr.show()
@see: DnaSegment_PropertyManager.show()
@see: self.setStructureName
"""
if self.hasValidStructure():
return self.struct.name
else:
return None
def setStructureName(self, name):
"""
Sets the name of self.struct to param <name> (if there is a valid
structure.
The PM of this command callss this method while closing itself
@param name: name of the structure to be set.
@type name: string
@see: DnaSegment_PropertyManager.close()
@see: self.getStructureName()
"""
#@BUG: We call this method in self.propMgr.close(). But propMgr.close()
#is called even when the command is 'cancelled'. That means the
#structure will get changed even when user hits cancel button or
#exits the command by clicking on empty space.
#This should really be done in self._finalizeStructure but that
#method doesn't get called when you click on empty space to exit
#the command. See DnaSegment_GraphicsMode.leftUp for a detailed
#comment.
if self.hasValidStructure():
self.struct.name = name
def getCursorText(self):
"""
This is used as a callback method in DnaLine mode
@see: DnaLineMode.setParams, DnaLineMode_GM.Draw
"""
#@TODO: Refactor this. Similar code exists in
#DnaStrand_EditCommand.getCursorText() -- Ninad 2008-04-12
if self.grabbedHandle is None:
return
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
duplexRise = self.struct.getDuplexRise()
#############
raw_numberOfBasePairsToAddOrRemove = self._determine_numberOfBasePairs_to_change(
)
#Following fixes bugs like 2904 and 2906
#Note that we are using numberOfBasePairsToAddOrRemove in self._modifyStructure()
#if self._determine_numberOfBasePairs_to_change() returns the number of basepairs
#to add, it returns 1 more than the actual number of basepairs. Because
#while creating the dna, it removes the first base pair of the newly created
#dna. So, for cursor text and for PM spinbox, we should make adjustments to the
#raw_numberOfBasePairsToAddOrRemove so that it reflects the correct value
#in the spinbox and in the PM
if raw_numberOfBasePairsToAddOrRemove > 1:
numberOfBasePairsToAddOrRemove = raw_numberOfBasePairsToAddOrRemove - 1
else:
numberOfBasePairsToAddOrRemove = raw_numberOfBasePairsToAddOrRemove
##############
current_numberOfBasePairs = self.struct.getNumberOfBasePairs()
numberOfBasePairs = current_numberOfBasePairs + numberOfBasePairsToAddOrRemove
#@TODO: The following updates the PM as the cursor moves.
#Need to rename this method so that you that it also does more things
#than just to return a textString -- Ninad 2007-12-20
self.propMgr.numberOfBasePairsSpinBox.setValue(numberOfBasePairs)
#Note: for Rattlesnake rc2, the text color is green when bases are added
#, red when subtracted black when no change. But this implementation is
#changed based on Mark's user experience. The text is now always shown
#in black color. -- Ninad 2008-04-17
textColor = black
text = ""
if not env.prefs[
dnaSegmentEditCommand_showCursorTextCheckBox_prefs_key]:
return '', black
#@@TODO: refactor.
#this duplex length canculation fixes bug 2906
duplexLength = getDuplexLength('B-DNA',
numberOfBasePairs,
duplexRise=duplexRise)
#Cursor text strings --
duplexLengthString = str(round(duplexLength, 3))
numberOfBasePairsString = self._getCursorText_numberOfBasePairs(
numberOfBasePairs)
duplexLengthString = self._getCursorText_length(duplexLength)
changedBasePairsString = self._getCursorText_changedBasePairs(
numberOfBasePairs)
#Add commas (to be refactored)
commaString = ", "
text = numberOfBasePairsString
if text and changedBasePairsString:
text += " " # commaString not needed here. Mark 2008-07-03
text += changedBasePairsString
if text and duplexLengthString:
text += commaString
text += duplexLengthString
return (text, textColor)
def _getCursorText_numberOfBasePairs(self, numberOfBasePairs):
"""
Return the cursor textstring that gives information about the number
of basepairs if the corresponding prefs_key returns True.
"""
numberOfBasePairsString = ''
if env.prefs[
dnaSegmentEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key]:
numberOfBasePairsString = "%db" % numberOfBasePairs
return numberOfBasePairsString
def _getCursorText_length(self, duplexLength):
"""
"""
duplexLengthString = ''
if env.prefs[
dnaSegmentEditCommand_cursorTextCheckBox_length_prefs_key]:
lengthUnitString = 'A'
#change the unit of length to nanometers if the length is > 10A
#fixes part of bug 2856
if duplexLength > 10.0:
lengthUnitString = 'nm'
duplexLength = duplexLength * 0.1
duplexLengthString = "%5.3f%s" % (duplexLength, lengthUnitString)
return duplexLengthString
def _getCursorText_changedBasePairs(self, numberOfBasePairs):
"""
"""
changedBasePairsString = ''
if env.prefs[
dnaSegmentEditCommand_cursorTextCheckBox_changedBasePairs_prefs_key]:
original_numberOfBasePairs = self.struct.getNumberOfBasePairs()
changed_basePairs = numberOfBasePairs - original_numberOfBasePairs
if changed_basePairs > 0:
changedBasePairsString = "(" + "+" + str(
changed_basePairs) + ")"
else:
changedBasePairsString = "(" + str(changed_basePairs) + ")"
return changedBasePairsString
def getDnaRibbonParams(self):
"""
Returns parameters for drawing the dna ribbon.
If the dna rubberband line should NOT be drawn (example when you are
removing basepairs from the segment
So the caller should check if the method return value is not None.
@see: DnaSegment_GraphicsMode._draw_handles()
"""
if self.grabbedHandle is None:
return None
if self.grabbedHandle.origin is None:
return None
direction_of_drag = norm(self.grabbedHandle.currentPosition - \
self.grabbedHandle.origin)
#If the segment is being shortened (determined by checking the
#direction of drag) , no need to draw the rubberband line.
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
return None
basesPerTurn = self.struct.getBasesPerTurn()
duplexRise = self.struct.getDuplexRise()
ladderEndAxisAtom = self.get_axisEndAtom_at_resize_end()
ladder = ladderEndAxisAtom.molecule.ladder
endBaseAtomList = ladder.get_endBaseAtoms_containing_atom(
ladderEndAxisAtom)
ribbon1_start_point = None
ribbon2_start_point = None
ribbon1_direction = None
ribbon2_direction = None
ribbon1Color = applegreen
ribbon2Color = applegreen
if endBaseAtomList and len(endBaseAtomList) > 2:
strand_atom1 = endBaseAtomList[0]
strand_atom2 = endBaseAtomList[2]
if strand_atom1:
ribbon1_start_point = strand_atom1.posn()
for bond_direction, neighbor in strand_atom1.bond_directions_to_neighbors(
):
if neighbor and neighbor.is_singlet():
ribbon1_direction = bond_direction
break
ribbon1Color = strand_atom1.molecule.color
if not ribbon1Color:
ribbon1Color = strand_atom1.element.color
if strand_atom2:
ribbon2_start_point = strand_atom2.posn()
for bond_direction, neighbor in strand_atom2.bond_directions_to_neighbors(
):
if neighbor and neighbor.is_singlet():
ribbon2_direction = bond_direction
break
ribbon2Color = strand_atom2.molecule.color
if not ribbon2Color:
ribbon2Color = strand_atom2.element.color
return (self.grabbedHandle.origin, self.grabbedHandle.currentPosition,
basesPerTurn, duplexRise, ribbon1_start_point,
ribbon2_start_point, ribbon1_direction, ribbon2_direction,
ribbon1Color, ribbon2Color)
def modifyStructure(self):
"""
Called when a resize handle is dragged to change the length of the
segment. (Called upon leftUp) . This method assigns the new parameters
for the segment after it is resized and calls
preview_or_finalize_structure which does the rest of the job.
Note that Client should call this public method and should never call
the private method self._modifyStructure. self._modifyStructure is
called only by self.preview_or_finalize_structure
@see: B{DnaSegment_ResizeHandle.on_release} (the caller)
@see: B{SelectChunks_GraphicsMode.leftUp} (which calls the
the relevent method in DragHandler API. )
@see: B{exprs.DraggableHandle_AlongLine}, B{exprs.DragBehavior}
@see: B{self.preview_or_finalize_structure }
@see: B{self._modifyStructure}
As of 2008-02-01 it recreates the structure
@see: a note in self._createStructure() about use of dnaSegment.setProps
"""
#TODO: need to cleanup this and may be use use something like
#self.previousParams = params in the end -- 2008-03-24 (midnight)
if self.grabbedHandle is None:
return
##self.propMgr.setParameters(params_to_set_in_propMgr)
#TODO: Important note: How does NE1 know that structure is modified?
#Because number of base pairs parameter in the PropMgr changes as you
#drag the handle . This is done in self.getCursorText() ... not the
#right place to do it. OR that method needs to be renamed to reflect
#this as suggested in that method -- Ninad 2008-03-25
self.preview_or_finalize_structure(previewing=True)
##self.previousParams = params_to_set_in_propMgr
self.glpane.gl_update()
def get_axisEndAtom_at_resize_end(self):
ladderEndAxisAtom = None
if self.grabbedHandle is not None:
ladderEndAxisAtom = self.struct.getAxisEndAtomAtPosition(
self.grabbedHandle.origin)
else:
endAtom1, endAtom2 = self.struct.getAxisEndAtoms()
ladderEndAxisAtom = endAtom2
return ladderEndAxisAtom
def _determine_numberOfBasePairs_to_change(self):
"""
"""
duplexRise = self.struct.getDuplexRise()
numberOfBasesToAddOrRemove = 0
#Following helps fixing bugs like 2904 and 2906 see also self.getCursorText()
#and TODO items in that method. Also note that the grabbed handle case
#is similar to the one in MultipleDnaSegmentResize_EditCommand.
#needs refactoring and overall cleanup.
if self.grabbedHandle is not None:
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
changedLength = vlen(currentPosition - self.grabbedHandle.origin)
direction_of_drag = norm(self.grabbedHandle.currentPosition - \
self.grabbedHandle.origin)
#Even when the direction of drag is negative (i.e. the basepairs being
#removed), make sure not to remove base pairs for very small movement
#of the grabbed handle
if changedLength < 0.2 * duplexRise:
return 0
#This check quickly determines if the grabbed handle moved by a distance
#more than the duplexRise and avoids further computations
#This condition is applicable only when the direction of drag is
#positive..i.e. bases bing added to the segment.
if changedLength < duplexRise and \
dot(self.grabbedHandle.direction, direction_of_drag) > 0:
return 0
#If the segment is being shortened (determined by checking the
#direction of drag)
numberOfBasesToAddOrRemove = \
getNumberOfBasePairsFromDuplexLength(
'B-DNA',
changedLength,
duplexRise = duplexRise)
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
numberOfBasesToAddOrRemove = -numberOfBasesToAddOrRemove
if numberOfBasesToAddOrRemove > 0:
#dna.modify will remove the first base pair it creates
#(that basepair will only be used for proper alignment of the
#duplex with the existing structure) So we need to compensate for
#this basepair by adding 1 to the new number of base pairs.
#UPDATE 2008-05-14: The following commented out code
#i.e. "##numberOfBasesToAddOrRemove += 1" is not required in this
#class , because the way we compute the number of base pairs to
#be added is different than than how its done at the moment in the
#superclass. In this method, we compute bases to be added from
#the resize end and that computation INCLUDES the resize end.
#so the number that it returns is already one more than the actual
#bases to be added. so commenting out the following line
# -- Ninad 2008-05-14
##numberOfBasesToAddOrRemove += 1
pass
else:
#The Property manager will be showing the current number
#of base pairs (w. May be we can use that number directly here?
#The following is safer to do so lets just recompute the
#number of base pairs. (if it turns out to be slow, we will consider
#using the already computed calue from the property manager
new_numberOfBasePairs = self.propMgr.numberOfBasePairsSpinBox.value(
)
endPoint1, endPoint2 = self.struct.getAxisEndPoints()
if endPoint1 is None or endPoint2 is None:
return 0
original_duplex_length = vlen(endPoint1 - endPoint2)
original_numberOfBasePairs = self.struct.getNumberOfBasePairs()
numberOfBasesToAddOrRemove = new_numberOfBasePairs - original_numberOfBasePairs
if numberOfBasesToAddOrRemove > 0:
#dna.modify will remove the first base pair it creates
#(that basepair will only be used for proper alignment of the
#duplex with the existing structure) So we need to compensate for
#this basepair by adding 1 to the new number of base pairs.
numberOfBasesToAddOrRemove += 1
return numberOfBasesToAddOrRemove
def makeMenus(self):
"""
Create context menu for this command. (Build Dna mode)
"""
if not hasattr(self, 'graphicsMode'):
return
selobj = self.glpane.selobj
if selobj is None:
return
self.Menu_spec = []
highlightedChunk = None
if isinstance(selobj, Chunk):
highlightedChunk = selobj
if isinstance(selobj, Atom):
highlightedChunk = selobj.molecule
elif isinstance(selobj, Bond):
chunk1 = selobj.atom1.molecule
chunk2 = selobj.atom2.molecule
if chunk1 is chunk2 and chunk1 is not None:
highlightedChunk = chunk1
if highlightedChunk is None:
return
if self.hasValidStructure():
dnaGroup = self.struct.parent_node_of_class(self.assy.DnaGroup)
if dnaGroup is None:
return
#following should be self.struct.getDnaGroup or self.struct.getDnaGroup
#need to formalize method name and then make change.
if not dnaGroup is highlightedChunk.parent_node_of_class(
self.assy.DnaGroup):
item = ("Edit unavailable: Member of a different DnaGroup",
noop, 'disabled')
self.Menu_spec.append(item)
return
highlightedChunk.make_glpane_context_menu_items(self.Menu_spec,
command=self)
class _cmd_MakeRect_BG(Highlightable):
"""Background event bindings for dragging out new Rects.
(Not involved with selecting/moving/editing/resizing rects after they're made,
even if that happens immediately to a rect this code makes from a single drag.)
"""
# args [needed for sharing state with something]
world = Option(World)
#e something to share state with a control panel in the PM - unless we just use prefs for that
# The drag event handlers modify the following state and/or derived objects (some documented with their defs):
# self.rubber_rect = None or a newly made Rect we're dragging out right now
# (implemented as a rubberband-object drawable -- NOT a model object -- since it has formulae to our state, not its own state)
#
# nim: self.newnode = None or a Model Object version of the Rect we're dragging out now, or last dragged out...
# in general this may be redundant with "the selection", if dragging out a rect selects it, or shift-dragging it adds it to sel...
# note, which of these are change-tracked? the ones used in drawing. that means all of them i guess.
startpoint = State(Point,
None,
doc="mousedown position; one corner of the rect"
) #e (or its center, for variants of this cmd)
curpoint = State(
Point,
None,
doc="last mouse position used for the other corner of the rect")
making_a_rect_now = State(
bool,
False,
doc="whether we're making a rect right now, using the current drag")
# formulae
whj = curpoint - startpoint # contains dims of current rect; only valid while we're making one, or after it's done before next press
w = whj[
0] ###k what if negative?? evidently we make a neg-width Rect and nothing complains and it draws properly... ###REVIEW
h = whj[1] # ditto
color = purple # for now -- will be a pref or PM control for the color to use for new rects
rubber_rect = Instance(
If(making_a_rect_now, Translate(Rect(w, h, color), startpoint)))
# this Instance is needed, at least by Highlightable
# appearance -- note, for superclass Highlightable, this is plain, not delegate, and must be an Instance.
# This means it's not good to subclass Highlightable rather than delegating to it. (Especially in example code!) ###FIX
## delegate = _self.rubber_rect
plain = _self.rubber_rect
# code for event handlers during the drag.
def on_press(self):
self.startpoint = self.current_event_mousepoint()
self.making_a_rect_now = False #k probably not needed
# don't make until we drag!
self.curpoint = None #k probably not needed, but might help to catch bugs where whj is used when it shouldn't be
#e change cursor, someday; sooner, change state to name the desired cursor, and display that cursorname in the PM
return
def on_drag(self):
self.curpoint = self.current_event_mousepoint(plane=self.startpoint)
self.making_a_rect_now = True
return
def on_release(self):
##e decide whether to really make one... here, assume we do, as long as we started one:
if self.making_a_rect_now:
node_expr = DraggableObject(
StatefulRect(self.rubber_rect)
) #e StatefulMovableRect? StatefulSnapshot(self.rubber_rect)??
###k can we just pass the rubber rect and assume StatefulRect can grab its state from it by taking a snapshot??
###WRONG for DraggableObject to be here, I think -- it's how we display it -- not sure, at least movability might be here...
### the posn is in the rubber_rect since it has Translate... this seems potentially bad/klugy tho...
# older cmts, related: ... also its state needs to include abs posn...
# maybe this means, split DraggableObject into event binding part (for this UI) and Movable part (for abs posn state). #k
self.newnode = self.world.make_and_add(node_expr, type="Rect")
###BUG (understood): type = "Rect" is not affecting sbar_text in DraggableObject. Need to add it in StatefulRect itself.
self.newnode.motion = self.startpoint ###KLUGE
self.making_a_rect_now = False # hide the rubber rect now that the real one is there
else:
print "fyi: click with no drag did nothing" ##e remove after debug
return
pass # end of class _cmd_MakeRect_BG
class polyline3d(
InstanceOrExpr
): # WARNING [070319]: duplicated code, demo_drag.py and demo_draw_on_surface.py [modified a bit]
"""A graphical object with an extendable (or resettable from outside I guess) list of points,
and a kid (end1) (supplied, but optional (leaving it out is ###UNTESTED)) that can serve as a drag handle by default.
(And which also picks up a cmenu from self. (kluge!))
Also some Options, see the code.
"""
# Note [070307]: this class will be superceded by class Polyline in demo_polyline.py,
# and the code that uses it below (eg the add_point call) will be superseded by other code in that file.
#
###BUGS: doesn't set color, depends on luck. end1 is not fully part of it so putting cmenu on it will be hard.
# could use cmenu to set the options.
# end1 might be in MT directly and also be our kid (not necessarily wrong, caller needn't add it to MT).
# when drawing on sphere, long line segs can go inside it and not be seen.
points = State(
list_Expr,
[]) ###k probably wrong way to say the value should be a list
## end1arg = Arg(StubType,None)
## end1 = Instance(eval_Expr( call_Expr(end1arg.copy,)( color = green) ))###HACK - works except color is ignored and orig obscures copy
end1 = Arg(
StubType,
None,
doc=
"KLUGE arg: optional externally supplied drag-handle, also is given our cmenu by direct mod"
)
closed = Option(bool, False, doc="whether to draw it as a closed loop")
_closed_state = State(bool, closed) ####KLUGE, needs OptionState
relative = Option(
bool,
True,
doc=
"whether to position it relative to the center of self.end1 (if it has one)"
)
def _init_instance(self):
end1 = self.end1
if end1:
end1.cmenu_maker = self
def _C__use_relative(self):
"compute self._use_relative (whether to use the relative option)"
if self.relative:
try:
center = self.end1.center
return True
except:
#e print?
return False
return False
def _C_origin(self): #070307 renamed this to origin from center
if self._use_relative:
return self.end1.center # this can vary!
return ORIGIN
## center = _self.origin #k might not be needed -- guessing it's not, 070307
def add_point(self, pos):
"add a point at the given 3d position"
pos = pos - self.origin
self.points = self.points + [
pos
] ### INEFFICIENT, but need to use '+' for now to make sure it's change-tracked
def draw(self):
###k is it wrong to draw both a kid and some opengl stuff?? not really, just suboptimal if opengl stuff takes long (re rendering.py)
self.drawkid(self.end1) # end1 node
if self._closed_state:
glBegin(GL_LINE_LOOP
) # note: nothing sets color. see drawline for how.
# in practice it's thin and dark gray - just by luck.
else:
glBegin(GL_LINE_STRIP)
if self._use_relative:
# general case - but also include origin (end1.center) as first point!
origin = self.origin
glVertex3fv(origin)
for pos in self.points:
glVertex3fv(pos + origin)
else:
# optim - but not equivalent since don't include origin!
for pos in self.points:
glVertex3fv(pos)
glEnd()
#e option to also draw dots on the points [useful if we're made differently, one click per point; and they might be draggable #e]
return
def make_selobj_cmenu_items(self, menu_spec, highlightable):
"""Add self-specific context menu items to <menu_spec> list when self is the selobj (or its delegate(?)... ###doc better).
Only works if this obj (self) gets passed to Highlightable's cmenu_maker option (which DraggableObject(self) will do).
[For more examples, see this method as implemented in chem.py, jigs*.py in cad/src.]
"""
menu_spec.extend([
(
"polyline3d", noop, 'disabled'
), # or 'checked' or 'unchecked'; item = None for separator; submenu possible
])
pass # end of class polyline3d
class Polyline(
SketchEntity
): #e rename -- 2D or general? [see also class polyline3d in demo_draw_on_surface.py]
#e assume SketchEntity super handles whatever relativity is needed? (even add_point coord transform??)
# more comments on relativity at end of file
# modified from: class polyline(InstanceOrExpr) in demo_drag.py, and some code therein that uses it (eg the add_point call)
"""A graphical model object with an extendable (or resettable from outside I guess) list of points.
(Q: Does it also consider that some of them are draggable control points and some are not??
Guess: not this class -- some other one might. This one considers all points to be equivalent independent state.)
Also might have some Options, see the code -- or those might belong in wrapper objects for various display/edit modes.
"""
###BUGS: doesn't set color, depends on luck.
# could use cmenu to set the options.
# end1 might be in MT directly and also be our kid (not necessarily wrong, caller needn't add it to MT).
# when drawing on sphere, long line segs can go inside it and not be seen.
points = State(
list_Expr,
[]) ###k probably wrong way to say the value should be a list
## end1arg = Arg(StubType,None)
## end1 = Instance(eval_Expr( call_Expr(end1arg.copy,)( color = green) ))###HACK - works except color is ignored and orig obscures copy
## end1 = Arg(StubType, None, doc = "KLUGE arg: optional externally supplied drag-handle, also is given our cmenu by direct mod")
# these style settings ought to be State attrs of self, changeable by cmenu and/or PM, as well as by construction (less important).
closed = Option(bool, False, doc="whether to draw it as a closed loop")
_closed_state = State(
bool, closed
) ####KLUGE -- closed and _closed_state should be a single OptionState attr [nim]
linecolor = blue ###KLUGE -- we want it to be a StateOption
###e name this linecolor or color?? even if linecolor, also accept color and use it for default??
# guess: I favor color for use as public option (but might like both to be there) and linecolor for use internally.
linewidth = 2 ###KLUGE -- we want it to be a StateOption
dashed = False ###KLUGE -- we want it to be a StateOption
## relative = Option(bool, True, doc = "whether to position it relative to the center of self.end1 (if it has one)")
## def _init_instance(self):
## end1 = self.end1
## if end1:
## end1.cmenu_maker = self
## def _C__use_relative(self):
## "compute self._use_relative (whether to use the relative option)"
## if self.relative:
## try:
## center = self.end1.center
## return True
## except:
## #e print?
## return False
## return False
def _C_center(self):
#e how do we define the center? center of bbox??
#e is the center of rotation necessarily the same? (guess: yes -- what *else* would center mean, or be needed for?)
# (if so, it ought to approximate the center of a minimal bounding circle -- ie its own bradius not be much larger than needed)
## if self._use_relative:
## return self.end1.center # this can vary!
## return ORIGIN
assert 0 # nim
def _C_origin(
self
): #070307 renamed this to origin from center (in demo_drag.py version); not sure if needed here at all
## if self._use_relative:
## return self.end1.center # this can vary!
return ORIGIN
def add_point(self, pos, replace=False):
"""add a point at the given 3d position pos; if replace is True, it replaces the existing last point.
If pos is None, then no point is added, and the last one is removed if replace is true.
"""
if replace:
self.points = self.points[:-1] #UNTESTED
if pos is not None:
pos = pos - self.origin ##e be more general -- but should be done by superclass or glue code or by calling transform method...
self.points = self.points + [
pos
] ### INEFFICIENT if lots of points, but need to use '+' for now to make sure it's change-tracked
return
def make_selobj_cmenu_items(self, menu_spec, highlightable):
"""Add self-specific context menu items to <menu_spec> list when self is the selobj (or its delegate(?)... ###doc better).
Only works if this obj (self) gets passed to Highlightable's cmenu_maker option (which DraggableObject(self) will do).
[For more examples, see this method as implemented in chem.py, jigs*.py in cad/src.]
"""
menu_spec.extend([
(
"Polyline", noop, 'disabled'
), # or 'checked' or 'unchecked'; item = None for separator; submenu possible
## ("show potential crossovers", self._cmd_show_potential_crossovers), #e disable if none (or all are already shown or real)
##
## ("change length", [
## ("left extend by 1 base", lambda self = self, left = 1, right = 0: self.extend(left, right)),
## ("left shrink by 1 base", lambda self = self, left = -1, right = 0: self.extend(left, right)),
## ("right extend by 1 base", lambda self = self, left = 0, right = 1: self.extend(left, right)),
## ("right shrink by 1 base", lambda self = self, left = 0, right = -1: self.extend(left, right)),
## ("both extend by 1 base", lambda self = self, left = 1, right = 1: self.extend(left, right)),
## ("both shrink by 1 base", lambda self = self, left = -1, right = -1: self.extend(left, right)),
## ] ),
])
pass # end of class Polyline
class DnaSegment_ResizeHandle(DraggableHandle_AlongLine):
"""
Provides a resize handle for editing the length of an existing DnaSegment.
"""
#Handle color will be changed depending on whether the the handle is grabbed
#So this is a 'State variable and its value is used in 'appearance'
#(given as an optional argument to 'Sphere')
handleColor = State(Color, olive)
#The state ref that determines the radius (of the sphere) of this handle.
#See DnaSegment_EditCommand._determine_resize_handle_radius() for more
#details
sphereRadius = Option(StateRef, 1.2)
discRadius = Option(StateRef, 1.2)
discThickness = Option(StateRef, 1.2)
#Stateusbar text. Variable needs to be renamed in superclass.
sbar_text = Option(str,
"Drag the handle to resize the segment",
doc="Statusbar text on mouseover")
#Command object specified as an 'Option' during instantiation of the class
#see DnaSegment_EditCommand class definition.
command = Option(Action, doc='The Command which instantiates this handle')
#Current position of the handle. i.e. it is the position of the handle
#under the mouse. (its differert than the 'orifinal position)
#This variable is used in self.command.graphicsMode to draw a rubberband
#line and also to specify the endPoint2 of the structure while modifying
#it. See DnaSegment_EditCommand.modifyStructure for details.
currentPosition = _self.origin + _self.direction * _self.height_ref.value
#Fixed end of the structure (self.command.struct) ..meaning that end won't
#move while user grabbs and draggs this handle (attached to a the other
#'moving endPoint) . This variable is used to specify endPoint1 of the
#structure while modifyin it. See DnaSegment_EditCommand.modifyStructure
#and self.on_release for details.
fixedEndOfStructure = Option(Point, V(0, 0, 0))
#If this is false, the 'highlightable' object i.e. this handle
#won't be drawn. See DraggableHandle.py for the declararion of
#the delegate(that defines a Highlightable) We define a If_Exprs to check
#whether to draw the highlightable object.
should_draw = State(bool, True)
pt = _self.direction * _self.discThickness
appearance = Overlay(
Sphere(_self.sphereRadius, handleColor, center=ORIGIN),
Cylinder((ORIGIN + pt, ORIGIN - pt),
radius=_self.discRadius,
color=handleColor,
opacity=0.5),
Arrow(color=handleColor,
arrowBasePoint=ORIGIN +
_self.direction * 2.0 * _self.sphereRadius,
tailPoint=ORIGIN,
tailRadius=_self.sphereRadius * 0.3,
tailRadiusLimits=(0.36, 3.0),
scale=_self.command.glpane.scale,
glpane=_self.command.glpane,
scale_to_glpane=True))
HHColor = env.prefs[hoverHighlightingColor_prefs_key]
appearance_highlighted = Option(
Drawable,
Overlay(
Sphere(_self.sphereRadius, HHColor, center=ORIGIN),
Cylinder((ORIGIN + pt, ORIGIN - pt),
radius=_self.discRadius,
color=HHColor),
Arrow(color=HHColor,
arrowBasePoint=ORIGIN +
_self.direction * 2.0 * _self.sphereRadius,
tailPoint=ORIGIN,
tailRadius=_self.sphereRadius * 0.3,
tailRadiusLimits=(0.36, 3.0),
scale=_self.command.glpane.scale,
glpane=_self.command.glpane,
scale_to_glpane=True)))
def on_press(self):
"""
Actions when handle is pressed (grabbed, during leftDown event)
@see: B{SelectChunks.GraphicsMode.leftDown}
@see: B{DnaSegment_EditCommand.grabbedHandle}
@see: B{DnaSegment_GraphicsMode.Draw} (which uses some attributes of
the current grabbed handle of the command.
@see: B{DragHandle_API}
"""
#Change the handle color when handle is grabbed. See declaration of
#self.handleColor in the class definition.
self.handleColor = env.prefs[selectionColor_prefs_key]
#assign 'self' as the curent grabbed handle of the command.
self.command.grabbedHandle = self
def on_drag(self):
"""
Method called while dragging this handle .
@see: B{DragHandle_API}
"""
#Does nothing at the moment.
pass
def on_release(self):
"""
This method gets called during leftUp (when the handle is released)
@see: B{DnaSegment_EditCommand.modifyStructure}
@see: self.on_press
@see: B{SelectChunks.GraphicsMode.leftUp}
@see: B{DragHandle_API}
"""
self.handleColor = olive
if self.command and hasattr(self.command, 'modifyStructure'):
self.command.modifyStructure()
#Clear the grabbed handle attribute (the handle is no longer
#grabbed)
self.command.grabbedHandle = None
def hasValidParamsForDrawing(self):
"""
Returns True if the handles origin and direction are not 'None'.
@see: DnaSesgment_GraphicsMode._draw_handles() where the caller
uses this to decide whether this handle can be drawn without
a problem.
"""
#NOTE: Better to do it in the drawing code of this class?
#But it uses a delegate to draw stuff (see class Highlightable)
#May be we should pass this method to that delegate as an optional
#argument -- Ninad 2008-04-02
#NOTES: See also:
#delegate in class DraggableHandle defined as --
#delegate = If_Exprs(_self.should_draw, Highlightable(....))
if self.origin is None:
self.should_draw = False
else:
self.should_draw = True
return self.should_draw
class Vertex(
ModelObject
): # renamed Node -> Vertex, to avoid confusion (tho it added some too, since localvars not all changed,
# and since the world ought to contain model objs anyway, in general, of which Vertex is only one type, and current implem
# also has its own graphics code)...
# see below about better ways to rename it...
"""It has a position, initializable from arg1 but also settable as state under name pos, and an arb appearance.
Position is relative to whatever coords it's drawn in.
When you drag it, it chooses depth just nearer than hitpoint -- which means if you wiggle it over itself,
it gets nearer and nearer (design flaw). [see comment for possible fix]
"""
# 070223 possible fix to seeing depth of self: during a drag, tell glpane not to draw dragobj into depth or during glselect
# mode... so it finds some other selobj besides dragobj. means it should draw dragobj last i guess... maybe transparent
# so you can see selobj behind it, or diff color when there is a selobj...
###e about what to rename it... Hmm, is it a general "Draggable"? .lookslike arg2 -> .islike or .thing arg1?
# BTW, the highlightability is not yet specified here ###nim; it relates to the fact that we can bind commands to it
# (as opposed to things it contains or is contained in, tho that should be permitted at the same time,
# tho implem requires nested glnames to sometimes ignore inner ones, when those are inactive);
# but we might add it in a wrapper which makes it into a view of it that lets commands be bound to it,
# except that World.draw assumes we draw the actual model objs, not wraps of them - also an issue if env says they
# look different -- so maybe World needs to wrap all it draws with glue to add looks and behavior to it, in fact.
# [update much later 070201: or maybe ModelObject knows about this and asks env whether to override default drawing code.]
# but for now, can we do this here?
pos0 = Arg(Position)
pos = State(
Position, pos0
) ###BUG -- does this work -- is pos0 set in time for this? not sure it's working... 061205 1009p
#e we probably want to combine pos0/pos into one StateArg so it's obvious how they relate,
# and only one gets saved in file, and only one self.attr name is used up and accessible
# the rest of this class is for drawing it and interacting with it.
# Can we move that code into e.g. VertexDrawable or VertexView
# and have Vertex itself just delegate (for sake of draw, lbox, etc) to some rule in the env for getting a Drawable for it,
# probably looking it up in a dynamic memoizing mapping in the env? ####e [070105]
# I think YES.
# - a main difference between a model & view object -- a view obj knows how to draw itself, a model obj asks the env.
# (and the answer is quite different in different envs, e.g. 3d area vs MT. but what if we mix those?)
# related notes:
# - it might want a different delegate for drawing purposes (draw, lbox) and sim purposes (or others).
# - does it also have an attr corresponding to its index/address/id in the model world?
# - and maybe some for relations to other model objs, eg MT-parent, tags, name, etc?
# - and maybe some graphics prefs like color or whatever, even if it's up to the drawing rule whether/how to use these?
# - and for that matter some arbitrary other data (named attrs), as we'll let any model object have?
# simplest thing that could work --
# - make some sort of MemoDict for model-view and put it into the env, even if we kluge how to set it up for now.
# how does demo_MT do it? With a hardcoded helper function using a MemoDict in a simple way -- no involvement of env.
# So see above for copied code from that... ###e
#e so now what we want is for this (in super modelobject) to delegate to a computed viewer from the helper func above
#e but also to have more args that can be used to set the color [do this only in Vertex_new, below]
## color = Option(Color, color)
## pass
## class VertexView(xx): -- SOMETHING LIKE THIS IS THE INTENT ####
#e and then we want this new class to have the hardcoded appearance & behavior which the code below now passes in lookslike arg
lookslike = ArgOrOption(Anything) # OrOption is so it's customizable
###BAD for lookslike to be an attr of the Vertex, at least if this should be a good example of editing a sketch. [070105]
# (a fancy sketch might have custom point types, but they'd have tags or typenames, with rules to control what they look like)
cmenu_maker = State(
Anything, None
) # meant to be set from outside; let's hope None is a legal value [070223 HACK]
## delegate = _self.lookslike #k
delegate = Highlightable(
Translate(lookslike, pos),
## eval_Expr( call_Expr(lookslike.copy,)( color = yellow) ), #####?? weird exc don't know why - reload?
## AssertionError: _this failed to find referent for '_this_Vertex'
on_drag=_self.on_drag, # 070103 kluge experiment, works (eg in _19d)
cmenu_maker=
cmenu_maker #070223 HACK [#e rename cmenu_maker to cmenu_obj as I guessed it was named??]
)
#e actions? or do this in a per-tool wrapper which knows the actions?
# or, do this here and make the actions delegate to the current tool for the current parent? guess: the latter.
##e digr: will we want to rename delegate so it's only for appearance? *is it*? does it sim like this too?
# Guess: it's for everything -- looks, sim qualities, etc -- except what we override or grab from special members.
# [if so, no need to rename, except to clarify, leaving it general.]
#e might need something for how to save it in a file, Undo policy, etc
def on_drag(
self
): # 070103 kluge experiment, copied/modified from on_drag_bg in bigger class below
# Note: this bug reported in BUGS breaks dragging of these nodes; worked around by increasing DZFUZZ:
# 070115 "highlightable-finder can be fooled due to check_target_depth_fudge_factor of 0.0001"
# where i am 070103 447p (one of two places with that comment)
# - sort of sometimes works, but posns are sometimes same as bg, not sure why that DZ would be needed,
# oh i guess the mousepos comes from the gray bg rect not the self unless we drag very slow...
point = self.current_event_mousepoint(
) ### MIGHT BE WRONG COORDS? guess: no
#k guess: will have snap-to-fixed-point bug for generic drag code
newpos = point + DZ * DZFUZZ # used for different things, depending #### DZ needed but might cause trouble too
self.pos = newpos
## print "in-node action set %r.pos = %r" % (self, newpos) # sometimes works
self.KLUGE_gl_update() #k needed?
return
pass # end of class Vertex
class MultipleDnaSegmentResize_EditCommand(DnaSegment_EditCommand):
#Graphics Mode
GraphicsMode_class = MultipleDnaSegmentResize_GraphicsMode
#Property Manager
PM_class = MultipleDnaSegmentResize_PropertyManager
cmdname = 'MULTIPLE_DNA_SEGMENT_RESIZE' # REVIEW: needed? correct?
commandName = 'MULTIPLE_DNA_SEGMENT_RESIZE'
featurename = "Edit Multiple Dna Segments"
from utilities.constants import CL_SUBCOMMAND
command_level = CL_SUBCOMMAND
command_parent = 'BUILD_DNA'
#This command operates on (resizes) multiple DnaSegments at once.
#It does that by looping through the DnaSegments and resizing them
#individually. self.currentStruct is set to the 'current' DnaSegment
#in that loop and then it is used in the resizing code.
#@see: DnaSegmentList class
#@see: self.modifyStructure()
currentStruct = None
handlePoint1 = State(Point, ORIGIN)
handlePoint2 = State(Point, ORIGIN)
#The minimum 'stopper'length used for resize handles
#@see: self._update_resizeHandle_stopper_length for details.
_resizeHandle_stopper_length = State(Width, -100000)
rotationHandleBasePoint1 = State(Point, ORIGIN)
rotationHandleBasePoint2 = State(Point, ORIGIN)
#See self._update_resizeHandle_radius where this gets changed.
#also see DnaSegment_ResizeHandle to see how its implemented.
handleSphereRadius1 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
handleSphereRadius2 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
cylinderWidth = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
cylinderWidth2 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
#@TODO: modify the 'State params for rotation_distance
rotation_distance1 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
rotation_distance2 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
leftHandle = Instance(
DnaSegment_ResizeHandle(
command=_self,
height_ref=call_Expr(ObjAttr_StateRef, _self, 'cylinderWidth'),
origin=handlePoint1,
fixedEndOfStructure=handlePoint2,
direction=norm_Expr(handlePoint1 - handlePoint2),
sphereRadius=handleSphereRadius1,
range=(_resizeHandle_stopper_length, 10000)))
rightHandle = Instance(
DnaSegment_ResizeHandle(
command=_self,
height_ref=call_Expr(ObjAttr_StateRef, _self, 'cylinderWidth2'),
origin=handlePoint2,
fixedEndOfStructure=handlePoint1,
direction=norm_Expr(handlePoint2 - handlePoint1),
sphereRadius=handleSphereRadius2,
range=(_resizeHandle_stopper_length, 10000)))
def _update_previousParams_in_model_changed(self):
"""
Overrides superclass method. Does nothing in this class.
@see: self.model_changed() which calls this method.
"""
pass
def isAddSegmentsToolActive(self):
"""
Returns True if the Add segments tool in the PM, that allows adding
dna segments from the resize segment list, is active.
@see: MultipleDnaSegmentResize_GraphicsMode.chunkLeftUp()
@see: MultipleDnaSegmentResize_GraphicsMode.end_selection_from_GLPane()
@see: self.isRemoveSegmentsToolActive()
@see: self.addSegmentToResizeSegmentList()
"""
if self.propMgr is None:
return False
return self.propMgr.isAddSegmentsToolActive()
def isRemoveSegmentsToolActive(self):
"""
Returns True if the Remove Segments tool in the PM, that allows removing
dna segments from the resize segment list, is active.
@see: MultipleDnaSegmentResize_GraphicsMode.chunkLeftUp()
@see: MultipleDnaSegmentResize_GraphicsMode.end_selection_from_GLPane()
@see: self.isAddSegmentsToolActive()
@see: self.removeSegmentFromResizeSegmentList()
"""
if self.propMgr is None:
return False
return self.propMgr.isRemoveSegmentsToolActive()
def addSegmentToResizeSegmentList(self, segment):
"""
Adds the given segment to the resize segment list
@param segment: The DnaSegment to be added to the resize segment list.
Also does other things such as updating resize handles etc.
@type sement: B{DnaSegment}
@see: self.isAddSegmentsToolActive()
"""
assert isinstance(segment, self.win.assy.DnaSegment)
self.struct.addToStructList(segment)
def removeSegmentFromResizeSegmentList(self, segment):
"""
Removes the given segment from the resize segment list
@param segment: The DnaSegment to be removed from the resize segment
list. Also does other things such as updating resize handles etc.
@type sement: B{DnaSegment}
@see: self.isRemoveSegmentsToolActive()
"""
assert isinstance(segment, self.win.assy.DnaSegment)
self.struct.removeFromStructList(segment)
def setResizeStructList(self, structList):
"""
Replaces the list of segments to be resized with the
given segmentList. Calls the related method of self.struct.
@param structList: New list of segments to be resized.
@type structList: list
@see: DnaSegmentList.setResizeStructList()
"""
if self.hasValidStructure():
self.struct.setStructList(structList)
self.updateHandlePositions()
def getResizeSegmentList(self):
"""
Returns a list of segments to be resized at once.
@see: DnaSegmentList.getStructList()
"""
if self.hasValidStructure():
return self.struct.getStructList()
return ()
def updateResizeSegmentList(self):
"""
Update the list of resize segments (maintained by self.struct)
"""
if self.hasValidStructure():
self.struct.updateStructList()
def editStructure(self, struct=None):
"""
Overrides superclass method. It first creates a B{DnaSegmentList} object
using the provided list (struct argument) The DnaSegmentList object
acts as self.struct.
@param struct: The caller of this method should provide a list of
containing all the structurs that need to be edited (resized) at
once. Caller also needs to make sure that this list contains
objects of class DnaSegment.
@type struct: list
@see: B{DnaSegmentList}
"""
if isinstance(struct, list):
dnaSegmentListObject = DnaSegmentList(self, structList=struct)
_superclass.editStructure(self, struct=dnaSegmentListObject)
def _updatePropMgrParams(self):
"""
Subclasses may override this method.
Update some property manager parameters with the parameters of
self.struct (which is being edited)
@see: self.editStructure()
@TODO: For multiple Dna segment resizing, this method does nothing as
of 2008-05-14. Need to be revised.
"""
#Commented out code as of 2008-05-14 ===========
#endPoint1, endPoint2 = self.struct.getAxisEndPoints()
#params_for_propMgr = (None,
#endPoint1,
#endPoint2)
##TODO 2008-03-25: better to get all parameters from self.struct and
##set it in propMgr? This will mostly work except that reverse is
##not true. i.e. we can not specify same set of params for
##self.struct.setProps ...because endPoint1 and endPoint2 are derived.
##by the structure when needed. Commenting out following line of code
##UPDATE 2008-05-06 Fixes a bug due to which the parameters in propMGr
##of DnaSegment_EditCommand are not same as the original structure
##(e.g. bases per turn and duplexrise)
###self.propMgr.setParameters(params_for_propMgr)
pass
def _update_resizeHandle_radius(self):
"""
Finds out the sphere radius to use for the resize handles, based on
atom /chunk or glpane display (whichever decides the display of the end
atoms. The default value is 1.2.
@see: self.updateHandlePositions()
@see: B{Atom.drawing_radius()}
@TODO: Refactor this. It does essentially same thing as the
superclass method. The problem is due to the use of the global constant
HANDLE_RADIUS_DEFAULT_VALUE which needs to be different (bigger) in this
class. So better to make it a class constant (need similar changes
in several commands. To be done in a refactoring project.
"""
atm1, atm2 = self.struct.getAxisEndAtoms()
if atm1 is not None:
self.handleSphereRadius1 = max(1.005 * atm1.drawing_radius(),
1.005 * HANDLE_RADIUS_DEFAULT_VALUE)
if atm2 is not None:
self.handleSphereRadius2 = max(1.005 * atm2.drawing_radius(),
1.005 * HANDLE_RADIUS_DEFAULT_VALUE)
def _modifyStructure(self, params):
"""
Modify the structure based on the parameters specified.
Overrides EditCommand._modifystructure. This method removes the old
structure and creates a new one using self._createStructure. This
was needed for the structures like this (Dna, Nanotube etc) . .
See more comments in the method.
"""
if self.currentStruct is None:
print_compact_stack("bug: self.currentStruct doesn't exist"\
"exiting self._modifyStructure")
return
assert isinstance(self.currentStruct, self.win.assy.DnaSegment)
self.dna = B_Dna_PAM3_Generator()
duplexRise = self.currentStruct.getDuplexRise()
basesPerTurn = self.currentStruct.getBasesPerTurn()
numberOfBasePairsToAddOrRemove = self._determine_numberOfBasePairs_to_change(
)
ladderEndAxisAtom = self.get_axisEndAtom_at_resize_end()
if ladderEndAxisAtom is None:
print_compact_stack("bug: unable to resize the DnaSegment"\
"%r, end axis ato not found"%self.currentStruct)
return
if numberOfBasePairsToAddOrRemove != 0:
resizeEnd_final_position = self._get_resizeEnd_final_position(
ladderEndAxisAtom, abs(numberOfBasePairsToAddOrRemove),
duplexRise)
self.dna.modify(self.currentStruct, ladderEndAxisAtom,
numberOfBasePairsToAddOrRemove, basesPerTurn,
duplexRise, ladderEndAxisAtom.posn(),
resizeEnd_final_position)
self.previousParams = params
return
def modifyStructure(self):
"""
Called when a resize handle is dragged to change the length of one
or more DnaSegments (to be resized together) Called upon leftUp .
To acheive this resizing, it loops through the DnaSegments to be resized
and calls self._modifyStructure() for individual DnaSegments.
Note that Client should call this public method and should never call
the private method self._modifyStructure.
@see: B{DnaSegment_ResizeHandle.on_release} (the caller)
@see: B{SelectChunks_GraphicsMode.leftUp} (which calls the
the relevent method in DragHandler API. )
@see: B{exprs.DraggableHandle_AlongLine}, B{exprs.DragBehavior}
@see: B{self._modifyStructure}
@see: B{DnaSegmentList.updateAverageEndPoints()}
"""
if self.grabbedHandle is None:
return
for segment in self.getResizeSegmentList():
#TODO 2008-05-14: DnaSegmentList class relies on self.currentStruct.
#See if there is a better way. Ok for now
self.currentStruct = segment
#self._modifyStructure needs 'param' argument. As of 2008-05-14
#it is not supported/needed for multiple dna segment resizing.
#So just pass an empty tuple.
params = ()
self._modifyStructure(params)
#Reset the self.currentStruct after use
self.currentStruct = None
#Update the average end points of the self.struct so that resize handles
#are placed at proper positions.
self.struct.updateAverageEndPoints()
self.win.assy.changed()
self.win.win_update()
def _get_resizeEnd_final_position(self, ladderEndAxisAtom, numberOfBases,
duplexRise):
"""
Returns the final position of the resize end.
Note that we can not use the grabbedHandle's currentPosition as the
final position because resize handle is placed at an 'average' position.
So we must compute the correct vector using the 'self.currentStruct'
"""
final_position = None
other_axisEndAtom = self.struct.getOtherAxisEndAtom(ladderEndAxisAtom)
if other_axisEndAtom is None:
return None
axis_vector = ladderEndAxisAtom.posn() - other_axisEndAtom.posn()
segment_length_to_add = getDuplexLength('B-DNA',
numberOfBases,
duplexRise=duplexRise)
signFactor = +1
##if self.grabbedHandle is not None:
##vec = self.grabbedHandle.currentPosition - \
## self.grabbedHandle.fixedEndOfStructure
##if dot(vec, axis_vector) < 0:
##signFactor = -1
##else:
##signFactor = +1
axis_vector = axis_vector * signFactor
final_position = ladderEndAxisAtom.posn() + \
norm(axis_vector)*segment_length_to_add
return final_position
def hasResizableStructure(self):
"""
"""
if len(self.struct.getStructList()) == 0:
why_not = 'Segment list is empty'
isResizable = False
return isResizable, why_not
return _superclass.hasResizableStructure(self)
def _getStructureType(self):
"""
Returns the type of the structure this command supports.
This is used in isinstance test.
@see: EditCommand._getStructureType()
"""
return DnaSegmentList
def getDnaRibbonParams(self):
"""
Overrides superclass method.
@TODO:[2008-05-14] This could SLOW things up! Its called multiple times
from the graphics mode (for all the DnaSegments to be resized at once).
There is no apparent solution to this, but we could try optimizing the
following code. Also needs some refactoring.
@see: MultipleDnaSegmentResize_GraphicsMode._drawHandles()
@see: self._determine_numberOfBasePairs_to_change()
"""
#Optimization: First test a few basic things to see if the dna ribbon
#should be drawn, before doing more computations -- Ninad 2008-05-14
params_when_adding_bases = None
params_when_removing_bases = None
if self.grabbedHandle is None:
return None, None
if self.grabbedHandle.origin is None:
return None, None
ladderEndAxisAtom = self.get_axisEndAtom_at_resize_end()
if ladderEndAxisAtom is None:
return None, None
numberOfBasePairsToAddOrRemove = self._determine_numberOfBasePairs_to_change(
)
if numberOfBasePairsToAddOrRemove == 0:
return None, None
direction_of_drag = norm(self.grabbedHandle.currentPosition - \
self.grabbedHandle.origin)
#@TODO: BUG: DO NOT use self._get_resizeEnd_final_position to compute
#the resizeEnd_final_position. It computes the segment length to add
#using the number of base pairs to add ... and it uses
#getDuplexLength method which in turn rounds off the length as an integer
#multiple of duplexRise. Although this is what we want in self._modify()
#the drawDnaRibbon draws the base pair only if step size is > 3.18!
#so no basepair is drawn at exact val of 3.18. This is BUG, harder to
#fix. for drawing dna ribbon, lets justcompute the resize end final
#position using the following code. -- Ninad 2008-05-14
other_axisEndAtom = self.struct.getOtherAxisEndAtom(ladderEndAxisAtom)
if other_axisEndAtom is None:
return None, None
axis_vector = ladderEndAxisAtom.posn() - other_axisEndAtom.posn()
currentPosition = self.grabbedHandle.currentPosition
changedLength = vlen(currentPosition - self.grabbedHandle.origin)
#NOTE: (TODO) we call self._determine_numberOfBasePairs_to_change() at the
#beginning of this method which checks various things such as
#total distance moved by the handle etc to determine whether to draw
#the ribbon. So those checks are not done here. If that call is removed
#then we need to do those checks.
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
signFactor = -1.0
else:
signFactor = 1.0
resizeEnd_final_position = ladderEndAxisAtom.posn() + \
norm(axis_vector)*changedLength*signFactor
#If the segment is being shortened (determined by checking the
#direction of drag) , no need to draw the rubberband line.
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
params_when_adding_bases = None
params_when_removing_bases = (resizeEnd_final_position)
return params_when_adding_bases, \
params_when_removing_bases
basesPerTurn = self.struct.getBasesPerTurn()
duplexRise = self.struct.getDuplexRise()
ladder = ladderEndAxisAtom.molecule.ladder
endBaseAtomList = ladder.get_endBaseAtoms_containing_atom(
ladderEndAxisAtom)
ribbon1_start_point = None
ribbon2_start_point = None
ribbon1_direction = None
ribbon2_direction = None
ribbon1Color = applegreen
ribbon2Color = applegreen
if endBaseAtomList and len(endBaseAtomList) > 2:
strand_atom1 = endBaseAtomList[0]
strand_atom2 = endBaseAtomList[2]
if strand_atom1:
ribbon1_start_point = strand_atom1.posn()
for bond_direction, neighbor in strand_atom1.bond_directions_to_neighbors(
):
if neighbor and neighbor.is_singlet():
ribbon1_direction = bond_direction
break
ribbon1Color = strand_atom1.molecule.color
if not ribbon1Color:
ribbon1Color = strand_atom1.element.color
if strand_atom2:
ribbon2_start_point = strand_atom2.posn()
for bond_direction, neighbor in strand_atom2.bond_directions_to_neighbors(
):
if neighbor and neighbor.is_singlet():
ribbon2_direction = bond_direction
break
ribbon2Color = strand_atom2.molecule.color
if not ribbon2Color:
ribbon2Color = strand_atom2.element.color
params_when_adding_bases = (ladderEndAxisAtom.posn(),
resizeEnd_final_position, basesPerTurn,
duplexRise, ribbon1_start_point,
ribbon2_start_point, ribbon1_direction,
ribbon2_direction, ribbon1Color,
ribbon2Color)
params_when_removing_bases = None
return params_when_adding_bases, params_when_removing_bases
def _determine_numberOfBasePairs_to_change(self):
"""
Overrides superclass method
@TODO: This is significantly different (and perhaps better)
than the superclass method. See how to incorporate changes in
this method in superclass.
@see: self.getDnaRibbonParams()
"""
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
duplexRise = self.struct.getDuplexRise()
changedLength = vlen(currentPosition - self.grabbedHandle.origin)
direction_of_drag = norm(self.grabbedHandle.currentPosition - \
self.grabbedHandle.origin)
#Even when the direction of drag is negative (i.e. the basepairs being
#removed), make sure not to remove base pairs for very small movement
#of the grabbed handle
if changedLength < 0.2 * duplexRise:
return 0
#This check quickly determines if the grabbed handle moved by a distance
#more than the duplexRise and avoids further computations
#This condition is applicable only when the direction of drag is
#positive..i.e. bases bing added to the segment.
if changedLength < duplexRise and \
dot(self.grabbedHandle.direction, direction_of_drag) > 0:
return 0
#If the segment is being shortened (determined by checking the
#direction of drag)
numberOfBasesToAddOrRemove = \
getNumberOfBasePairsFromDuplexLength(
'B-DNA',
changedLength,
duplexRise = duplexRise)
if dot(self.grabbedHandle.direction, direction_of_drag) < 0:
numberOfBasesToAddOrRemove = -numberOfBasesToAddOrRemove
if numberOfBasesToAddOrRemove > 0:
#dna.modify will remove the first base pair it creates
#(that basepair will only be used for proper alignment of the
#duplex with the existing structure) So we need to compensate for
#this basepair by adding 1 to the new number of base pairs.
#UPDATE 2008-05-14: The following commented out code
#i.e. "##numberOfBasesToAddOrRemove += 1" is not required in this
#class , because the way we compute the number of base pairs to
#be added is different than than how its done at the moment in the
#superclass. In this method, we compute bases to be added from
#the resize end and that computation INCLUDES the resize end.
#so the number that it returns is already one more than the actual
#bases to be added. so commenting out the following line
# -- Ninad 2008-05-14
##numberOfBasesToAddOrRemove += 1
##print "*** numberOfBasesToAddOrRemove = ", numberOfBasesToAddOrRemove
##print "**** changedLength =", changedLength
pass
###UPDATE 2008-06-26: for some reason, when the number of base pairs
###to be added (i.e. value of numberOfBasesToAddOrRemove) is 1 more
###than the actual number of base pairs to be added. So subtract 1
###from this number. Cause not debugged. -- Ninad
##if numberOfBasesToAddOrRemove > 1:
##numberOfBasesToAddOrRemove -= 1
#UPDATE 2008-08-20: Note that DnaSegment_EditCommand.getCursorText()
#does the job of removing the extra basepair from numberOfBasesToAddOrRemove
#It(subtracting 1 basePair) is not done here as
#self._modifyStructure() needs it without the subtraction. This is
#prone to bugs and need to be cleaned up. -- Ninad
return numberOfBasesToAddOrRemove
class DraggableHandle_AlongLine(DelegatingInstanceOrExpr): ### TODO: all options might need renaming! replace "height" everywhere.
"""
A kind of draggable handle which can be dragged along a line
to change the value of a single floating point parameter
(representing position along the line, using a scale and origin
determined by our arguments).
### TODO: add epydoc parameters to this docstring? not sure that will work for a class!
Maybe we need to synthesize those (from the doc options below) into a fake __init__ method for its sake??
"""
# == args and options
# options for appearance of handle
appearance = Option( Drawable,
Center(Rect(0.2, 0.2, white)),
doc = "our appearance, when not highlighted") ###e take other args of Highlightable?
appearance_highlighted = Option( Drawable,
appearance,
doc = "our appearance, when highlighted")
sbar_text = Option(str, "draggable handle", doc = "our statusbar text on mouseover")
# state variable controlled by dragging
height_ref = Option(StateRef, doc = "stateref to a height variable") # TODO: rename, redoc
range = Option(tuple_Expr, None, doc = "range limit of height (tuple)")
### MAYBE: RENAME to avoid conflict with python range in this code
### TODO: take values from the stateref if this option is not provided
# action options, for Highlightable to do after the ones that come from
# DragBehavior_AlongLine [new feature of this and Highlightable, 080129]
on_press = Option(Action)
on_drag = Option(Action)
on_release = Option(Action)
on_release_in = Option(Action, on_release)
on_release_out = Option(Action, on_release)
on_doubleclick = Option(Action)
# line along which to drag it, and how to interpret the state as a position along that line (origin and scale)
origin = Option( Point, ORIGIN)
direction = Option( Vector, DX, doc = "vector giving direction and scale")
# providing a default value is mainly just for testing
#If this is false, the 'highlightable' object i.e. this handle
#won't be drawn. The delegate (that defines a Highlightable)
#We define an If_expr to check whether to draw the highlightable object.
#[by Ninad]
# [this should probably be revised, with hasValidParamsForDrawing replaced
# with an overridable compute method, for robustness -- current implem
# is suspected of causing tracebacks from insufficient update of this
# state. Need to review whether methodname needs to be hasValidParamsForDrawing
# to conform with any API. -- bruce 080409 comment]
should_draw = State(bool, True)
# == internal instances and formulae (modified from test_statearray_3.py)
_drag_handler = Instance( DragBehavior_AlongLine(
_self._delegate,
height_ref,
call_Expr(Ray, origin, direction),
# note: we need call_Expr since Ray is an ordinary class, not an expr! ###FIX
range = range
))
# note: _drag_handler is also being used to compute the translation from the height, even between drags.
#@see: DnaStrand_ResizeHandle.hasValidParamsForDrawing
#@see: definition of State attr should_draw
delegate = \
If_expr(
_self.should_draw,
Highlightable(
Translate(
appearance,
_drag_handler._translation #k ok?? only if that thing hangs around even in between drags, i guess!
#e #k not sure if this code-commoning is good, but it's tempting. hmm.
),
highlighted = Translate(
appearance_highlighted,
_drag_handler._translation
),
sbar_text = sbar_text,
behavior = _drag_handler,
on_press = _self.on_press,
on_drag = _self.on_drag,
# (note: no need to pass on_release)
on_release_in = _self.on_release_in,
on_release_out = _self.on_release_out,
on_doubleclick = _self.on_doubleclick
) #end of Highlightable
) #end of If_expr
def hasValidParamsForDrawing(self):
"""
Overridden in subclasses. Default implementation returns True
if this object (the highlightable) can be drawn without any known
issues
@see: DnaStrand_ResizeHandle.hasValidParamsForDrawing for more notes.
"""
self.should_draw = True
return self.should_draw
pass # end of class
class NanotubeSegment_EditCommand(State_preMixin, EditCommand):
"""
Command to edit a NanotubeSegment object.
To edit a segment, first enter BuildNanotube_EditCommand (accessed using
Build > Nanotube) then, select an existing NanotubeSegment within the
NanotubeGroup you are editing. When you select the NanotubeSegment, it
enters NanotubeSegment_Editcommand and shows the property manager with its
widgets showing the properties of selected segment.
"""
cmd = 'Nanotube Segment'
sponsor_keyword = 'Nanotube'
prefix = 'NanotubeSegment' # used for gensym
cmdname = "NANOTUBE_SEGMENT"
commandName = 'NANOTUBE_SEGMENT'
featurename = 'Edit Nanotube Segment'
command_should_resume_prevMode = True
command_has_its_own_gui = True
command_can_be_suspended = False
create_name_from_prefix = True
call_makeMenus_for_each_event = True
#Graphics Mode
GraphicsMode_class = NanotubeSegment_GraphicsMode
#This is set to BuildDna_EditCommand.flyoutToolbar (as of 2008-01-14,
#it only uses
flyoutToolbar = None
_parentNanotubeGroup = None
handlePoint1 = State( Point, ORIGIN)
handlePoint2 = State( Point, ORIGIN)
#The minimum 'stopper'length used for resize handles
#@see: self._update_resizeHandle_stopper_length for details.
_resizeHandle_stopper_length = State(Width, -100000)
rotationHandleBasePoint1 = State( Point, ORIGIN)
rotationHandleBasePoint2 = State( Point, ORIGIN)
#See self._update_resizeHandle_radius where this gets changed.
#also see NanotubeSegment_ResizeHandle to see how its implemented.
handleSphereRadius1 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
handleSphereRadius2 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
cylinderWidth = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
cylinderWidth2 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
#@TODO: modify the 'State params for rotation_distance
rotation_distance1 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
rotation_distance2 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
leftHandle = Instance(
NanotubeSegment_ResizeHandle(
command = _self,
height_ref = call_Expr( ObjAttr_StateRef, _self, 'cylinderWidth'),
origin = handlePoint1,
fixedEndOfStructure = handlePoint2,
direction = norm_Expr(handlePoint1 - handlePoint2),
sphereRadius = handleSphereRadius1,
range = (_resizeHandle_stopper_length, 10000)
))
rightHandle = Instance(
NanotubeSegment_ResizeHandle(
command = _self,
height_ref = call_Expr( ObjAttr_StateRef, _self, 'cylinderWidth2'),
origin = handlePoint2,
fixedEndOfStructure = handlePoint1,
direction = norm_Expr(handlePoint2 - handlePoint1),
sphereRadius = handleSphereRadius2,
range = (_resizeHandle_stopper_length, 10000)
))
rotationHandle1 = Instance(
RotationHandle(
command = _self,
rotationDistanceRef = call_Expr( ObjAttr_StateRef,
_self,
'rotation_distance1'),
center = handlePoint1,
axis = norm_Expr(handlePoint1 - handlePoint2),
origin = rotationHandleBasePoint1,
radiusVector = norm_Expr(rotationHandleBasePoint1 - handlePoint1)
))
rotationHandle2 = Instance(
RotationHandle(
command = _self,
rotationDistanceRef = call_Expr( ObjAttr_StateRef,
_self,
'rotation_distance2'),
center = handlePoint2,
axis = norm_Expr(handlePoint2 - handlePoint1),
origin = rotationHandleBasePoint2,
radiusVector = norm_Expr(rotationHandleBasePoint2 - handlePoint2)
))
def __init__(self, commandSequencer, struct = None):
"""
Constructor for DnaDuplex_EditCommand
"""
glpane = commandSequencer
State_preMixin.__init__(self, glpane)
EditCommand.__init__(self, commandSequencer)
self.struct = struct
#Graphics handles for editing the structure .
self.handles = []
self.grabbedHandle = None
#Initialize DEBUG preference
pref_nt_segment_resize_by_recreating_nanotube()
return
def init_gui(self):
"""
Initialize gui.
"""
#Note that NanotubeSegment_EditCommand only act as an edit command for an
#existing structure. The call to self.propMgr.show() is done only during
#the call to self.editStructure ..i .e. only after self.struct is
#updated. This is done because of the following reason:
# - self.init_gui is called immediately after entering the command.
# - self.init_gui in turn, initialized propMgr object and may also
# show the property manager. The self.propMgr.show routine calls
# an update widget method just before the show. This update method
# updates the widgets based on the parameters from the existing
# structure of the command (self.editCommand.struct)
# Although, it checks whether this structure exists, the editCommand
# could still have a self.struct attr from a previous run. (Note that
# EditCommand API was written before the command sequencer API and
# it has some loose ends like this. ) -- Ninad 2008-01-22
self.create_and_or_show_PM_if_wanted(showPropMgr = False)
return
def editStructure(self, struct = None):
EditCommand.editStructure(self, struct)
if self.hasValidStructure():
#When the structure (segment) is finalized (after the modifications)
#it will be added to the original NanotubeGroup to which it belonged
#before we began editing (modifying) it.
self._parentNanotubeGroup = self.struct.getNanotubeGroup()
#Set the endpoints
#@ DOES THIS DO ANYTHING? I don't think so. --Mark 2008-04-01
#@endPoint1, endPoint2 = self.struct.nanotube.getEndPoints()
#@params_for_propMgr = (endPoint1, endPoint2)
#TODO 2008-03-25: better to get all parameters from self.struct and
#set it in propMgr? This will mostly work except that reverse is
#not true. i.e. we can not specify same set of params for
#self.struct.setProps ...because endPoint1 and endPoint2 are derived.
#by the structure when needed. Commenting out following line of code
self.propMgr.setParameters(self.struct.getProps())
#Store the previous parameters. Important to set it after you
#set nanotube attrs in the propMgr.
#self.previousParams is used in self._previewStructure and
#self._finalizeStructure to check if self.struct changed.
self.previousParams = self._gatherParameters()
self._updateHandleList()
self.updateHandlePositions()
return
def keep_empty_group(self, group):
"""
Returns True if the empty group should not be automatically deleted.
otherwise returns False. The default implementation always returns
False. Subclasses should override this method if it needs to keep the
empty group for some reasons. Note that this method will only get called
when a group has a class constant autdelete_when_empty set to True.
(and as of 2008-03-06, it is proposed that dna_updater calls this method
when needed.
@see: Command.keep_empty_group() which is overridden here.
@see: BreakStrands_Command.keep_empty_group
@see: Group.autodelete_when_empty.. a class constant used by the
dna_updater (the dna updater then decides whether to call this
method to see which empty groups need to be deleted)
"""
bool_keep = EditCommand.keep_empty_group(self, group)
if not bool_keep:
if self.hasValidStructure():
if group is self.struct:
bool_keep = True
elif group is self.struct.parent_node_of_class(self.assy.NanotubeGroup):
bool_keep = True
#If this command doesn't have a valid structure, as a fall back,
#lets instruct it to keep ALL the NanotubeGroup objects even when empty
#Reason? ..see explanation in BreakStrands_Command.keep_empty_group
elif isinstance(group, self.assy.NanotubeGroup):
bool_keep = True
return bool_keep
def hasValidStructure(self):
"""
Tells the caller if this edit command has a valid structure.
Overrides EditCommand.hasValidStructure()
"""
#(By Bruce 2008-02-13)
isValid = EditCommand.hasValidStructure(self)
if not isValid:
return isValid
# would like to check here whether it's empty of axis chunks;
# instead, this will do for now (probably too slow, though):
p1, p2 = self.struct.nanotube.getEndPoints()
return (p1 is not None)
def _getStructureType(self):
"""
Subclasses override this method to define their own structure type.
Returns the type of the structure this editCommand supports.
This is used in isinstance test.
@see: EditCommand._getStructureType() (overridden here)
"""
return self.win.assy.NanotubeSegment
def _updateHandleList(self):
"""
Updates the list of handles (self.handles)
@see: self.editStructure
@see: NanotubeSegment_GraphicsMode._drawHandles()
"""
# note: if handlePoint1 and/or handlePoint2 can change more often than this
# runs, we'll need to rerun the two assignments above whenever they
# change and before the handle is drawn. An easy way would be to rerun
# these assignments in the draw method of our GM. [bruce 080128]
self.handles = [] # guess, but seems like a good idea [bruce 080128]
self.handles.append(self.leftHandle)
self.handles.append(self.rightHandle)
if DEBUG_ROTATION_HANDLES:
self.handles.append(self.rotationHandle1)
self.handles.append(self.rotationHandle2)
return
def updateHandlePositions(self):
"""
Update handle positions and also update the resize handle radii and
their 'stopper' lengths.
@see: self._update_resizeHandle_radius()
@see: self._update_resizeHandle_stopper_length()
@see: NanotubeSegment_GraphicsMode._drawHandles()
"""
self.handlePoint1 = None # Needed!
self.handlePoint2 = None
#TODO: Call this method less often by implementing model_changed
#see bug 2729 for a planned optimization
self.cylinderWidth = CYLINDER_WIDTH_DEFAULT_VALUE
self.cylinderWidth2 = CYLINDER_WIDTH_DEFAULT_VALUE
self._update_resizeHandle_radius()
handlePoint1, handlePoint2 = self.struct.nanotube.getEndPoints()
if 0: # Debug prints
print "updateHandlePositions(): handlePoint1=", handlePoint1
print "updateHandlePositions(): handlePoint2=", handlePoint2
if handlePoint1 is not None and handlePoint2 is not None:
# (that condition is bugfix for deleted axis segment, bruce 080213)
self.handlePoint1, self.handlePoint2 = handlePoint1, handlePoint2
#Update the 'stopper' length where the resize handle being dragged
#should stop. See self._update_resizeHandle_stopper_length()
#for more details
self._update_resizeHandle_stopper_length()
if DEBUG_ROTATION_HANDLES:
self.rotation_distance1 = CYLINDER_WIDTH_DEFAULT_VALUE
self.rotation_distance2 = CYLINDER_WIDTH_DEFAULT_VALUE
#Following computes the base points for rotation handles.
#to be revised -- Ninad 2008-02-13
unitVectorAlongAxis = norm(self.handlePoint1 - self.handlePoint2)
v = cross(self.glpane.lineOfSight, unitVectorAlongAxis)
self.rotationHandleBasePoint1 = self.handlePoint1 + norm(v) * 4.0
self.rotationHandleBasePoint2 = self.handlePoint2 + norm(v) * 4.0
return
def _update_resizeHandle_radius(self):
"""
Finds out the sphere radius to use for the resize handles, based on
atom /chunk or glpane display (whichever decides the display of the end
atoms. The default value is 1.2.
@see: self.updateHandlePositions()
"""
self.handleSphereRadius1 = HANDLE_RADIUS_DEFAULT_VALUE
self.handleSphereRadius2 = HANDLE_RADIUS_DEFAULT_VALUE
return
def _update_resizeHandle_stopper_length(self):
"""
Update the limiting length at which the resize handle being dragged
should 'stop' without proceeding further in the drag direction.
The segment resize handle stops when you are dragging it towards the
other resizeend and the distance between the two ends reaches two
duplexes.
The self._resizeHandle_stopper_length computed in this method is
used as a lower limit of the 'range' option provided in declaration
of resize handle objects (see class definition for the details)
@see: self.updateHandlePositions()
"""
total_length = vlen(self.handlePoint1 - self.handlePoint2)
nanotubeRise = self.struct.nanotube.getRise()
self._resizeHandle_stopper_length = - total_length + nanotubeRise
return
def _createPropMgrObject(self):
"""
Creates a property manager object (that defines UI things) for this
editCommand.
"""
assert not self.propMgr
propMgr = self.win.createNanotubeSegmentPropMgr_if_needed(self)
return propMgr
def _gatherParameters(self):
"""
Return the parameters from the property manager UI.
@return: The endpoints of the nanotube.
@rtype: tuple (endPoint1, endPoint2).
"""
return self.propMgr.getParameters()
def _createStructure(self):
"""
Creates and returns the structure (in this case a L{NanotubeSegment}
object.
@return : Nanotube segment that include the nanotube chunk.
@rtype: L{NanotubeSegment}
"""
# self.name needed for done message
if self.create_name_from_prefix:
# create a new name
name = self.name = gensym(self.prefix, self.win.assy) # (in _build_struct)
self._gensym_data_for_reusing_name = (self.prefix, name)
else:
# use externally created name
self._gensym_data_for_reusing_name = None
# (can't reuse name in this case -- not sure what prefix it was
# made with)
name = self.name
# Create the model tree group node.
# Make sure that the 'topnode' of this part is a Group (under which the
# DNa group will be placed), if the topnode is not a group, make it a
# a 'Group' (applicable to Clipboard parts).See part.py
# --Part.ensure_toplevel_group method. This is an important line
# and it fixes bug 2585
self.win.assy.part.ensure_toplevel_group()
ntSegment = NanotubeSegment(self.name,
self.win.assy,
self.win.assy.part.topnode,
editCommand = self )
try:
# Make the NanotubeSegment.
n, m, type, endings, endPoint1, endPoint2 = self._gatherParameters()
from cnt.model.Nanotube import Nanotube
self.nanotube = Nanotube()
nanotube = self.nanotube
nanotube.setChirality(n, m)
nanotube.setType(type)
nanotube.setEndings(endings)
nanotube.setEndPoints(endPoint1, endPoint2)
position = V(0.0, 0.0, 0.0)
ntChunk = nanotube.build(self.name, self.win.assy, position)
nanotube.computeEndPointsFromChunk(ntChunk)
ntSegment.addchild(ntChunk)
#set some properties such as nanotubeRise
#This information will be stored on the NanotubeSegment object so that
#it can be retrieved while editing this object.
#Should these props be assigned to the NanotubeSegment in
#Nanotube.build() itself? This needs to be answered while modifying
#build() method to fit in the dna data model. --Ninad 2008-03-05
#WARNING 2008-03-05: Since self._modifyStructure calls
#self._createStructure()
#If in the near future, we actually permit modifying a
#structure (such as dna) without actually recreating the whole
#structure, then the following properties must be set in
#self._modifyStructure as well. Needs more thought.
props =(nanotube.getChirality(),
nanotube.getType(),
nanotube.getEndings(),
nanotube.getEndPoints())
ntSegment.setProps(props)
return ntSegment
except (PluginBug, UserError):
# Why do we need UserError here? Mark 2007-08-28
ntSegment.kill()
raise PluginBug("Internal error while trying to create a NanotubeSegment.")
return
def _modifyStructure(self, params):
"""
Modify the structure based on the parameters specified.
Overrides EditCommand._modifystructure. This method removes the old
structure and creates a new one using self._createStructure. This
was needed for the structures like this (Dna, Nanotube etc) . .
See more comments in the method.
"""
if not pref_nt_segment_resize_by_recreating_nanotube():
self._modifyStructure_NEW_SEGMENT_RESIZE(params)
return
assert self.struct
# parameters have changed, update existing structure
self._revertNumber()
# self.name needed for done message
if self.create_name_from_prefix:
# create a new name
name = self.name = gensym(self.prefix, self.win.assy) # (in _build_struct)
self._gensym_data_for_reusing_name = (self.prefix, name)
else:
# use externally created name
self._gensym_data_for_reusing_name = None
# (can't reuse name in this case -- not sure what prefix it was
# made with)
name = self.name
#@NOTE: Unlike editcommands such as Plane_EditCommand, this
#editCommand actually removes the structure and creates a new one
#when its modified. -- Ninad 2007-10-24
self._removeStructure()
self.previousParams = params
self.struct = self._createStructure()
# Now append the new structure in self._segmentList (this list of
# segments will be provided to the previous command
# (BuildDna_EditCommand)
# TODO: Should self._createStructure does the job of appending the
# structure to the list of segments? This fixes bug 2599
# (see also BuildDna_PropertyManager.Ok
if self._parentNanotubeGroup is not None:
#Should this be an assertion? (assert self._parentNanotubeGroup is not
#None. For now lets just print a warning if parentNanotubeGroup is None
self._parentNanotubeGroup.addSegment(self.struct)
return
def _modifyStructure_NEW_SEGMENT_RESIZE(self, params): #@ NOT FIXED
"""
Modify the structure based on the parameters specified.
Overrides EditCommand._modifystructure. This method removes the old
structure and creates a new one using self._createStructure. This
was needed for the structures like this (Dna, Nanotube etc) . .
See more comments in the method.
@attention: is not implemented.
"""
#@TODO: - rename this method from _modifyStructure_NEW_SEGMENT_RESIZE
#to self._modifyStructure, after more testing
#This method is used for debug prefence:
#'Nanotube Segment: resize without recreating whole duplex'
#see also self.modifyStructure_NEW_SEGMENT_RESIZE
assert self.struct
from utilities.debug import print_compact_stack
print_compact_stack("_modifyStructure_NEW_SEGMENT_RESIZE() not fixed!" )
print "Params =", params
self.nanotube = params #@
length_diff = self._determine_how_to_change_length() #@
if length_diff == 0:
print_compact_stack("BUG: length_diff is always ZERO." )
return
elif length_diff > 0:
print "Nanotube longer by ", length_diff, ", angstroms."
else:
print "Nanotube shorter by ", length_diff, ", angstroms."
return
if numberOfBasePairsToAddOrRemove != 0: #@@@@ Not reached.
resizeEnd_final_position = self._get_resizeEnd_final_position(
ladderEndAxisAtom,
abs(numberOfBasePairsToAddOrRemove),
nanotubeRise )
self.nanotube.modify(self.struct,
length_diff,
ladderEndAxisAtom.posn(),
resizeEnd_final_position)
#Find new end points of structure parameters after modification
#and set these values in the propMgr.
new_end1 , new_end2 = self.struct.nanotube.getEndPoints() #@
params_to_set_in_propMgr = (new_end1,
new_end2)
#TODO: Need to set these params in the PM
#and then self.previousParams = params_to_set_in_propMgr
self.previousParams = params
return
def _get_resizeEnd_final_position(self,
ladderEndAxisAtom,
numberOfBases,
nanotubeRise):
final_position = None
if self.grabbedHandle:
final_position = self.grabbedHandle.currentPosition
else:
other_axisEndAtom = self.struct.getOtherAxisEndAtom(ladderEndAxisAtom)
axis_vector = ladderEndAxisAtom.posn() - other_axisEndAtom.posn()
segment_length_to_add = 0 #@
final_position = ladderEndAxisAtom.posn() + norm(axis_vector)*segment_length_to_add
return final_position
def getStructureName(self):
"""
Returns the name string of self.struct if there is a valid structure.
Otherwise returns None. This information is used by the name edit field
of this command's PM when we call self.propMgr.show()
@see: NanotubeSegment_PropertyManager.show()
@see: self.setStructureName
"""
if self.hasValidStructure():
return self.struct.name
return None
def setStructureName(self, name):
"""
Sets the name of self.struct to param <name> (if there is a valid
structure.
The PM of this command callss this method while closing itself
@param name: name of the structure to be set.
@type name: string
@see: NanotubeSegment_PropertyManager.close()
@see: self.getStructureName()
"""
#@BUG: We call this method in self.propMgr.close(). But propMgr.close()
#is called even when the command is 'cancelled'. That means the
#structure will get changed even when user hits cancel button or
#exits the command by clicking on empty space.
#This should really be done in self._finalizeStructure but that
#method doesn't get called when you click on empty space to exit
#the command. See NanotubeSegment_GraphicsMode.leftUp for a detailed
#comment.
if self.hasValidStructure():
self.struct.name = name
return
def getCursorText(self):
"""
This is used as a callback method in NanotubeLine mode
@see: NanotubeLineMode.setParams, NanotubeLineMode_GM.Draw
"""
if self.grabbedHandle is None:
return
if not env.prefs[nanotubeSegmentEditCommand_showCursorTextCheckBox_prefs_key]:
return '', black
text = ""
textColor = black
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
nanotubeLength = vlen( currentPosition - fixedEndOfStructure )
nanotubeLengthString = self._getCursorText_length(nanotubeLength)
text = nanotubeLengthString
#@TODO: The following updates the PM as the cursor moves.
#Need to rename this method so that you that it also does more things
#than just to return a textString -- Ninad 2007-12-20
self.propMgr.ntLengthLineEdit.setText(nanotubeLengthString)
return text, textColor
def _getCursorText_length(self, nanotubeLength):
"""
Returns a string that gives the length of the Nanotube for the cursor
text
"""
nanotubeLengthString = ''
if env.prefs[nanotubeSegmentEditCommand_cursorTextCheckBox_length_prefs_key]:
lengthUnitString = 'A'
#change the unit of length to nanometers if the length is > 10A
#fixes part of bug 2856
if nanotubeLength > 10.0:
lengthUnitString = 'nm'
nanotubeLength = nanotubeLength * 0.1
nanotubeLengthString = "%5.3f%s"%(nanotubeLength, lengthUnitString)
return nanotubeLengthString
def modifyStructure(self):
"""
Called when a resize handle is dragged to change the length of the
segment. (Called upon leftUp) . This method assigns the new parameters
for the segment after it is resized and calls
preview_or_finalize_structure which does the rest of the job.
Note that Client should call this public method and should never call
the private method self._modifyStructure. self._modifyStructure is
called only by self.preview_or_finalize_structure
@see: B{NanotubeSegment_ResizeHandle.on_release} (the caller)
@see: B{SelectChunks_GraphicsMode.leftUp} (which calls the
the relevent method in DragHandler API. )
@see: B{exprs.DraggableHandle_AlongLine}, B{exprs.DragBehavior}
@see: B{self.preview_or_finalize_structure }
@see: B{self._modifyStructure}
As of 2008-02-01 it recreates the structure
@see: a note in self._createStructure() about use of ntSegment.setProps
"""
if not pref_nt_segment_resize_by_recreating_nanotube():
self.modifyStructure_NEW_SEGMENT_RESIZE()
return
if self.grabbedHandle is None:
return
self.propMgr.endPoint1 = self.grabbedHandle.fixedEndOfStructure
self.propMgr.endPoint2 = self.grabbedHandle.currentPosition
#@length = vlen(self.propMgr.endPoint1 - self.propMgr.endPoint2 ) #@
self.preview_or_finalize_structure(previewing = True)
self.updateHandlePositions()
self.glpane.gl_update()
return
def modifyStructure_NEW_SEGMENT_RESIZE(self): #@ NOT FIXED
"""
Called when a resize handle is dragged to change the length of the
segment. (Called upon leftUp) . This method assigns the new parameters
for the segment after it is resized and calls
preview_or_finalize_structure which does the rest of the job.
Note that Client should call this public method and should never call
the private method self._modifyStructure. self._modifyStructure is
called only by self.preview_or_finalize_structure
@see: B{NanotubeSegment_ResizeHandle.on_release} (the caller)
@see: B{SelectChunks_GraphicsMode.leftUp} (which calls the
the relevent method in DragHandler API. )
@see: B{exprs.DraggableHandle_AlongLine}, B{exprs.DragBehavior}
@see: B{self.preview_or_finalize_structure }
@see: B{self._modifyStructure}
As of 2008-02-01 it recreates the structure
@see: a note in self._createStructure() about use of ntSegment.setProps
"""
#TODO: need to cleanup this and may be use use something like
#self.previousParams = params in the end -- 2008-03-24 (midnight)
#@TODO: - rename this method from modifyStructure_NEW_SEGMENT_RESIZE
#to self.modifyStructure, after more testing
#This method is used for debug prefence:
#'Nanotube Segment: resize without recreating whole duplex'
#see also self._modifyStructure_NEW_SEGMENT_RESIZE
if self.grabbedHandle is None:
return
self.propMgr.endPoint1 = self.grabbedHandle.fixedEndOfStructure
self.propMgr.endPoint2 = self.grabbedHandle.currentPosition
DEBUG_DO_EVERYTHING_INSIDE_MODIFYSTRUCTURE_METHOD = False
if DEBUG_DO_EVERYTHING_INSIDE_MODIFYSTRUCTURE_METHOD:
# TO DO: this entire block of code. --Mark 2008-04-03
print_compact_stack("modifyStructure_NEW_SEGMENT_RESIZE(): NOT FIXED")
length = vlen(self.grabbedHandle.fixedEndOfStructure - \
self.grabbedHandle.currentPosition )
endAtom1, endAtom2 = self.struct.getAxisEndAtoms() #@
for atm in (endAtom1, endAtom2):
if not same_vals(self.grabbedHandle.fixedEndOfStructure, atm.posn()):
ladderEndAxisAtom = atm
break
endPoint1, endPoint2 = self.struct.nanotube.getEndPoints()
old_dulex_length = vlen(endPoint1 - endPoint2)
nanotubeRise = self.struct.getProps() #@
params_to_set_in_propMgr = (
self.grabbedHandle.origin,
self.grabbedHandle.currentPosition,
)
##self._modifyStructure(params)
############################################
self.nanotube = Nanotube() #@ Creates 5x5 CNT. Miisng PM params.
length_diff = self._determine_how_to_change_length()
ladderEndAxisAtom = self.get_axisEndAtom_at_resize_end() #@
#@ Nanotube class needs modify() method.
self.nanotube.modify(self.struct,
length_diff,
ladderEndAxisAtom.posn(),
self.grabbedHandle.currentPosition)
#TODO: Important note: How does NE1 know that structure is modified?
#Because number of base pairs parameter in the PropMgr changes as you
#drag the handle . This is done in self.getCursorText() ... not the
#right place to do it. OR that method needs to be renamed to reflect
#this as suggested in that method -- Ninad 2008-03-25
self.preview_or_finalize_structure(previewing = True)
##self.previousParams = params_to_set_in_propMgr
self.glpane.gl_update()
return
def get_axisEndAtom_at_resize_end(self):
ladderEndAxisAtom = None
if self.grabbedHandle is not None:
ladderEndAxisAtom = self.struct.getAxisEndAtomAtPosition(self.grabbedHandle.origin)
else:
endAtom1, endAtom2 = self.struct.getAxisEndAtoms()
ladderEndAxisAtom = endAtom2
return ladderEndAxisAtom
def _determine_how_to_change_length(self): #@ NEEDS WORK
"""
Returns the difference in length between the original nanotube and the
modified nanotube, where:
0 = no change in length
> 0 = lengthen
< 0 = trim
"""
nanotubeRise = self.struct.nanotube.getRise()
endPoint1, endPoint2 = self.struct.nanotube.getEndPoints() #@
original_nanotube_length = vlen(endPoint1 - endPoint2)
new_nanotube_length = vlen(endPoint1 - endPoint2) #@
return new_nanotube_length - original_nanotube_length #@ ALWAYS RETURNS ZERO
def makeMenus(self):
"""
Create context menu for this command. (Build Dna mode)
"""
if not hasattr(self, 'graphicsMode'):
return
selobj = self.glpane.selobj
if selobj is None:
return
self.Menu_spec = []
highlightedChunk = None
if isinstance(selobj, Chunk):
highlightedChunk = selobj
if isinstance(selobj, Atom):
highlightedChunk = selobj.molecule
elif isinstance(selobj, Bond):
chunk1 = selobj.atom1.molecule
chunk2 = selobj.atom2.molecule
if chunk1 is chunk2 and chunk1 is not None:
highlightedChunk = chunk1
if highlightedChunk is None:
return
if self.hasValidStructure():
nanotubeGroup = self.struct.parent_node_of_class(self.assy.NanotubeGroup)
if nanotubeGroup is None:
return
#following should be self.struct.getNanotubeGroup or self.struct.getNanotubeGroup
#need to formalize method name and then make change.
if not nanotubeGroup is highlightedChunk.parent_node_of_class(self.assy.NanotubeGroup):
item = ("Edit unavailable: Member of a different NanotubeGroup",
noop, 'disabled')
self.Menu_spec.append(item)
return
highlightedChunk.make_glpane_context_menu_items(self.Menu_spec,
command = self)
return
class test_connectWithState(State_preMixin, ExampleCommand):
# class constants needed by mode API for example commands
commandName = 'test_connectWithState-commandName'
default_mode_status_text = "test_connectWithState"
featurename = "Prototype: Test connectWithState"
PM_class = test_connectWithState_PM
# tracked state -- this initializes specially defined instance variables
# which will track all their uses and changes so that connectWithState
# works for them:
cylinderVertical = State(bool, False)
cylinderWidth = State(float, CYLINDER_WIDTH_DEFAULT_VALUE)
# TODO: soon this will be the only use of this constant, so it can be inlined
cylinderColor = State('color-stub', pink) # type should be Color (nim), but type is not yet used
# note: you can add _e_debug = True to one or more of these State definitions
# to see debug prints about some accesses to this state.
GraphicsMode_class = _test_connectWithState_GM
# init methods
def __init__(self, glpane):
# I don't know why this method is needed. ##### REVIEW (super semantics), FIX or clean up
super(test_connectWithState, self).__init__(glpane) # State_preMixin.__init__
ExampleCommand.__init__(self, glpane) # (especially this part)
return
## def __init__(self, glpane):
## super(test_connectWithState, self).__init__(glpane)
#### # that only calls some mode's init method,
#### # so (for now) call this separately:
#### IorE_guest_mixin.__init__(self, glpane)
## return
# exprs-based formulae (and some compute methods)
direction = If_expr( cylinderVertical, DY, DX )
def _C_width_direction(self):
"""
compute self.width_direction
"""
# Note: to do this with a formula expr instead
# would require cross_Expr to be defined,
# and glpane.lineOfSight to be tracked.
return cross( self.direction, self.env.glpane.lineOfSight )
width_direction = _self.width_direction # so it can be used in formulae below
# stub for handle test code [070912]
widthHandleEnabled = True # stub
## widthHandle = Instance(Rect()) # stub
h_offset = 0.5 + 0.2 # get it from handle? nah (not good if that changes with time); just make it fit.
# or we could decide that handles ought to have useful fixed bounding boxes...
## widthHandle = Instance(Translate(Center(Rect(0.5)),
## width_direction * (cylinderWidth / 2.0 + h_offset) )) #stub
widthHandle = Instance( DraggableHandle_AlongLine(
appearance = Center(Rect(0.5, 0.5, white)),
### REVIEW:
# Can't we just replace the following with something based on the formula for the position,
# width_direction * (cylinderWidth / 2.0 + h_offset)
# ?
# As it is, I have to manually solve that formula for origin and direction to pass in,
# i.e. rewrite it as
# position = origin + direction * cylinderWidth
## height_ref = cylinderWidth, ###WRONG
## height_ref = ObjAttr_StateRef( _self, 'cylinderWidth'),
## ## AssertionError: ObjAttr_StateRef fallback is nim -- needed for S._self
height_ref = call_Expr( ObjAttr_StateRef, _self, 'cylinderWidth'), # guess at workaround; #e we need a more principled way!
### REVIEW: efficient enough? (guess: overhead only happens once, so yes)
# could we say instead something like: height_ref = Variable(cylinderWidth) ?? Or VariableRef? Or StateRef_to ?
origin = width_direction * h_offset, # note: also includes cylinder center, but that's hardcoded at ORIGIN
direction = width_direction / 2.0,
sbar_text = "cylinder width", ### TODO: make it a formula, include printed value of width?
range = (0.1, 10),
### TODO: DraggableHandle_AlongLine should take values from the stateref if this option is not provided;
# meanwhile, we ought to pass a consistent value!
))
# Note: the Instance is required; but I'm not sure if it would be
# if we were using a fuller exprs superclass or init code. [bruce 070912]
def cmd_Bigger(self):
self.cylinderWidth += 0.5
set_cylinder_height( cylinder_height() + 0.5)
# TODO: enforce maxima
return
def cmd_Smaller(self):
self.cylinderWidth -= 0.5
set_cylinder_height( cylinder_height() - 0.5)
# enforce minima (###BUG: not the same ones as declared in the PM)
### REVISE: min & max should be declared in State macro and (optionally) enforced by it
if self.cylinderWidth < 0.1:
self.cylinderWidth = 0.1
if cylinder_height() < 0.1:
set_cylinder_height(0.1)
return
pass
class MakeCrossovers_Handle(DelegatingInstanceOrExpr):
should_draw = State(bool, True)
radius = 0.8
point1 = Arg(Point)
point2 = Arg(Point)
scale = Arg(float)
crossoverSite_marker = Option(
Action,
doc='The CrossoverSite Marker class which instantiates this handle')
#Command object specified as an 'Option' during instantiation of the class
#see DnaSegment_EditCommand class definition.
command = Option(Action, doc='The Command which instantiates this handle')
crossoverPairs = Option(tuple, ())
#Stateusbar text. Variable needs to be renamed in superclass.
sbar_text = Option(str,
"Click on the handle to create this crossover",
doc="Statusbar text on mouseover")
delegate = If_expr(
_self.should_draw,
Highlightable(Overlay(
Cylinder((call_Expr(_self.crossoverPairs[0].posn),
call_Expr(_self.crossoverPairs[3].posn)),
radius=radius,
color=silver),
Cylinder((call_Expr(_self.crossoverPairs[1].posn),
call_Expr(_self.crossoverPairs[2].posn)),
radius=radius,
color=silver)),
Overlay(
Cylinder((call_Expr(_self.crossoverPairs[0].posn),
call_Expr(_self.crossoverPairs[3].posn)),
radius=radius,
color=banana),
Cylinder((call_Expr(_self.crossoverPairs[1].posn),
call_Expr(_self.crossoverPairs[2].posn)),
radius=radius,
color=banana)),
on_press=_self.on_press,
on_release=_self.on_release,
sbar_text=sbar_text))
##delegate = If_expr(_self.should_draw,
##Highlightable(Cylinder((point1, point2),
##radius = radius,
##color = silver),
##Cylinder((point1, point2),
##radius = radius,
##color = banana),
##on_press = _self.on_press,
##on_release = _self.on_release))
##delegate = \
##If_expr(
##_self.should_draw,
##Highlightable(Arrow(
##color = silver,
##arrowBasePoint = point1,
####tailPoint = norm(vector)*1.0,
##tailPoint = point2,
##radius = radius,
##scale = scale),
##Arrow(
##color = banana,
##arrowBasePoint = point1,
####tailPoint = norm(vector)*1.0,
##tailPoint = point2,
##radius = radius,
##scale = scale),
##on_press = _self.on_press,
##on_release = _self.on_release ) ) #
def hasValidParamsForDrawing(self):
"""
Overridden in subclasses. Default implementation returns True
if this object (the highlightable) can be drawn without any known
issues
@see: DnaStrand_ResizeHandle.hasValidParamsForDrawing for more notes.
"""
##self.should_draw = True
return self.should_draw
def on_press(self):
pass
def on_release(self):
self.command.makeCrossover(self.crossoverPairs)
self.crossoverSite_marker.removeHandle(self)
class TextState(InstanceMacro): # rename?
text = State(str, "initial text", doc="text")
_value = TextRect(text) # need size?
pass
class _MT_try2_node_helper(DelegatingInstanceOrExpr):
"""
[private helper expr class for MT_try2]
One MT item view -- specific to one node, one whole MT, and one (possibly time-varying) position with it.
"""
# args ####e REORDER THEM
node = Arg(ModelNode, doc = "any node that needs to be displayed in this MT")
###e NOTE: type coercion to this is nim; while that's true, we use helper functions like node_name(node) below;
# once type coercion is implemented
# (or simulated by hand by wrapping this arg with a helper expr like ModelTreeNode_trivial_glue),
# we could instead use node.mt_name, etc.)
mt = Arg(MT_try2, doc = "the whole MT view, in which we store MT items for nodes, and keep other central state or prefs if needed")
name_suffix = Option(str, "")
initial_open = Option(bool, False, doc = "initial value of boolean state 'open'; only used when this item is first created")
##e should ask the node itself for the initial value of open (e.g. so new groups, trying to start open, can do so),
# and also advise it when we open/close it, in case it wants to make that state persistent in some manner
# WARNING: compare to MT_try1 -- lots of copied code after this point
# WARNING: the comments are also copied, and not yet reviewed much for their new context! (so they could be wrong or obs) ###k
# state refs
open = State(bool, initial_open)
# other formulae
###e optim: some of these could have shared instances over this class, since they don't depend on _self; should autodetect this
# Note, + means openable (ie closed), - means closable (ie open) -- this is the Windows convention (I guess; not sure about Linux)
# and until now I had them reversed. This is defined in two files and in more than one place in one of them. [bruce 070123]
open_icon = Overlay(Rect(0.4), TextRect('-',1,1))
closed_icon = Overlay(Rect(0.4), TextRect('+',1,1))
openclose_spacer = Spacer(0.4)
#e or Invisible(open_icon); otoh that's no simpler, since open_icon & closed_icon have to be same size anyway
# the openclose icon, when open or close is visible (i.e. for openable nodes)
openclose_visible = Highlightable(
If( open, open_icon, closed_icon ),
on_press = Set(open, not_Expr(open)),
sbar_text = getattr_Expr( _self, '_e_serno') #070301 this permits finding out how often MT gets remade/shared
# (results as of 070301: remade when main instance is, even if going back to a prior testexpr, out of _19i & _30i)
)
openclose_slot = If( call_Expr(node_openable, node), openclose_visible, openclose_spacer )
if 0:
# cross-highlighting experiment, 070210, but disabled since approach seems wrong (as explained in comment)
yellow = DZ = 'need to import these'
indicator_over_obj_center = Center(Rect(0.4, 0.4, yellow))
position_over_obj_center = node.center + DZ * 3 ###BUG: DZ does not point towards screen if trackballing was done
###STUB:
# - should be drawn in a fixed close-to-screen plane, or cov plane (if obscuring is not an issue),
# - so indicator size is constant in pixels, even in perspective view (I guess),
# - also so it's not obscured (especially by node itself) -- or, draw it in a way visible behind obscuring things (might be a better feature)
# - what we draw here should depend on what node is
# - we also want to draw a line from type icon to node indicator (requires transforming coords differently)
# - needs to work if node.center is not defined (use getattr_Expr - but what dflt? or use some Ifs about it)
pointer_to_obj = DrawInCenter( Translate( indicator_over_obj_center, position_over_obj_center))
#bug: Translate gets neutralized by DrawInCorner [fixed now]
###BUG: fundamentally wrong -- wrong coord system. We wanted DrawInAbsCoords or really DrawInThingsCoords,
# but this is not well-defined (if thing drawn multiply) or easy (see comments about the idea in projection.py).
else:
# What we want instead is to set a variable which affects how the obj is drawn.
# If this was something all objs compared themselves to, then all objs would track its use (when they compared)
# and therefore want to redraw when we changed it! Instead we need only the involved objs (old & new value) to redraw,
# so we need a dict from obj to this flag (drawing prefs set by this MT). Maybe the app would pass this dict to MT_try2
# as an argument. It would be a dict of individually trackable state elements. (Key could be node_id, I guess.)
# ### TRY IT SOMETIME -- for now, cross-highlighting experiment is disabled.
pointer_to_obj = None
# selection indications can use this
node_is_selected = call_Expr( mt_node_selected, node)
kluge_icon_color = If( node_is_selected, blue, green)
sbar_format_for_name = If( node_is_selected, "%s (selected)", "%s")
###STUB for the type_icon ##e the Highlightable would be useful on the label too
icon = Highlightable(
Rect(0.4, 0.4, kluge_icon_color), ##stub; btw, would be easy to make color show hiddenness or type, bfr real icons work
Overlay( Rect(0.4, 0.4, ave_colors(0.1, white, kluge_icon_color)),
#070216 mix white into the color like DraggableObject does
pointer_to_obj ),
sbar_text = format_Expr( sbar_format_for_name, call_Expr(node_name, node) )
)
##e selection behavior too
label = DisplayListChunk(
# added DisplayListChunk 070213 late -- does it speed it up? not much; big new-item slowness bug remains. retain, since doesn't hurt.
TextRect( call_Expr(node_name, node) + name_suffix )
)
###e will need revision to Node or proxy for it, so node.name is usage/mod-tracked
##e selection behavior too --
#e probably not in these items but in the surrounding Row (incl invis bg? maybe not, in case model appears behind it!)
##e italic for disabled nodes
##e support cmenu
delegate = SimpleRow(
CenterY(openclose_slot),
SimpleColumn(
SimpleRow(CenterY(icon), CenterY(label)),
#070124 added CenterY, hoping to improve text pixel alignment (after drawfont2 improvements) -- doesn't work
If( open,
_MT_try2_kids_helper( call_Expr(node_kids, node) , _self.mt ), # 070218 added _self.mt -- always intended, first used now
None
# Note: this None used to be Spacer(0), due to a bug mentioned in a comment in ToggleShow.py
# (but unfortunately not explained there -- it just says "I wanted None here, but it exposes a logic bug,
# not trivial to fix, discuss in If or Column" -- my recollected bug-theory is described just below).
# On 070302 I confirmed that None seems to work (even in testexpr_18i with a group of 2 chunks, plus two more below).
# I don't fully know why it works, since I thought the bug was that SimpleColumn's None specialcase
# didn't run, since the element was not None but the If, and then delegating lbox attrs to None didn't work.
# (Fixable by using the newer If that evals, but for some reason that's not yet standard, I guess just because
# I didn't have time to test it enough or think it through fully re ipath or instance caching or something.)
# But as long as it works, use it -- ask Qs later. A recent perhaps-related change: None is allowed in drawkid.
# (A memory scrap -- does instantiating None conceivably produce a spacer?? ###k)
)
)
)
pass # end of class _MT_try2_node_helper
class EditNanotube_EditCommand(State_preMixin, EditCommand):
"""
Command to edit a NanotubeSegment (nanotube).
"""
# class constants
GraphicsMode_class = EditNanotube_GraphicsMode
PM_class = EditNanotube_PropertyManager
commandName = 'EDIT_NANOTUBE'
featurename = "Edit Nanotube"
from utilities.constants import CL_SUBCOMMAND
command_level = CL_SUBCOMMAND
command_parent = 'BUILD_NANOTUBE'
command_should_resume_prevMode = True
command_has_its_own_PM = True
flyoutToolbar = None
call_makeMenus_for_each_event = True
handlePoint1 = State( Point, ORIGIN)
handlePoint2 = State( Point, ORIGIN)
#The minimum 'stopper'length used for resize handles
#@see: self._update_resizeHandle_stopper_length for details.
_resizeHandle_stopper_length = State(Width, -100000)
rotationHandleBasePoint1 = State( Point, ORIGIN)
rotationHandleBasePoint2 = State( Point, ORIGIN)
#See self._update_resizeHandle_radius where this gets changed.
#also see EditNanotube_ResizeHandle to see how its implemented.
handleSphereRadius1 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
handleSphereRadius2 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
cylinderWidth = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
cylinderWidth2 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
#@TODO: modify the 'State params for rotation_distance
rotation_distance1 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
rotation_distance2 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
leftHandle = Instance(
EditNanotube_ResizeHandle(
command = _self,
height_ref = call_Expr( ObjAttr_StateRef, _self, 'cylinderWidth'),
origin = handlePoint1,
fixedEndOfStructure = handlePoint2,
direction = norm_Expr(handlePoint1 - handlePoint2),
sphereRadius = handleSphereRadius1,
range = (_resizeHandle_stopper_length, 10000)
))
rightHandle = Instance(
EditNanotube_ResizeHandle(
command = _self,
height_ref = call_Expr( ObjAttr_StateRef, _self, 'cylinderWidth2'),
origin = handlePoint2,
fixedEndOfStructure = handlePoint1,
direction = norm_Expr(handlePoint2 - handlePoint1),
sphereRadius = handleSphereRadius2,
range = (_resizeHandle_stopper_length, 10000)
))
rotationHandle1 = Instance(
RotationHandle(
command = _self,
rotationDistanceRef = call_Expr( ObjAttr_StateRef,
_self,
'rotation_distance1'),
center = handlePoint1,
axis = norm_Expr(handlePoint1 - handlePoint2),
origin = rotationHandleBasePoint1,
radiusVector = norm_Expr(rotationHandleBasePoint1 - handlePoint1)
))
rotationHandle2 = Instance(
RotationHandle(
command = _self,
rotationDistanceRef = call_Expr( ObjAttr_StateRef,
_self,
'rotation_distance2'),
center = handlePoint2,
axis = norm_Expr(handlePoint2 - handlePoint1),
origin = rotationHandleBasePoint2,
radiusVector = norm_Expr(rotationHandleBasePoint2 - handlePoint2)
))
def __init__(self, commandSequencer):
"""
Constructor for InsertDna_EditCommand
"""
glpane = commandSequencer.assy.glpane
State_preMixin.__init__(self, glpane)
EditCommand.__init__(self, commandSequencer)
#Graphics handles for editing the structure .
self.handles = []
self.grabbedHandle = None
#Initialize DEBUG preference
pref_nt_segment_resize_by_recreating_nanotube()
return
def editStructure(self, struct = None):
EditCommand.editStructure(self, struct)
if self.hasValidStructure():
#TODO 2008-03-25: better to get all parameters from self.struct and
#set it in propMgr? This will mostly work except that reverse is
#not true. i.e. we can not specify same set of params for
#self.struct.setProps ...because endPoint1 and endPoint2 are derived.
#by the structure when needed.
self.propMgr.setParameters(self.struct.getProps())
#Store the previous parameters. Important to set it after you
#set nanotube attrs in the propMgr.
#self.previousParams is used in self._previewStructure and
#self._finalizeStructure to check if self.struct changed.
self.previousParams = self._gatherParameters()
self._updateHandleList()
self.updateHandlePositions()
return
def hasValidStructure(self):
"""
Tells the caller if this edit command has a valid structure.
Overrides EditCommand.hasValidStructure()
"""
#(By Bruce 2008-02-13)
isValid = EditCommand.hasValidStructure(self)
if not isValid:
return isValid
# would like to check here whether it's empty of axis chunks;
# instead, this will do for now (probably too slow, though):
p1, p2 = self.struct.nanotube.getEndPoints()
return (p1 is not None)
def _getStructureType(self):
"""
Subclasses override this method to define their own structure type.
Returns the type of the structure this editCommand supports.
This is used in isinstance test.
@see: EditCommand._getStructureType() (overridden here)
"""
return self.win.assy.NanotubeSegment
def _updateHandleList(self):
"""
Updates the list of handles (self.handles)
@see: self.editStructure
@see: EditNanotube_GraphicsMode._drawHandles()
"""
# note: if handlePoint1 and/or handlePoint2 can change more often than this
# runs, we'll need to rerun the two assignments above whenever they
# change and before the handle is drawn. An easy way would be to rerun
# these assignments in the draw method of our GM. [bruce 080128]
self.handles = [] # guess, but seems like a good idea [bruce 080128]
self.handles.append(self.leftHandle)
self.handles.append(self.rightHandle)
if DEBUG_ROTATION_HANDLES:
self.handles.append(self.rotationHandle1)
self.handles.append(self.rotationHandle2)
return
def updateHandlePositions(self):
"""
Update handle positions and also update the resize handle radii and
their 'stopper' lengths.
@see: self._update_resizeHandle_radius()
@see: self._update_resizeHandle_stopper_length()
@see: EditNanotube_GraphicsMode._drawHandles()
"""
self.handlePoint1 = None # Needed!
self.handlePoint2 = None
#TODO: Call this method less often by implementing model_changed
#see bug 2729 for a planned optimization
self.cylinderWidth = CYLINDER_WIDTH_DEFAULT_VALUE
self.cylinderWidth2 = CYLINDER_WIDTH_DEFAULT_VALUE
self._update_resizeHandle_radius()
handlePoint1, handlePoint2 = self.struct.nanotube.getEndPoints()
if 0: # Debug prints
print "updateHandlePositions(): handlePoint1=", handlePoint1
print "updateHandlePositions(): handlePoint2=", handlePoint2
if handlePoint1 is not None and handlePoint2 is not None:
# (that condition is bugfix for deleted axis segment, bruce 080213)
self.handlePoint1, self.handlePoint2 = handlePoint1, handlePoint2
#Update the 'stopper' length where the resize handle being dragged
#should stop. See self._update_resizeHandle_stopper_length()
#for more details
self._update_resizeHandle_stopper_length()
if DEBUG_ROTATION_HANDLES:
self.rotation_distance1 = CYLINDER_WIDTH_DEFAULT_VALUE
self.rotation_distance2 = CYLINDER_WIDTH_DEFAULT_VALUE
#Following computes the base points for rotation handles.
#to be revised -- Ninad 2008-02-13
unitVectorAlongAxis = norm(self.handlePoint1 - self.handlePoint2)
v = cross(self.glpane.lineOfSight, unitVectorAlongAxis)
self.rotationHandleBasePoint1 = self.handlePoint1 + norm(v) * 4.0
self.rotationHandleBasePoint2 = self.handlePoint2 + norm(v) * 4.0
return
def _update_resizeHandle_radius(self):
"""
Finds out the sphere radius to use for the resize handles, based on
atom /chunk or glpane display (whichever decides the display of the end
atoms. The default value is 1.2.
@see: self.updateHandlePositions()
"""
self.handleSphereRadius1 = HANDLE_RADIUS_DEFAULT_VALUE
self.handleSphereRadius2 = HANDLE_RADIUS_DEFAULT_VALUE
return
def _update_resizeHandle_stopper_length(self):
"""
Update the limiting length at which the resize handle being dragged
should 'stop' without proceeding further in the drag direction.
The segment resize handle stops when you are dragging it towards the
other resizeend and the distance between the two ends reaches two
duplexes.
The self._resizeHandle_stopper_length computed in this method is
used as a lower limit of the 'range' option provided in declaration
of resize handle objects (see class definition for the details)
@see: self.updateHandlePositions()
"""
total_length = vlen(self.handlePoint1 - self.handlePoint2)
nanotubeRise = self.struct.nanotube.getRise()
self._resizeHandle_stopper_length = - total_length + nanotubeRise
return
def _gatherParameters(self):
"""
Return the parameters from the property manager UI.
@return: The endpoints of the nanotube.
@rtype: tuple (endPoint1, endPoint2).
"""
return self.propMgr.getParameters()
def _createStructure(self):
"""
Returns the current NanotubeSegment being edited with a new nanotube
chunk.
@return : Nanotube segment that include the new nanotube chunk.
@rtype: L{NanotubeSegment}
"""
try:
# Create a new nanotube chunk using new params.
n, m, type, endings, endPoint1, endPoint2 = self._gatherParameters()
from cnt.model.NanotubeParameters import NanotubeParameters
self.nanotube = NanotubeParameters()
nanotube = self.nanotube
nanotube.setChirality(n, m)
nanotube.setType(type)
nanotube.setEndings(endings)
nanotube.setEndPoints(endPoint1, endPoint2)
position = V(0.0, 0.0, 0.0)
ntChunk = nanotube.build(self.struct.name, self.win.assy, position)
nanotube.computeEndPointsFromChunk(ntChunk) # Needed.
self.struct.addchild(ntChunk)
#WARNING 2008-03-05:
#When we actually permit modifying a nanotube without recreating it,
#then the following properties must be set in self._modifyStructure
#as well. Needs more thought.
props =(nanotube.getChirality(),
nanotube.getType(),
nanotube.getEndings(),
nanotube.getEndPoints())
self.struct.setProps(props)
return self.struct
except (PluginBug, UserError):
self.struct.kill()
raise PluginBug("Internal error while trying to recreate a NanotubeSegment.")
return None
def _modifyStructure(self, params):
"""
Modify the structure based on the parameters specified.
Overrides EditCommand._modifystructure. This method removes the old
nanotube and replaces it with a new one using self._createStructure.
"""
if not pref_nt_segment_resize_by_recreating_nanotube():
self._modifyStructure_NEW_SEGMENT_RESIZE(params)
return
# To modify the structure, we need to:
# 1. Delete the current nanotube chunk inside the NanotubeSegment group.
# 2. Create a new new nanotube chunk using nanotube.build()
# 3. Add the newly generated nanotube to this NanotubeSegment.
# 4. Update all the nanotube parameters.
# Note: Steps 2-4 are done in self._createStructure()
assert self.struct
self.struct.members[0].kill() # Delete the current nanotube chunk.
self.previousParams = params
self.struct = self._createStructure()
return
def _modifyStructure_NEW_SEGMENT_RESIZE(self, params): #@ NOT FIXED
"""
This resizes without recreating whole nanotube
Overrides EditCommand._modifystructure.
@attention: is not implemented.
"""
#@TODO: - rename this method from _modifyStructure_NEW_SEGMENT_RESIZE
#to self._modifyStructure, after more testing
#This method is used for debug prefence:
#'Nanotube Segment: resize without recreating whole nanotube'
#see also self.modifyStructure_NEW_SEGMENT_RESIZE
assert self.struct
from utilities.debug import print_compact_stack
print_compact_stack("_modifyStructure_NEW_SEGMENT_RESIZE() not fixed!" )
print "Params =", params
self.nanotube = params #@
length_diff = self._determine_how_to_change_length() #@
if length_diff == 0:
print_compact_stack("BUG: length_diff is always ZERO." )
return
elif length_diff > 0:
print "Nanotube longer by ", length_diff, ", angstroms."
else:
print "Nanotube shorter by ", length_diff, ", angstroms."
return
if numberOfBasePairsToAddOrRemove != 0: #@@@@ Not reached.
resizeEnd_final_position = self._get_resizeEnd_final_position(
ladderEndAxisAtom,
abs(numberOfBasePairsToAddOrRemove),
nanotubeRise )
self.nanotube.modify(self.struct,
length_diff,
ladderEndAxisAtom.posn(),
resizeEnd_final_position)
#Find new end points of structure parameters after modification
#and set these values in the propMgr.
new_end1 , new_end2 = self.struct.nanotube.getEndPoints() #@
params_to_set_in_propMgr = (new_end1,
new_end2)
#TODO: Need to set these params in the PM
#and then self.previousParams = params_to_set_in_propMgr
self.previousParams = params
return
def _get_resizeEnd_final_position(self,
ladderEndAxisAtom,
numberOfBases,
nanotubeRise):
final_position = None
if self.grabbedHandle:
final_position = self.grabbedHandle.currentPosition
else:
other_axisEndAtom = self.struct.getOtherAxisEndAtom(ladderEndAxisAtom)
axis_vector = ladderEndAxisAtom.posn() - other_axisEndAtom.posn()
segment_length_to_add = 0 #@
final_position = ladderEndAxisAtom.posn() + norm(axis_vector)*segment_length_to_add
return final_position
def getStructureName(self):
"""
Returns the name string of self.struct if there is a valid structure.
Otherwise returns None. This information is used by the name edit field
of this command's PM when we call self.propMgr.show()
@see: EditNanotube_PropertyManager.show()
@see: self.setStructureName
"""
if self.hasValidStructure():
return self.struct.name
return None
def setStructureName(self, name):
"""
Sets the name of self.struct to param <name> (if there is a valid
structure.
The PM of this command callss this method while closing itself
@param name: name of the structure to be set.
@type name: string
@see: EditNanotube_PropertyManager.close()
@see: self.getStructureName()
"""
#@BUG: We call this method in self.propMgr.close(). But propMgr.close()
#is called even when the command is 'cancelled'. That means the
#structure will get changed even when user hits cancel button or
#exits the command by clicking on empty space.
#This should really be done in self._finalizeStructure but that
#method doesn't get called when you click on empty space to exit
#the command. See EditNanotube_GraphicsMode.leftUp for a detailed
#comment.
if self.hasValidStructure():
self.struct.name = name
return
def getCursorText(self):
"""
This is used as a callback method in NanotubeLine mode
@see: NanotubeLineMode.setParams, NanotubeLineMode_GM.Draw
"""
if self.grabbedHandle is None:
return
text = ''
textColor = env.prefs[cursorTextColor_prefs_key]
if not env.prefs[editNanotubeEditCommand_showCursorTextCheckBox_prefs_key]:
return text, textColor
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
nanotubeLength = vlen( currentPosition - fixedEndOfStructure )
nanotubeLengthString = self._getCursorText_length(nanotubeLength)
text = nanotubeLengthString
#@TODO: The following updates the PM as the cursor moves.
#Need to rename this method so that you that it also does more things
#than just to return a textString -- Ninad 2007-12-20
self.propMgr.ntLengthLineEdit.setText(nanotubeLengthString)
return text, textColor
def _getCursorText_length(self, nanotubeLength):
"""
Returns a string that gives the length of the Nanotube for the cursor
text
"""
nanotubeLengthString = ''
if env.prefs[editNanotubeEditCommand_cursorTextCheckBox_length_prefs_key]:
lengthUnitString = 'A'
#change the unit of length to nanometers if the length is > 10A
#fixes part of bug 2856
if nanotubeLength > 10.0:
lengthUnitString = 'nm'
nanotubeLength = nanotubeLength * 0.1
nanotubeLengthString = "%5.3f%s"%(nanotubeLength, lengthUnitString)
return nanotubeLengthString
def modifyStructure(self):
"""
Called when a resize handle is dragged to change the length of the
segment. (Called upon leftUp) . This method assigns the new parameters
for the segment after it is resized and calls
preview_or_finalize_structure which does the rest of the job.
Note that Client should call this public method and should never call
the private method self._modifyStructure. self._modifyStructure is
called only by self.preview_or_finalize_structure
@see: B{EditNanotube_ResizeHandle.on_release} (the caller)
@see: B{SelectChunks_GraphicsMode.leftUp} (which calls the
the relevent method in DragHandler API. )
@see: B{exprs.DraggableHandle_AlongLine}, B{exprs.DragBehavior}
@see: B{self.preview_or_finalize_structure }
@see: B{self._modifyStructure}
As of 2008-02-01 it recreates the structure
@see: a note in self._createStructure() about use of ntSegment.setProps
"""
if not pref_nt_segment_resize_by_recreating_nanotube():
self.modifyStructure_NEW_SEGMENT_RESIZE()
return
if self.grabbedHandle is None:
return
self.propMgr.endPoint1 = self.grabbedHandle.fixedEndOfStructure
self.propMgr.endPoint2 = self.grabbedHandle.currentPosition
#@length = vlen(self.propMgr.endPoint1 - self.propMgr.endPoint2 ) #@
self.preview_or_finalize_structure(previewing = True)
self.updateHandlePositions()
self.glpane.gl_update()
return
def modifyStructure_NEW_SEGMENT_RESIZE(self): #@ NOT FIXED
"""
Called when a resize handle is dragged to change the length of the
segment. (Called upon leftUp) . This method assigns the new parameters
for the segment after it is resized and calls
preview_or_finalize_structure which does the rest of the job.
Note that Client should call this public method and should never call
the private method self._modifyStructure. self._modifyStructure is
called only by self.preview_or_finalize_structure
@see: B{EditNanotube_ResizeHandle.on_release} (the caller)
@see: B{SelectChunks_GraphicsMode.leftUp} (which calls the
the relevent method in DragHandler API. )
@see: B{exprs.DraggableHandle_AlongLine}, B{exprs.DragBehavior}
@see: B{self.preview_or_finalize_structure }
@see: B{self._modifyStructure}
As of 2008-02-01 it recreates the structure
@see: a note in self._createStructure() about use of ntSegment.setProps
"""
#TODO: need to cleanup this and may be use use something like
#self.previousParams = params in the end -- 2008-03-24 (midnight)
#@TODO: - rename this method from modifyStructure_NEW_SEGMENT_RESIZE
#to self.modifyStructure, after more testing
#This method is used for debug prefence:
#'Nanotube Segment: resize without recreating whole duplex'
#see also self._modifyStructure_NEW_SEGMENT_RESIZE
if self.grabbedHandle is None:
return
self.propMgr.endPoint1 = self.grabbedHandle.fixedEndOfStructure
self.propMgr.endPoint2 = self.grabbedHandle.currentPosition
DEBUG_DO_EVERYTHING_INSIDE_MODIFYSTRUCTURE_METHOD = False
if DEBUG_DO_EVERYTHING_INSIDE_MODIFYSTRUCTURE_METHOD:
# TO DO: this entire block of code. --Mark 2008-04-03
print_compact_stack("modifyStructure_NEW_SEGMENT_RESIZE(): NOT FIXED")
length = vlen(self.grabbedHandle.fixedEndOfStructure - \
self.grabbedHandle.currentPosition )
endAtom1, endAtom2 = self.struct.getAxisEndAtoms() #@
for atm in (endAtom1, endAtom2):
if not same_vals(self.grabbedHandle.fixedEndOfStructure, atm.posn()):
ladderEndAxisAtom = atm
break
endPoint1, endPoint2 = self.struct.nanotube.getEndPoints()
old_dulex_length = vlen(endPoint1 - endPoint2)
nanotubeRise = self.struct.getProps() #@
params_to_set_in_propMgr = (
self.grabbedHandle.origin,
self.grabbedHandle.currentPosition,
)
##self._modifyStructure(params)
############################################
self.nanotube = NanotubeParameters() #@ Creates 5x5 CNT. Missing PM params.
length_diff = self._determine_how_to_change_length()
ladderEndAxisAtom = self.get_axisEndAtom_at_resize_end() #@
#@ Nanotube class needs modify() method.
self.nanotube.modify(self.struct,
length_diff,
ladderEndAxisAtom.posn(),
self.grabbedHandle.currentPosition)
#TODO: Important note: How does NE1 know that structure is modified?
#Because number of base pairs parameter in the PropMgr changes as you
#drag the handle . This is done in self.getCursorText() ... not the
#right place to do it. OR that method needs to be renamed to reflect
#this as suggested in that method -- Ninad 2008-03-25
self.preview_or_finalize_structure(previewing = True)
##self.previousParams = params_to_set_in_propMgr
self.glpane.gl_update()
return
def get_axisEndAtom_at_resize_end(self):
ladderEndAxisAtom = None
if self.grabbedHandle is not None:
ladderEndAxisAtom = self.struct.getAxisEndAtomAtPosition(self.grabbedHandle.origin)
else:
endAtom1, endAtom2 = self.struct.getAxisEndAtoms()
ladderEndAxisAtom = endAtom2
return ladderEndAxisAtom
def _determine_how_to_change_length(self): #@ NEEDS WORK
"""
Returns the difference in length between the original nanotube and the
modified nanotube, where:
0 = no change in length
> 0 = lengthen
< 0 = trim
"""
nanotubeRise = self.struct.nanotube.getRise()
endPoint1, endPoint2 = self.struct.nanotube.getEndPoints() #@
original_nanotube_length = vlen(endPoint1 - endPoint2)
new_nanotube_length = vlen(endPoint1 - endPoint2) #@
return new_nanotube_length - original_nanotube_length #@ ALWAYS RETURNS ZERO
def makeMenus(self):
"""
Create context menu for this command.
"""
if not hasattr(self, 'graphicsMode'):
return
selobj = self.glpane.selobj
if selobj is None:
return
self.Menu_spec = []
highlightedChunk = None
if isinstance(selobj, Chunk):
highlightedChunk = selobj
if isinstance(selobj, Atom):
highlightedChunk = selobj.molecule
elif isinstance(selobj, Bond):
chunk1 = selobj.atom1.molecule
chunk2 = selobj.atom2.molecule
if chunk1 is chunk2 and chunk1 is not None:
highlightedChunk = chunk1
if highlightedChunk is None:
return
highlightedChunk.make_glpane_cmenu_items(self.Menu_spec, self)
return
class RotationHandle(DraggableHandle_AlongCircle):
"""
Provides a resize handle for editing the length of an existing DnaSegment.
"""
#Handle color will be changed depending on whether the the handle is grabbed
#So this is a 'State variable and its value is used in 'appearance'
#(given as an optional argument to 'Sphere')
handleColor = State(Color, purple)
if DEBUG_FANCY_HANDLES:
appearance = Overlay(
Sphere(1.2, handleColor, center=ORIGIN + _self.axis * 3 * DX),
Cylinder((ORIGIN, ORIGIN + _self.axis * 2 * DX), 0.5, handleColor))
HHColor = env.prefs[hoverHighlightingColor_prefs_key]
appearance_highlighted = Option(
Drawable,
Overlay(
Sphere(1.2, HHColor, center=ORIGIN + _self.axis * 3 * DX),
Cylinder((ORIGIN, ORIGIN + _self.axis * 2 * DX), 0.5,
HHColor)),
doc="handle appearance when highlighted")
else:
#Appearance of the handle. (note that it uses all the code from exprs module
# and needs more documentation there).
#See exprs.Rect.Sphere for definition of a drawable 'Sphere' object.
appearance1 = Option(Drawable,
Sphere(1.2, handleColor),
doc="handle appearance when not highlighted")
#Handle appearance when highlighted
appearance_highlighted1 = Option(
Drawable,
Sphere(1.2, yellow),
doc="handle appearance when highlighted")
#Stateusbar text. Variable needs to be renamed in superclass.
sbar_text = Option(str,
"Drag the handle to rotate the segment around axis",
doc="Statusbar text on mouseover")
#Command object specified as an 'Option' during instantiation of the class
#see DnaSegment_EditCommand class definition.
command = Option(Action, doc='The Command which instantiates this handle')
def on_press(self):
"""
Actions when handle is pressed (grabbed, during leftDown event)
@see: B{SelectChunks.GraphicsMode.leftDown}
@see: B{DnaSegment_EditCommand.grabbedHandle}
@see: B{DnaSegment_GraphicsMode.Draw} (which uses some attributes of
the current grabbed handle of the command.
@see: B{DragHandle_API}
"""
#Change the handle color when handle is grabbed. See declaration of
#self.handleColor in the class definition.
self.handleColor = env.prefs[selectionColor_prefs_key]
#assign 'self' as the curent grabbed handle of the command.
self.command.grabbedHandle = self
def on_drag(self):
"""
Method called while dragging this handle .
@see: B{DragHandle_API}
"""
#Does nothing at the moment.
pass
def on_release(self):
"""
This method gets called during leftUp (when the handle is released)
@see: B{DnaSegment_EditCommand.modifyStructure}
@see: self.on_press
@see: B{SelectChunks.GraphicsMode.leftUp}
@see: B{DragHandle_API}
"""
self.handleColor = purple
if self.command:
#Clear the grabbed handle attribute (the handle is no longer
#grabbed)
self.command.grabbedHandle = None
class World(InstanceOrExpr
): #070205 revised, public nodelist -> private _nodeset
"""maintains the set of objects in the model; provides general operations on them
"""
#k is this 070401 change ok: ModelObject -> InstanceOrExpr? At least it doesn't seem to have caused trouble.
###e Q: Is it ok for this to inherit _CoordsysHolder and have .draw save the coords? Or to own one of those to hold them?
# The goal is for some external thing to be able to copy the coords we will draw a newly made thing under.
# that's partly misguided given that we might in theory draw things in more than one place
# and/or in a different place than in the prior frame. The external thing that wants to do this
# is self._newobj.copy_saved_coordsys_from( self.world) in class PalletteWell.on_press as of 070401.
# It wants to use the right coordsys to turn a mouseray into that obj's initial position in the World. Hmm.
# A: In principle, if we're drawing the world twice (eg in stereo), we'd better be able to tell from a mouseray
# used to put something into it, which world-instance we're putting it into! and each of those needs to know
# where mouse events would drop things (based on where it was last drawn -- no ambiguity there).
# So it's correct for something to save that and reveal it -- it just needs to be a world-drawn-instance
# which would somehow show up (as selobj?) when interpreting that mouseray. For now, it's ok to kluge this
# by assuming this class is taking the role of world-drawn-instance and being drawn only once. Alternatively,
# we could say that the recipient of the mouseray should also be told what background it's over (whether or not it
# hit the background or some object drawn over it) (this might be "one of several background objects" for stereo)
# so it would know how to find "absolute model coords" in a canonical way. Or a third way is for the World client code
# to include an invisible object drawn just to capture the coords. In the multi-world-drawn-instance case, we'd have to combine
# this object with our knowledge of which worldinstance was drawn, by storing the drawn coords under the crossproduct
# of that and the object...
# ... Trying one of these solutions with self._coordsys_holder below. Seems to work & fix the pallette bug. Comment needs cleanup.
# [070401]
#
###FLAW: logically, this should store exprs needed to remake its instances, merely caching the instances,
# but in fact, stores the instances themselves. This will make save/load harder, and means instances survive code-reloading.
# Probably it should be fixed before trying to do save/load. [070206 comment]
_nodeset = State(
Anything, {}
) # self._nodeset is private; it's changetracked but only when entirely replaced (not just modified!)
# (###e optim: can that be fixed? we need a way to access the LvalForState and inval it)
###e we'll need to put that State on a different state-layer (i.e. kind of StatePlace) when we start saving/loading this
_coordsys_holder = Instance(SavedCoordsys(
)) #070401 -- see long comment above, about _CoordsysHolder
def _init_instance(self):
super(World, self)._init_instance()
set_default_attrs(self.untracked_model_state, _index_counter=4000
) #070213; could State() do this for us instead? #e
def _C_number_of_objects(self):
"""Compute self.number_of_objects, defined as the total number of objects explicitly stored in self,
of all types, in all Parts and configurations (but not including objects removed by Undo but present in Undo history).
WARNING: Parts, configurations, and Undo are nim for this class as of 070206.
Note: probably not very useful, due to that lack of qualification by anything.
Perhaps useful to know whether self is entirely empty,
or as a ballpark estimate of how much data it might contain.
"""
return len(self._nodeset)
def list_all_objects_of_type(self, model_type):
"""Return a nominally read-only list of all objects in self of the given model_type (or IorE class, as a special case),
in a deterministic order not yet decided on (might be creation order, world-index order, MT order).
[Current implem uses creation order as an Instance, as told by _e_serno; this order will become unideal as new kinds of
object ops are added, like potential objs or moving them from other worlds (if possible). ##e 070206]
##e needs options for "not just this config", "not just this Part" (and revised implem, once we support configs or Parts)
#e optim: extend API to be able to specify ordering -- otherwise it has to be sorted twice (here, and often in caller).
"""
type_predicate = model_type_predicate(
model_type
) # this permits model_type to be an IorE subclass (or its name)
###BAD: not enough kinds of type exprs can be passed, and error checking on model_type (not being garbage) is nim
return filter(
type_predicate, self._sorted_objects
) ##e optim: filter first (or keep them already type-separated), then sort
def _append_node(self, index,
node): #070201 new feature ###e SHOULD RENAME [070205]
"not sure if this should be private... API revised 070205, ought to rename it more (and #doc it)"
## self._nodeset = dict(self._nodeset)
## ###KLUGE: copy it first, to make sure it gets change-tracked. Inefficient when long!
###BUG in the above:
# doesn't work, since the change to it is not tracked, since the old and new values compare equal! (guess)
#k note that LvalForState may also not keep a deep enough copy of the old value in doing the compare,
# to not be fooled by the direct modification of the dict (in the sense of that mod escaping its notice, even later)!
# (i'm not sure -- needs review, e.g. about whether bugs of this kind will go undetected and be too hard to catch)
## self._nodeset[index] = node
newset = dict(self._nodeset)
newset[index] = node
self._nodeset = newset # this ought to compare different and cause changetracking (assuming the index was in fact new)
###e OPTIM IDEA: can we modify it, then set it to itself? No, because LvalForState will compare saved & new value --
# the same mutable object! We need to fix that, but a workaround is to set it to None and then set it to itself again.
# That ought to work fine. ####TRYIT but then fix LvalForState so we can tell it we modified its mutable contents. [070228]
return
def _C__sorted_objects(self):
"""compute private self._sorted_objects (a list, ordered by something not yet decided,
probably creation time; probably should be the same order used by list_all_objects_of_type)
"""
res = self._nodeset.values()
res = sorted_by(res, lambda obj: obj._e_serno)
###KLUGE: use _e_serno in place of .creation_order, not yet defined --
# works now, but wrong in general due to potential objects or moved-from-elsewhere objects.
# (Q: Would index-in-world be ordered the same way? A: Yes for now, but not good to require this in the future.)
return res
def draw(self):
# draw all the nodes [#e 070228 ###e in future we're more likely to draw X(node) for X supplied from caller & subset of nodes]
# [optim idea 070103 late: have caller put this in a DisplayListChunk; will it actually work?
# the hope is, yes for animating rotation, with proper inval when nodelist changes. It ought to work! Try it. It works!]
self._coordsys_holder.save_coords_if_safe() #070401
for node in self._sorted_objects:
# print "%r is drawing %r at %r" % (self, node, node.pos) # suspicious: all have same pos ... didn't stay true, nevermind
self.drawkid(node) ## node.draw()
# this assumes the items in the list track their own posns, which might not make perfect sense;
# otoh if they didn't we'd probably replace them with container objs for our view of them, which did track their pos;
# so it doesn't make much difference in our code. we can always have a type "Vertex for us" to coerce them to
# which if necessary adds the pos which only we see -- we'd want this if one Vertex could be in two Worlds at diff posns.
# (Which is likely, due to Configuration Management.)
if 0 and node is self._sorted_objects[-1]:
print "drew last node in list, %r, ipath[0] %r, pos %r" % (
node, node.ipath[0], node.pos)
###e see comment above: "maybe World needs to wrap all it draws with glue to add looks and behavior to it"
return
def make_and_add(
self,
expr,
type=None
): #070206 added type option -- required for now (temporary); semantics not fully defined
"""Make a new model object instance from expr, add it to the world at a local index we choose, and return it.
This is the main public method for making new model objects.
[As a temporary ###KLUGE (070206), the type needs to be passed, for purposes of methods like self.list_all_objects_of_type.
This will no longer be needed once we can reliably infer the type (including supertypes) from the made instance of expr.
But that probably requires altering delegation to specify which attrs to delegate (based on which interface they're part of),
including a new attr for model object type. ###e Even once that's done, the caller may want to pass type-like info, perhaps
"tags" -- e.g. one current caller passes type = "dot" which could not be inferred from expr it passes. ###e Callers may also
want to pass desired relations, like a parent object, for convenience, or to influence details of how we make and index
the new instance. ##e callers will also want to wrap objects with type-nicknames (see code comment for details).
[WARNING: the API may be revised to also return the index. Or, we might store that in object, or store a back-dict here.]
"""
index, node = self._make(expr)
# that picks a unique index (using a counter in transient_state); I think that's ok
# (but its change/usage tracking needs review ####k)
self._append_node(index, node) # revised 070205
if 'model_type_on_object_kluge_070206': ###KLUGE -- store type on object (simulates later inferring it from object)
# update 070213: the right thing to do is probably not this, but to wrap the object itself with a type-nickname
# (before passing it to us), so not only this world (self), but everything that sees it (MT default label, commands/ops,
# selobj checks, etc), can react to its type-nickname.
if type is not None:
# node._i_model_type is defined on all Instances, and node should be one
## if not hasattr(node, '_i_model_type'):
## node._i_model_type = None # this is how much of a kluge it is -- we're not even sure which classes need this attr
if node._i_model_type is not None:
assert node._i_model_type == type, "make_and_add type %r inconsistent with existing type %r on %r" % \
(type, node._i_model_type, node)
node._i_model_type = type
pass
return node
def _make(self, expr): # moved here from demo_drag 070202
"""[private]
Allocate a new index, use it as the localmost component of ipath while making
[or finding?? I THINK NOT ####k] expr,
and return (index, new-expr-instance).
Note that it's up to expr whether to actually make use of the suggested ipath
in the new instance. The case of one instance stored with different indices in World
is not reviewed, and not recommended until it is, but it's up to the caller to
worry about. I don't know it's wrong, just never thought about it and assumed it would not happen
when analyzing the code.
"""
index = None
#e rename? #e move to some superclass
#e worry about lexenv, eg _self in the expr, _this or _my in it... is expr hardcoded or from an arg?
#e revise implem in other ways eg eval vs instantiate
#e default unique index?? (unique in the saved stateplace, not just here)
# (in fact, is reuse of index going to occur from a Command and be a problem? note *we* are acting as command...
#e use in other recent commits that inlined it
if index is None:
# usual case I hope (due to issues mentioned above [maybe here or maybe in demo_drag.py]): allocate one
index = self.untracked_model_state._index_counter
if 'index should be modified [070203]':
# see comments above dated 070203
index = index + 1
self.untracked_model_state._index_counter = index
# 070213 changed implem of _index_counter to make sure it's not change/usage-tracked.
# (Fyi, I don't know whether or not it was before (using State()), in a way that mattered.
# The tracking danger would be that whenever you make any new object,
# the old objects see that the index they used is different
# and think they too need remaking, or something like that! This needs thinking through
# since it probably covers all make-data, not just the index. All make-data is being snapshotted.
# For that matter, things used by "commands" are in general different than things used to recompute.
# Maybe entire commands need to have tracked usage discarded or kept in a new kind of place. #####FIGURE OUT)
#
# Note (language design flaw): to set this attr (using current code),
# you have to refer to it directly in the stateplace,
# rather than using the kind of abbrev that (in Highlightable glname) seems to work for get:
# _index_counter = _self.untracked_model_state._index_counter
# This could possibly be fixed in C_rule_for_formula (not sure), or by making the abbrev in a fancier manner.
# (If you try to set the abbrev, you get
# "AssertionError: subclass [C_rule_for_formula] ... should implement set_for_our_cls".)
#
###BUG: even for get, the abbreviated form (self._index_counter) is not updated when the spelled out form is!!
# See this debug print from when we tried that here:
## print "after set to %r, self._index_counter = %r, self.untracked_model_state._index_counter = %r" % \
## (index, self._index_counter, self.untracked_model_state._index_counter )
## # it prints: after set to 4002, self._index_counter = 4001, self.untracked_model_state._index_counter = 4002
# This is weird, since Highlightable seems to succeed using a similar glname abbrev for get.
# (Unless it doesn't, and I never noticed?? To check, I just added debug code for that -- so far untriggered.)
pass
###e LOGIC ISSUE: should assert the resulting ipath has never been used,
# or have a more fundamental mechanism to guarantee that
env = self.env # maybe wrong, esp re _self
ipath = (index, self.ipath)
return index, env.make(expr,
ipath) # note: does eval before actual make
# ==
def _C_mt_kids(
self): # 070206 experiment related to ModelTreeNodeInterface (sp?)
###e how do we depend on the mt display prefs? note we need to be drawn twice, once in graphics area using .draw
# and once in MT using the mt_* methods, but with independent envs provided! Self.env might have room in attr namespace,
# but it has a single origin. Besides there might be two indep MT views or graphics views -- each of those also needs
# separate envs (of the same kind). But that makes us two instances! I guess we need separate World data obj vs World viewer,
# to handle that! I'm not even sure it makes sense to put the viewing methods in the same object... but maybe it does
# with this concept of partial instantiation [nim], in which we could instantiate the viewing layer(?) (interface??) twice,
# and the data layer just once, letting it (an instance) serve as the expr for instantiating the viewing layer in two places.
# (But this makes it clear that the env would need to be split into separate parts, one for each partially instantiable
# layer -- hopefully these parts would correspond to interfaces (or sets of them), i.e. an interface's attrs would
# have to all be instantiated at the same time, and decls would control which ones were instantiated together in which
# partial-instantiation layers.)
#
# So for now let's pretend self.env can tell us... tho as initial kluge, the global env.prefs (get_pref?) could tell us.
# But even sooner, just pretend we don't care and always show all the kids.
return self._sorted_objects
mt_name = "testmode" #e or maybe something like State(str, "Untitled"), or a stateref # or "Untitled" as it was before 070208
mt_openable = True
## mt_node_id = getattr_Expr( _self, '_e_serno')
mt_node_id = getattr_Expr(
_self, 'ipath'
) #e optim: should intern the ipath ###e move this to IorE? btw redundant w/ def mt_node_id
# 070218 -- by test, using ipath (a bugfix) makes world.open persistent (as hoped/predicted);
# probably doesn't affect open-MT newnode slowness (but now that's fixed in different way in demo_MT)
# ==
def _cmd_Clear(
self
): #070106 experimental naming convention for a "cmd method" -- a command on this object (requiring no args/opts, by default)
if self._nodeset:
# avoid gratuitous change-track by only doing it if it does something (see also _cmd_Clear_nontrivial)
# NOTE: this cond is probably not needed, since (IIRC) LvalForState only invalidates if a same_vals comparison fails. ###k
self._nodeset = {}
return
# related formulae for that command
# (names are related by convention, only used in this file, so far; prototype for wider convention, but not yet well thought through)
_cmd_Clear_nontrivial = not_Expr(
not_Expr(_nodeset)
) #KLUGE: need a more direct boolean coercion (not that it's really needed at all)
# can be used to enable (vs disable) a button or menu item for this command on this object
_cmd_Clear_legal = True # whether giving the command to this object from a script would be an error
_cmd_Clear_tooltip = "clear all objects" # a command button or menu item could use this as its tooltip ###e is this client-specific??
def _cmd_Make(self):
print "world make is nim" ###
_cmd_Make_tooltip = "make something [nim]" ###e when we know the source of what to make, it can also tell us this tooltip
pass # end of class World
class main_ui_layout(DelegatingInstanceOrExpr):
#e rename? is it not only the ui, but the entire app? (selection, files, etc)
#e merge in the App obj from test.py, and the _recent_tests system in some form?
# args (none yet)
# internal state - permanent
###e note: when we reload and remake this instance, we'd prefer it if the world state stayed unchanged (as i presume it does)
# but if the default_tool instance and toolstack state got remade. The lack of the latter has been confusing me
# since changes to ui code aren't working. I think this is a difference between a ui and operations layer (should change)
# vs model data layer (should not change even tho the op methods on it can change). So when I can put these things into layers
# (not only State, but even Instance or attrs within them) and make those sensitive to reload, that will help.
# In the meantime -- if I could kluge Instance and State to take an option to control this
# (like index = exprs_globals.reload_counter)
# it might help.... #####TRYIT SOMETIME, and BE CAREFUL UNTIL I DO.
world = Instance(World())
default_tool = Instance(DefaultToolRun())
# internal state - varying
toolstack = State(list_Expr, [
default_tool
]) # always has at least one tool on it; a stack of Instances not exprs
# maybe the better term for this is something like command & subcommand
current_tool = toolstack[
-1] # last tool on the stack is current; exiting it will pop the stack (Instance not expr)
##e (add a type-assertion (as opposed to type-coercion) primitive, so I can say "this is an Instance" in the code?)
# NOTE: this is not strictly speaking a tool, but ONE RUN of a tool. That might be important enough to rename it for,
# to ToolRun or maybe ActiveTool or RunningTool or ToolInUse or ToolBeingUsed...
# [but note, obj might remain around on history or in Undo stack, even when no longer being used],
# since we also have to deal with Tools in the sense of Tool Run Producers, eg toolbuttons. ###e
# parts of the appearance
registry = find_or_make_global_command_registry(
) ## None ###STUB, will fail --
## AttributeError: 'NoneType' object has no attribute 'command_for_toolname'
toolstack_ref = None ###STUB
toolbar = Instance(
MainToolbar(registry, ["Features", "Build", "Sketch"],
toolstack_ref)) #e arg order?
###e args/opts for what tools to show -- maybe their cmdnames & it loads them from elsewhere
#e add row of tool buttons, and flyout toolbar; use ChoiceRow?? the things should probably look pressed...
# they might need cmenus (find out what the deal is with the cmenus i see in the ui mockup - related to flyouts?
# yes, it's like this: main tools have cmenus with subtools, and if you pick one, main tool and its subtool both look pressed
# I'll need new specialized controls.py classes for these; new super Control for all kinds of controls?? (not sure why...)
propmgr = SimpleColumn(
TextRect(
"(property manager)"), #e possibly to become a tab control tab
DebugPrintAttrs(
current_tool.property_manager
) # must be None if we don't want one visible; otherwise an Instance
###BUG: DebugPrintAttrs shows that it's a spacer -- I guess IorE turns None into one when it instantiates? Make it a false one??
)
mt = SimpleColumn(
TextRect(
"(model tree)"
), #e possibly to become a tab control tab, but only when we're in the left channel
MT_try2(world) #e rename to "Feature Manager" ??
##e soon, MT should be not on whole world but on model or cur. part, a specific obj in the world
)
graphics_area = _self.world
##e ditto for what we show here, except it might not be the exact same object, and it will really be shown in a way
# that depends on both the current display style and the current tool (command & subcommand)
graphics_area_topright_buttons = current_tool.graphics_area_topright_buttons
# overall appearance
delegate = Overlay(
# stuff in the corners -- note, these don't use the corner constants for standalone tests like PM_CORNER
DrawInCorner(corner=UPPER_LEFT)(
SimpleColumn(
toolbar,
#e add tab control
SimpleRow(
If(
current_tool.property_manager, Top(propmgr), None
), #k None?? prob ok now, see demo_MT comment 070302 ###k
Top(mt)
), #e actually we'd then put a splitter & glpane-like-thing...
#e anything just below the propmgr?
)),
DrawInCorner(corner=UPPER_RIGHT)
( ##e of graphics area, not entire screen...
graphics_area_topright_buttons ### WRONG, these should go under the main toolbar area on the right
# (but we don't yet have any 2dwidgets which expand to fill the available space, except DrawInCorner of entire screen)
# (this won't matter once the toolbar is done entirely in Qt, so we don't need to correct it for now)
),
#e other corners? "... an area (view) on the right side
# of the main window for accessing the part library, on-line documentation, etc"
# the main graphics area
#e [this too ought to go under the toolbar and to the right of the propmgr, but that can wait until they're fully in Qt]
graphics_area)
pass