path: root/cad/src/modelTree/TreeModel.py

# Copyright 2004-2008 Nanorex, Inc.  See LICENSE file for details. 
"""
TreeModel.py - tree of nodes and rules for its appearance and behavior,
for use in NE1 model tree

@version: $Id$
@copyright: 2004-2008 Nanorex, Inc.  See LICENSE file for details.

History:

For earlier history, see ModelTree.py.

Bruce 081216 is doing some cleanup and refactoring, including splitting
ModelTree and TreeModel into separate objects with separate classes and
_api classes, and splitting some code into separate files.

TODO:

As of 081218 (just after fixing bug 2948),
there are unexplained bugs in gl_update after MT selection click
(it happens, but the changed selection status is not redrawn;
might be a bug in other code) and non-undoability of MT selection
click (could it be lack of calls to change the selection counter in assy?)

"""

import foundation.env as env
from foundation.Group import Group
from foundation.wiki_help import wiki_help_menuspec_for_object

from model.chunk import Chunk
from model.jigs import Jig
from model.jigs_planes import RectGadget

from modelTree.TreeModel_api import TreeModel_api
from modelTree.mt_statistics import all_attrs_act_as_counters
from modelTree.mt_statistics import mt_accumulate_stats

from operations.ops_select import selection_from_part

from platform_dependent.PlatformDependent import fix_plurals

from utilities import debug_flags
from utilities.GlobalPreferences import pref_show_highlighting_in_MT
from utilities.Log import orangemsg
from utilities.constants import gensym
from utilities.constants import noop
from utilities.debug import print_compact_traceback

from widgets.widget_helpers import RGBf_to_QColor

# ===

class TreeModel(TreeModel_api):
    """
    """
    #bruce 081216 split ModelTree and TreeModel into separate objects

    def __init__(self, modeltree, win):
        self._modeltree = modeltree # only needed for .mt_update and .modelTreeGui
        self.win = win # used often
        self.assy = self.win.assy # review: might not be needed, since set in get_topnodes
        return

    def mt_update(self):
        return self._modeltree.mt_update()

    # == callbacks from self._modeltree.modelTreeGui to help it update the display
    
    def get_topnodes(self):
        self.assy = self.win.assy #k need to save it like this?
        self.assy.tree.name = self.assy.name
            #k is this still desirable, now that we have PartGroup
            # so it's no longer needed for safety?
        self.assy.kluge_patch_toplevel_groups( assert_this_was_not_needed = True)
            # fixes Group subclasses of assy.shelf and assy.tree
        self.tree_node, self.shelf_node = self.assy.tree, self.assy.shelf
        topnodes = [self.assy.tree, self.assy.shelf]
        return topnodes

    def get_nodes_to_highlight(self): #bruce 080507
        """
        Return a dictionary of nodes which should be drawn as highlighted right now.
        (The keys are those nodes, and the values are arbitrary.)
        """
        if not pref_show_highlighting_in_MT():
            return {}
        glpane = self.win.glpane
        nodes_containing_selobj = glpane.get_nodes_containing_selobj()
            # note: can contain duplicate nodes
        topnodes = self.get_topnodes()
            # these happen to be the nodes we consider to be
            # too high in the tree to show highlighted
            # (at least when the highlighting comes from
            #  them containing glpane.selobj -- for mouseover
            #  of these nodes in MT iself, we'd still show them
            #  as highlighted, once that's implemented)
        res = {}
        for node in nodes_containing_selobj:
            if not node in topnodes:
                res[node] = True
        return res
    
    def get_current_part_topnode(self): #bruce 070509 added this to the API
        return self.win.assy.part.topnode
    
    # ===
    
    # methods related to context menu -- menu maker, and handlers for each op
    
    def make_cmenuspec_for_set(self, nodeset, nodeset_whole, optflag):
        """
        #doc... see superclass docstring, and the term "menu_spec"
        """
        # Note: we use nodeset_whole (a subset of nodeset, or equal to it)
        # for operations which might be unsafe on partly-selected "whole nodes"
        # (i.e. unopenable nodes such as DnaStrand).
        # (Doing this on the Group operation is part of fixing bug 2948.)
        # These menu commands need corresponding changes in their cm methods,
        # namely, calling deselect_partly_picked_whole_nodes at the start.
        # All cm_duplicate methods (on individual nodes) also may need to do
        # this if they care about the selection.
        # [bruce 081218]
        
        #e some advice [bruce]: put "display changes" (eg Hide) before "structural changes" (such as Group/Ungroup)...
        #e a context-menu command "duplicate" which produces
        ##a copy of them, with related names and a "sibling" position.
        ##Whereas the menu command called "copy" produces a copy of the selected
        ##things in the system-wide "clipboard" shared by all apps.)

        # I think we might as well remake this every time, for most kinds of menus,
        # so it's easy for it to depend on current state.
        # I really doubt this will be too slow. [bruce 050113]

        if not nodeset:
            #e later we'll add useful menu commands for no nodes,
            # i.e. for a "context menu of the background".
            # In fact, we'll probably remove this special case
            # and instead let each menu command decide whether it applies
            # in this case.
            res = [('Model Tree (nothing selected)',noop,'disabled')]
            #bruce 050505 adding some commands here (cm_delete_clipboard is a just-reported NFR from Mark)
            res.append(( 'Create new empty clipboard item', self.cm_new_clipboard_item ))
            lenshelf = len(self.assy.shelf.MT_kids()) #bruce 081217 use MT_kids
            if lenshelf:
                if lenshelf > 2:
                    text = 'Delete all %d clipboard items' % lenshelf
                else:
                    text = 'Delete all clipboard items'
                res.append(( text, self.cm_delete_clipboard ))
            return res

        res = []

        if len(nodeset_whole) < len(nodeset):
            # alert user to presence of partly-selected items [bruce 081218]
            # (which are not marked as selected on nodes seeable in MT)
            # (review: should we mark them in some other way?)
            #
            # (note about older text,
            #  "deselect %d partly-selected item(s)":
            #  the count is wrong if one partly-selected leaflike group
            #  contains more than one selected node, and nothing explains
            #  the situation well to the user)
            #
            # (about this text: it might be ambiguous whether they're too deep
            #  because of groups being closed, or being leaflike; mitigated
            #  by saying "shown" rather than "visible")
            text = "Deselect %d node(s) too deep to be shown" % \
                   (len(nodeset) - len(nodeset_whole))
            text = fix_plurals(text)
            res.append(( text, self.cm_deselect_partly_selected_items ))
            res.append(None)
            pass
        
        # old comment, not recently reviewed/updated as of 081217:
        # first put in a Hide item, checked or unchecked. But what if the hidden-state is mixed?
        # then there is a need for two menu commands! Or, use the command twice, fully hide then fully unhide -- not so good.
        # Hmm... let's put in Hide (with checkmark meaning "all hidden"), then iff that's not enough, Unhide.
        # So how do we know if a node is hidden -- this is only defined for leaf nodes now!
        # I guess we figure it out... I guess we might as well classify nodeset and its kids.
        # [update, bruce 080108/080306: does "and its kids" refer to members, or MT_kids?
        #  It might be some of each -- we would want to include members present but not shown
        #  in the MT (like the members of DnaGroup or DnaStrand), which are in members but not in
        #  MT_kids, but we might also want to cover "shared members", like DnaStrandChunks,
        #  which *might* be included in both strands and segments for this purpose (in the future;
        #  shared members are NIM now).]
        
        allstats = all_attrs_act_as_counters()
        
        for node in nodeset:
            node_stats = all_attrs_act_as_counters()
            node.apply2all( lambda node1: mt_accumulate_stats( node1, node_stats) )
            allstats += node_stats # totals to allstats

        # Hide command (and sometimes Unhide)
        
        # now can we figure out how much is/could be hidden, etc
        #e (later, modularize this, make assertfails only affect certain menu commands, etc)
        nleafs = allstats.n - allstats.ngroups
        assert nleafs >= 0
        nhidden = allstats.nhidden
        nunhidden = nleafs - nhidden # since only leafs can be hidden
        assert nunhidden >= 0

        # We'll always define a Hide item. Checked means all is hidden (and the command will be unhide);
        # unchecked means not all is hidden (and the command will be hide).
        # First handle degenerate case where there are no leafs selected.
        if nleafs == 0:
            res.append(( 'Hide', noop, 'disabled')) # nothing that can be hidden
        elif nunhidden == 0:
            # all is hidden -- show that, and offer to unhide it all
            ## res.append(( 'Hidden', self.cm_unhide, 'checked'))
            res.append(( 'Unhide', self.cm_unhide)) # will this be better?
            ##e do we want special cases saying "Unhide All", here and below,
            # when all hidden items would be unhidden, or vice versa?
            # (on PartGroup, or in other cases, so detect by comparing counts for sel and tree_node.)
        elif nhidden > 0:
            # some is not hidden, some is hidden -- make this clear & offer both extremes
            ## res.append(( 'Hide (' + fix_plurals('%d item(s)' % nunhidden) + ')', self.cm_hide )) #e fix_plurals bug, worked around
            res.append(( fix_plurals('Unhide %d item(s)' % nhidden), self.cm_unhide ))
            res.append(( fix_plurals('Hide %d item(s)' % nunhidden), self.cm_hide ))
        else:
            # all is unhidden -- just offer to hide it
            res.append(( 'Hide', self.cm_hide ))

        try:
            njigs = allstats.njigs
            if njigs == 1 and allstats.n == 1:
                # exactly one jig selected. Show its disabled state, with option to change this if permitted.
                # warning: depends on details of Jig.is_disabled() implem. Ideally we should ask Jig to contribute
                # this part of the menu-spec itself #e. [bruce 050421]
                jig = nodeset[0]
                if not isinstance(jig, RectGadget): # remove this menu item for RectGadget [Huaicai 10/11/05]
                    disabled_must = jig.disabled_by_atoms() # (by its atoms being in the wrong part)
                    disabled_choice = jig.disabled_by_user_choice
                    disabled_menu_item = disabled_must # menu item is disabled iff jig disabled state can't be changed, ie is "stuck on"
                    checked = disabled_must or disabled_choice # menu item is checked if it's disabled for whatever reason (also affects text)
                    if checked:
                        command = self.cm_enable
                        if disabled_must:
                            text = "Disabled (atoms in other Part)"
                        else:
                            text = "Disabled"
                    else:
                        command = self.cm_disable
                        text = "Disable"
                    res.append(( text, command, checked and 'checked' or None, disabled_menu_item and 'disabled' or None ))
        except:
            print "bug in MT njigs == 1, ignored"
            ## raise # just during devel
            pass

        if nodeset_whole:

            res.append(None) # separator
                # (from here on, only add these at start of optional items
                #  or sets of items)

            # Group command -- only offered for 2 or more subtrees of any Part,
            # or for exactly one clipboard item topnode itself if it's not already a Group.
            # [rules loosened by bruce 050419-050421]

            if optflag or len(nodeset_whole) >= 2:
                # note that these nodes are always in the same Part and can't include its topnode
                ok = True
            else:
                # exactly one node - ok iff it's a clipboard item and not a group
                node = nodeset_whole[0]
                ok = (node.dad is self.shelf_node and not node.is_group())
            if not ok:
                res.append(( 'Group', noop, 'disabled' ))
            else:
                res.append(( 'Group', self.cm_group ))

            # Ungroup command -- only when exactly one picked Group is what we have, of a suitable kind.
            # (As for Group, later this can become more general, tho in this case it might be general
            #  enough already -- it's more "self-contained" than the Group command can be.)

            offered_ungroup = False # modified below; used by other menu items farther below
            
            if len(nodeset_whole) == 1 and nodeset_whole[0].permits_ungrouping():
                # (this implies it's a group, or enough like one)
                node = nodeset_whole[0]
                if not node.members: #bruce 080207
                    #REVIEW: use MT_kids? [same issue in many places in this file, as of 080306]
                    #reply, bruce 081217: not yet; really we need a new Node or Group API method
                    # "offer to remove as empty Group"; meanwhile, be conservative by using .members
                    text = "Remove empty Group"
                elif node.dad == self.shelf_node and len(node.members) > 1:
                    # todo: "Ungroup into %d separate clipboard item(s)"
                    text = "Ungroup into separate clipboard items" #bruce 050419 new feature (distinct text in this case)
                else:
                    # todo: "Ungroup %d item(s)"
                    text = "Ungroup"
                res.append(( text, self.cm_ungroup ))
                offered_ungroup = True
            else:
                # review: is this clear enough for nodes that are internally Groups
                # but for which permits_ungrouping is false, or would some other
                # text be better, or would leaving this item out be better?
                # An old suggestion of "Ungroup (unsupported)" seems bad now,
                # since it might sound like "a desired feature that's nim".
                # [bruce 081212 comment]
                res.append(( "Ungroup", noop, 'disabled' ))

            # Remove all %d empty Groups (which permit ungrouping) [bruce 080207]
            count_holder = [0]
            def func(group, count_holder = count_holder):
                if not group.members and group.permits_ungrouping():
                    count_holder[0] += 1 # UnboundLocalError when this was count += 1
            for node in nodeset_whole:
                node.apply_to_groups(func) # note: this descends into groups that don't permit ungrouping, e.g. DnaStrand
            count = count_holder[0]
            if count == 1 and len(nodeset_whole) == 1 and not nodeset_whole[0].members:
                # this is about the single top selected node,
                # so it's redundant with the Ungroup command above
                # (and if that was not offered, this should not be either)
                pass
            elif count:
                res.append(( 'Remove all %d empty Groups' % count, self.cm_remove_empty_groups ))
                    # lack of fix_plurals seems best here; review when seen
            else:
                pass

            pass
        
        # Edit Properties command -- only provide this when there's exactly one thing to apply it to,
        # and it says it can handle it.
        ###e Command name should depend on what the thing is, e.g. "Part Properties", "Chunk Properties".
        # Need to add methods to return that "user-visible class name".
        res.append(None) # separator

        if debug_flags.atom_debug:
            if len(nodeset) == 1:
                res.append(( "debug._node =", self.cm_set_node ))
            else:
                res.append(( "debug._nodeset =", self.cm_set_node ))
        
        if len(nodeset) == 1 and nodeset[0].editProperties_enabled():
            res.append(( 'Edit Properties...', self.cm_properties ))
        else:
            res.append(( 'Edit Properties...', noop, 'disabled' )) # nim for multiple items
        
        #ninad 070320 - context menu option to edit color of multiple chunks
        if allstats.nchunks:
            res.append(("Edit Chunk Color...", self.cmEditChunkColor))
        if allstats.canShowOverlayText:
            res.append(("Show Overlay Text", self.cmShowOverlayText))
        if allstats.canHideOverlayText:
            res.append(("Hide Overlay Text", self.cmHideOverlayText))

        #bruce 070531 - rename node -- temporary workaround for inability to do this in MT, or, maybe we'll like it to stay
        if len(nodeset) == 1:
            node = nodeset[0]
            if node.rename_enabled():
                res.append(("Rename node...", self.cmRenameNode)) ##k should it be called node or item in this menu text?

        # subsection of menu (not a submenu unless they specify one)
        # for node-class-specific menu items, when exactly one node
        # (old way, based on methodnames that start with __CM;
        #  and new better way, using Node method ModelTree_context_menu_section)
        if len(nodeset) == 1:
            node = nodeset[0]
            submenu = []
            attrs = filter( lambda attr: "__CM_" in attr, dir( node.__class__ )) #e should do in order of superclasses
            attrs.sort() # ok if empty list
            #bruce 050708 -- provide a way for these custom menu items to specify a list of menu_spec options (e.g. 'disabled') --
            # they should define a method with the same name + "__options" and have it return a list of options, e.g. ['disabled'],
            # or [] if it doesn't want to provide any options. It will be called again every time the context menu is shown.
            # If it wants to remove the menu item entirely, it can return the special value (not a list) 'remove'.
            opts = {}
            for attr in attrs: # pass 1 - record menu options for certain commands
                if attr.endswith("__options"):
                    boundmethod = getattr( node, attr)
                    try:
                        lis = boundmethod()
                        assert type(lis) == type([]) or lis == 'remove'
                        opts[attr] = lis # for use in pass 2
                    except:
                        print_compact_traceback("exception ignored in %r.%s(): " % (node, attr))
                        pass
            for attr in attrs: # pass 2
                if attr.endswith("__options"):
                    continue
                classname, menutext = attr.split("__CM_",1)
                boundmethod = getattr( node, attr)
                if callable(boundmethod):
                    lis = opts.get(attr + "__options") or []
                    if lis != 'remove':
                        mitem = tuple([menutext.replace('_',' '), boundmethod] + lis)
                        submenu.append(mitem)
                elif boundmethod is None:
                    # kluge: None means remove any existing menu items (before the submenu) with this menutext!
                    res = filter( lambda text_cmd: text_cmd and text_cmd[0] != menutext, res ) # text_cmd might be None
                    while res and res[0] == None:
                        res = res[1:]
                    #e should also remove adjacent Nones inside res
                else:
                    assert 0, "not a callable or None: %r" % boundmethod
            if submenu:
                ## res.append(( 'other', submenu )) #e improve submenu name, ordering, location
                res.extend(submenu) # changed append to extend -- Mark and Bruce at Retreat 050621
            
            # new system, used in addition to __CM above (preferred in new code):
            # [bruce 080225]
            try:
                submenu = node.ModelTree_context_menu_section()
                assert submenu is not None # catch a likely possible error specifically
                assert type(submenu) is type([]) # it should be a menu_spec list
            except:
                print_compact_traceback("exception ignored in %r.%s() " \
                                        "or in checking its result: " % \
                                        (node, 'ModelTree_context_menu_section'))
                submenu = []
            if submenu:
                res.extend(submenu)
            pass            

        if nodeset_whole:
            # copy, cut, delete, maybe duplicate...
            # bruce 050704 revisions:
            # - these are probably ok for clipboard items; I'll enable them there and let them be tested there.
            # - I'll remove Copy when the selection only contains jigs that won't copy themselves
            #   unless some of their atoms are copied (which for now is true of all jigs).
            #   More generally (in principle -- the implem is not general), Copy should be removed
            #   when the selection contains nothing which makes sense to copy on its own,
            #   only things which make sense to copy only in conjunction with other things.
            #   I think this is equivalent to whether all the selected things would fail to get copied,
            #   when the copy command was run.
            # - I'll add Duplicate for single selected jigs which provide an appropriate method,
            #   and show it dimmed for those that don't.
            
            res.append(None) # separator

            # figure out whether Copy would actually copy anything.
            part = nodeset_whole[0].part # the same for all nodes in nodeset_whole
            sel = selection_from_part(part, use_selatoms = False) #k should this be the first code to use selection_from_MT() instead?
            doit = False
            for node in nodeset_whole:
                if node.will_copy_if_selected(sel, False):
                    #wware 060329 added realCopy arg, False here (this is not a real copy, so do not issue a warning).
                    #bruce 060329 points out about realCopy being False vs True that at this point in the code we don't
                    # yet know whether the real copy will be made, and when we do, will_copy_if_selected
                    # might like to be re-called with True, but that's presently nim. ###@@@
                    # 
                    # if this test is too slow, could inline it by knowing about Jigs here; but better to speed it up instead!
                    doit = True
                    break
            if doit:
                res.append(( 'Copy', self.cm_copy ))
            # For single items, add a Duplicate command and enable it if they support the method. [bruce 050704 new feature]
            # For now, hardly anything offers this command, so I'm changing the plan, and removing it (not disabling it)
            # when not available. This should be reconsidered if more things offer it.
            if len(nodeset_whole) == 1:
                node = nodeset_whole[0]
                try:
                    method = node.cm_duplicate
                        # Warning 1: different API than self.cm_xxx methods (arg differs)
                        # or __CM_ methods (disabled rather than missing, if not defined).
                        # Warning 2: if a class provides it, no way for a subclass to stop
                        # providing it. This aspect of the API is bad, should be revised.
                        # Warning 3: consider whether each implem of this needs to call
                        # self.deselect_partly_picked_whole_nodes().
                    assert callable(method)
                except:
                    dupok = False
                else:
                    dupok = True
                if dupok:
                    res.append(( 'Duplicate', method ))
                else:
                    pass ## res.append(( 'Duplicate', noop, 'disabled' ))
            # Cut (unlike Copy), and Delete, should always be ok.
            res.append(( 'Cut', self.cm_cut ))
            res.append(( 'Delete', self.cm_delete ))
        
        #ninad060816 added option to select all atoms of the selected chunks. 
        #I don't know how to handle a case when a whole group is selected.
        #So putting a condition allstats.nchunks == allstats.n.
        #Perhaps, I should unpick the groups while picking atoms?
        if allstats.nchunks == allstats.n and allstats.nchunks : 
            res.append((fix_plurals("Select all atoms of %d chunk(s)" %
                                    allstats.nchunks),
                        self.cmSelectAllAtomsInChunk))
        
        # add basic info on what's selected at the end
        # (later might turn into commands related to subclasses of nodes)

        if allstats.nchunks + allstats.njigs:
            # otherwise, nothing we can yet print stats on... (e.g. clipboard)

            res.append(None) # separator

            res.append(( "selection:", noop, 'disabled' ))
                        
            if allstats.nchunks:
                res.append(( fix_plurals("%d chunk(s)" % allstats.nchunks), noop, 'disabled' ))
            
            if allstats.njigs:
                res.append(( fix_plurals("%d jig(s)" % allstats.njigs), noop, 'disabled' ))
            
            if allstats.nhidden:
                res.append(( "(%d of these are hidden)" % allstats.nhidden, noop, 'disabled' ))

            if allstats.njigs == allstats.n and allstats.njigs:
                # only jigs are selected -- offer to select their atoms [bruce 050504]
                # (text searches for this code might like to find "Select this jig's" or "Select these jigs'")
                want_select_item = True #bruce 051208
                if allstats.njigs == 1:
                    jig = nodeset[0]
                    if isinstance(jig, RectGadget): # remove menu item for RectGadget [Huaicai 10/11/05]
                        ## return res  -- this 'return' was causing bug 1189 by skipping the rest of the menu, not just this item.
                        # Try to do something less drastic. [bruce 051208]
                        want_select_item = False
                    else:
                        natoms = len(nodeset[0].atoms)
                        myatoms = fix_plurals( "this jig's %d atom(s)" % natoms )
                else:
                    myatoms = "these jigs' atoms"
                if want_select_item:
                    res.append(('Select ' + myatoms, self.cm_select_jigs_atoms ))

##        ##e following msg is not true, since nodeset doesn't include selection under selected groups!
##        # need to replace it with a better breakdown of what's selected,
##        # incl how much under selected groups is selected. Maybe we'll add a list of major types
##        # of selected things, as submenus, lower down (with commands like "select only these", "deselect these").
##        
##        res.append(( fix_plurals("(%d selected item(s))" % len(nodeset)), noop, 'disabled' ))

        # for single items that have a featurename, add wiki-help command [bruce 051201]
        if len(nodeset) == 1:
            node = nodeset[0]
            ms = wiki_help_menuspec_for_object(node) # will be [] if this node should have no wiki help menu items
                #review: will this func ever need to know which widget is asking?
            if ms:
                res.append(None) # separator
                res.extend(ms)

        return res # from make_cmenuspec_for_set

    # Context menu handler functions [bruce 050112 renamed them; e.g. old name "hide" overrode a method of QWidget!]
    #
    # Note: these must do their own updates (win_update, gl_update, mt_update) as needed.

    def cm_deselect_partly_selected_items(self): #bruce 081218
        # todo: call statusbar_message in modeltreegui
        self.deselect_partly_picked_whole_nodes()
        self.win.win_update()
        
    def cm_hide(self):
        env.history.message("Hide: %d selected items or groups" % \
                            len(self.topmost_selected_nodes()))
        #bruce 050517/081216 comment: doing self.assy.permit_pick_parts() here
        # (by me, unknown when or why) caused bug 500; removing it seems ok.
        self.assy.Hide() # includes win_update
        
    def cm_unhide(self):
        env.history.message("Unhide: %d selected items or groups" % \
                            len(self.topmost_selected_nodes()))
        ## self.assy.permit_pick_parts() #e should not be needed here [see same comment above]
        self.assy.Unhide() # includes win_update

    def cm_set_node(self): #bruce 050604, for debugging
        import utilities.debug as debug
        nodeset = self.topmost_selected_nodes()
        if len(nodeset) == 1:
            debug._node = nodeset[0]
            print "set debug._node to", debug._node
        else:
            debug._nodeset = nodeset
            print "set debug._nodeset to list of %d items" % len(debug._nodeset)
        return
    
    def cm_properties(self):
        nodeset = self.topmost_selected_nodes()
        if len(nodeset) != 1:
            env.history.message("error: cm_properties called on no or multiple items")
                # (internal error, not user error)
        else:
            node = nodeset[0]
            #UM 20080730: if its a protein chunk, enter build protein mode
            # (REVIEW: shouldn't this special case be done inside Chunk.edit instead? [bruce 090106 comment])
            if hasattr(node, 'isProteinChunk') and node.isProteinChunk():
                res = node.protein.edit(self.win)
            else:
                res = node.edit()
            if res:
                env.history.message(res) # added by bruce 050121 for error messages
            else:
                self.win.win_update()
        return

    def cm_group(self): # bruce 050126 adding comments and changing behavior; 050420 permitting exactly one subtree
        """
        put the selected subtrees (one or more than one) into a new Group (and update)
        """
        ##e I wonder if option/alt/middleButton should be like a "force" or "power" flag
        # for cmenus; in this case, it would let this work even for a single element,
        # making a 1-item group. That idea can wait. [bruce 050126]
        #bruce 050420 making this work inside clipboard items too
        # TEST if assy.part updated in time ####@@@@ -- no, change to selgroup!
        self.deselect_partly_picked_whole_nodes()
        sg = self.assy.current_selgroup()
        node = sg.hindmost() # smallest nodetree containing all picked nodes 
        if not node:
            env.history.message("nothing selected to Group") # should never happen
            return
        if node.picked:
            #bruce 050420: permit this case whenever possible (formation of 1-item group);
            # cmenu constructor should disable or leave out the menu command when desired.
            if node != sg:
                assert node.dad # in fact, it'll be part of the same sg subtree (perhaps equal to sg)
                node = node.dad
                assert not node.picked
                # fall through -- general case below can handle this.
            else:
                # the picked item is the topnode of a selection group.
                # If it's the main part, we could make a new group inside it
                # containing all its children (0 or more). This can't happen yet
                # so I'll be lazy and save it for later.
                assert node != self.assy.tree
                # Otherwise it's a clipboard item. Let the Part take care of it
                # since it needs to patch up its topnode, choose the right name,
                # preserve its view attributes, etc.
                assert node.part.topnode == node
                newtop = node.part.create_new_toplevel_group()
                env.history.message("made new group %s" % newtop.name) ###k see if this looks ok with autogenerated name
                self.mt_update()
                return
        # (above 'if' might change node and then fall through to here)
        # node is an unpicked Group inside (or equal to) sg;
        # more than one of its children (or exactly one if we fell through from the node.picked case above)
        # are either picked or contain something picked (but maybe none of them are directly picked).
        # We'll make a new Group inside node, just before the first child containing
        # anything picked, and move all picked subtrees into it (preserving their order;
        # but losing their structure in terms of unpicked groups that contain some of them).
        ###e what do we do with the picked state of things we move? worry about the invariant! ####@@@@

        # make a new Group (inside node, same assy)
        ###e future: require all assys the same, or, do this once per topnode or assy-node.
        # for now: this will have bugs when done across topnodes!
        # so the caller doesn't let that happen, for now. [050126]
        new = Group(gensym("Group", node.assy), node.assy, node) # was self.assy
        assert not new.picked

        # put it where we want it -- before the first node member-tree with anything picked in it
        for m in node.members:
            if m.haspicked():
                assert m != new
                ## node.delmember(new) #e (addsibling ought to do this for us...) [now it does]
                m.addsibling(new, before = True)
                break # (this always happens, since something was picked under node)
        node.apply2picked(lambda(x): x.moveto(new))
            # this will have skipped new before moving anything picked into it!
            # even so, I'd feel better if it unpicked them before moving them...
            # but I guess it doesn't. for now, just see if it works this way... seems to work.
            # ... later [050316], it evidently does unpick them, or maybe delmember does.
        msg = fix_plurals("grouped %d item(s) into " % len(new.members)) + "%s" % new.name
        env.history.message( msg)

        # now, should we pick the new group so that glpane picked state has not changed?
        # or not, and then make sure to redraw as well? hmm...
        # - possibility 1: try picking the group, then see if anyone complains.
        # Caveat: future changes might cause glpane redraw to occur anyway, defeating the speed-purpose of this...
        # and as a UI feature I'm not sure what's better.
        # - possibility 2: don't pick it, do update glpane. This is consistent with Ungroup (for now)
        # and most other commands, so I'll do it.
        #
        # BTW, the prior code didn't pick the group
        # and orginally didn't unpick the members but now does, so it had a bug (failure to update
        # glpane to show new picked state), whose bug number I forget, which this should fix.
        # [bruce 050316]
        ## new.pick() # this will emit an undesirable history message... fix that?
        self.win.glpane.gl_update() #k needed? (e.g. for selection change? not sure.)
        self.mt_update()
        return
    
    def cm_ungroup(self):
        self.deselect_partly_picked_whole_nodes()
        nodeset = self.topmost_selected_nodes()
        assert len(nodeset) == 1 # caller guarantees this
        node = nodeset[0]
        assert node.permits_ungrouping() # ditto
        need_update_parts = []
        pickme = None
        if node.is_top_of_selection_group():
            # this case is harder, since dissolving this node causes its members to become
            # new selection groups. Whether there's one or more members, Part structure needs fixing;
            # if more than one, interpart bonds need breaking (or in future might keep some subsets of
            # members together; more likely we'd have a different command for that).
            # simplest fix -- just make sure to update the part structure when you're done.
            # [bruce 050316]
            need_update_parts.append( node.assy)
            #bruce 050419 comment: if exactly one child, might as well retain the same Part... does this matter?
            # Want to retain its name (if group name was automade)? think about this a bit before doing it...
            # maybe fixing bugs for >1 child case will also cover this case. ###e
            #bruce 050420 addendum: I did some things in Part.__init__ which might handle all this well enough. We'll see. ###@@@ #k
            #bruce 050528 addendum: it's not handled well enough, so try this: hmm, it's not enough! try adding pickme too... ###@@@
            if len(node.members) == 1 and node.part.topnode is node:
                node.part.topnode = pickme = node.members[0]
        if node.is_top_of_selection_group() and len(node.members) > 1:
            msg = "splitting %r into %d new clipboard items" % (node.name, len(node.members))
        else:
            msg = fix_plurals("ungrouping %d item(s) from " % len(node.members)) + "%s" % node.name
        env.history.message( msg)
        node.ungroup()
        # this also unpicks the nodes... is that good? Not really, it'd be nice to see who they were,
        # and to be consistent with Group command, and to avoid a glpane redraw.
        # But it's some work to make it pick them now, so for now I'll leave it like that.
        # BTW, if this group is a clipboard item and has >1 member, we couldn't pick all the members anyway!
        #bruce 050528 addendum: we can do it in this case, temporarily, just to get selgroup changed:
        if pickme is not None:
            pickme.pick() # just to change selgroup (too lazy to look up the official way to only do that)
            pickme.unpick() # then make it look the same as for all other "ungroup" ops
        #e history.message?
        for assy in need_update_parts:
            assy.update_parts() # this should break new inter-part bonds
        self.win.glpane.gl_update() #k needed? (e.g. for selection change? not sure. Needed if inter-part bonds break!)
        self.mt_update()
        return

    def cm_remove_empty_groups(self): #bruce 080207
        self.deselect_partly_picked_whole_nodes()
        nodeset = self.topmost_selected_nodes()
        empties = []
        def func(group):
            if not group.members and group.permits_ungrouping():
                empties.append(group)
        for node in nodeset:
            node.apply_to_groups(func)
        for group in empties:
            group.kill()
        msg = fix_plurals("removed %d empty Group(s)" % len(empties))
        env.history.message( msg)
        self.mt_update()
        return
    
    # copy and cut and delete are doable by tool buttons
    # so they might as well be available from here as well;
    # anyway I tried to fix or mitigate their bugs [bruce 050131]:
    
    def cm_copy(self):
        self.deselect_partly_picked_whole_nodes()
        self.assy.copy_sel(use_selatoms = False) # does win_update
    
    def cm_cut(self):
        self.deselect_partly_picked_whole_nodes()
        self.assy.cut_sel(use_selatoms = False) # does win_update
    
    def cm_delete(self): # renamed from cm_kill which was renamed from kill
        self.deselect_partly_picked_whole_nodes()
        # note: after this point, this is now the same code as MWsemantics.killDo. [bruce 050131]
        self.assy.delete_sel(use_selatoms = False) #bruce 050505 don't touch atoms, to fix bug (reported yesterday in checkin mail)
        ##bruce 050427 moved win_update into delete_sel as part of fixing bug 566
        ##self.win.win_update()
        
    def cmSelectAllAtomsInChunk(self): #Ninad060816
        """
        Selects all the atoms preseent in the selected chunk(s)
        """
        nodeset = self.topmost_selected_nodes()
        self.assy.part.permit_pick_atoms()
        for m in nodeset:
            for a in m.atoms.itervalues():
                a.pick()
        self.win.win_update()
    
    def cmEditChunkColor(self): #Ninad 070321
        """
        Edit the color of the selected chunks using the Model Tree context menu
        """        
        nodeset = self.topmost_selected_nodes()
        chunkList = []
        #Find the chunks in the selection and store them temporarily
        for m in nodeset:
            if isinstance(m, Chunk):
                chunkList.append(m)
        #Following selects the current color of the chunk 
        #in the QColor dialog. If multiple chunks are selected, 
        #it simply sets the selected color in the dialog as 'white'
        if len(chunkList) == 1:
            m = chunkList[0]            
            if m.color:
                m_QColor =  RGBf_to_QColor(m.color)
            else:
                m_QColor = None
               
            self.win.dispObjectColor(initialColor = m_QColor)
        else:         
            self.win.dispObjectColor()

    def cmShowOverlayText(self):
        """
        Context menu entry for chunks.  Turns on the showOverlayText
        flag in each chunk which has overlayText in some of its atoms.
        """
        nodeset = self.topmost_selected_nodes()
        for m in nodeset:
            if isinstance(m, Chunk):
                m.showOverlayText = True

    def cmHideOverlayText(self):
        """
        Context menu entry for chunks.  Turns off the showOverlayText
        flag in each chunk which has overlayText in some of its atoms.
        """
        nodeset = self.topmost_selected_nodes()
        for m in nodeset:
            if isinstance(m, Chunk):
                m.showOverlayText = False
        

    def cmRenameNode(self): #bruce 070531
        """
        Put up a dialog to let the user rename the selected node. (Only one node for now.)
        """
        nodeset = self.topmost_selected_nodes()
        assert len(nodeset) == 1 # caller guarantees this
        node = nodeset[0]
        self._modeltree.modelTreeGui.rename_node_using_dialog( node) # note: this checks node.rename_enabled() first
        return
    
    def cm_disable(self): #bruce 050421
        nodeset = self.topmost_selected_nodes()
        assert len(nodeset) == 1 # caller guarantees this
        node = nodeset[0]
        jig = node # caller guarantees this is a jig; if not, this silently has no effect
        jig.set_disabled_by_user_choice( True) # use Node method as part of fixing bug 593 [bruce 050505]
        self.win.win_update()

    def cm_enable(self): #bruce 050421
        nodeset = self.topmost_selected_nodes()
        assert len(nodeset) == 1, "len nodeset should be 1, but nodeset is %r" % nodeset
        node = nodeset[0]
        jig = node
        jig.set_disabled_by_user_choice( False)
        self.win.win_update()

    def cm_select_jigs_atoms(self): #bruce 050504
        nodeset = self.topmost_selected_nodes()
        otherpart = {} #bruce 050505 to fix bug 589
        did_these = {}
        nprior = len(self.assy.selatoms)
        for jig in nodeset:
            assert isinstance( jig, Jig) # caller guarantees they are all jigs
            # If we didn't want to desel the jig, I'd have to say:
                # note: this does not deselect the jig (good); and permit_pick_atoms would deselect it (bad);
                # so to keep things straight (not sure this is actually needed except to avoid a debug message),
                # just set SELWHAT_ATOMS here; this is legal because no chunks are selected. Actually, bugs might occur
                # in which that's not true... I forget whether I fixed those recently or only analyzed them (due to delays
                # in update event posting vs processing)... but even if they can occur, it's not high-priority to fix them,
                # esp since selection rules might get revised soon.
                ## self.assy.set_selwhat(SELWHAT_ATOMS)
            # but (I forgot when I wrote that) we *do* desel the jig,
            # so instead I can just say:
            self.assy.part.permit_pick_atoms() # changes selwhat and deselects all chunks, jigs, and groups
            # [bruce 050519 8pm]
            for atm in jig.atoms:
                if atm.molecule.part == jig.part:
                    atm.pick()
                    did_these[atm.key] = atm
                else:
                    otherpart[atm.key] = atm
            ## jig.unpick() # not done by picking atoms [no longer needed since done by permit_pick_atoms]
        msg = fix_plurals("Selected %d atom(s)" % len(did_these)) # might be 0, that's ok
        if nprior: #bruce 050519
            #e msg should distinguish between atoms already selected and also selected again just now,
            # vs already and not now; for now, instead, we just try to be ambiguous about that
            msg += fix_plurals(" (%d atom(s) remain selected from before)" % nprior)
        if otherpart:
            msg += fix_plurals(" (skipped %d atom(s) which were not in this Part)" % len(otherpart))
            msg = orangemsg(msg) # the whole thing, I guess
        env.history.message(msg)
        self.win.win_update()
        # note: caller (which puts up context menu) does
        # self.win.update_select_mode(); we depend on that. [### still true??]
        return

    def cm_new_clipboard_item(self): #bruce 050505
        name = self.assy.name_autogrouped_nodes_for_clipboard( [] ) # will this end up being the part name too? not sure... ###k
        self.assy.shelf.addchild( Group(name, self.assy, None) )
        self.assy.update_parts()
        self.mt_update()

    def cm_delete_clipboard(self): #bruce 050505; docstring added 050602
        """
        Delete all clipboard items
        """
        ###e get confirmation from user?
        for node in self.assy.shelf.MT_kids()[:]: #bruce 081217 use MT_kids
            node.kill() # will this be safe even if one of these is presently displayed? ###k
        self.mt_update()
    
    pass # end of class TreeModel

# end