555 lines
20 KiB
Python
555 lines
20 KiB
Python
import pygtk
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import gtk
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import gtk.gdk
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import gtk.glade
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import gnome
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import gnome.ui
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import gobject
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import logger, dataset
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import annotations
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from lib import hypergeom
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class SimpleMenu(gtk.Menu):
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def __init__(self):
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gtk.Menu.__init__(self)
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def add_simple_item(self, title, function, *args):
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item = gtk.MenuItem(title)
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item.connect('activate', function, *args)
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self.append(item)
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item.show()
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class IdListController:
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"""Controller class for the identifier list."""
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def __init__(self, idlist):
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self._idlist = idlist
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# dimname: current_annotation_name
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self._annotation = {}
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# current dimension
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self._dimension = None
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# id, annotation
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self._idstore = gtk.ListStore(gobject.TYPE_STRING,
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gobject.TYPE_STRING,)
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# Annotation tree column
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self._annotation_column = None
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## Set up identifier list
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idlist.set_model(self._idstore)
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renderer = gtk.CellRendererText()
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dim_column = gtk.TreeViewColumn('Identifiers', renderer, text=0)
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idlist.insert_column(dim_column, 0)
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idlist.connect('button-press-event', self._button_pressed)
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## Set up identifier list context menu
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menu = self._menu = SimpleMenu()
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menu.add_simple_item('Import...', self._on_import_list)
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menu.add_simple_item('Export...', self._on_export_list)
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item = gtk.MenuItem('Show annotations')
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menu.append(item)
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item.show()
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self._menu_ann = item
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##
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## Public interface
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##
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def set_dimension(self, dimname):
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"""Set dimension"""
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if dimname == self._dimension:
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return
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self.set_annotation(self._annotation.get(dimname, None))
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if not self._annotation.has_key(dimname):
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self._annotation[dimname] = None
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self._dimension = dimname
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def set_annotation(self, annotation):
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"""Set the displayed annotation to annotation. If annotation is None,
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the annotation column is hidden. Otherwise the annotation column is
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shown and filled with values from the given annotation field."""
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if annotation == None:
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if self._annotation_column != None:
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self._idlist.remove_column(self._annotation_column)
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self._annotation_column = None
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else:
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idlist = [x[0] for x in self._idstore]
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annlist = annotations.get_dim_annotations(self._dimension,
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annotation,
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idlist)
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for i, x in enumerate(self._idstore):
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x[1] = annlist[i]
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if self._annotation_column == None:
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renderer = gtk.CellRendererText()
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col = gtk.TreeViewColumn(annotation, renderer, text=1)
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self._idlist.append_column(col)
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self._annotation_column = col
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self._annotation_column.set_title(annotation)
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self._annotation[self._dimension] = annotation
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def set_selection(self, selection):
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"""Set the selection to be displayed.
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The selection is not stored, the values are copied into the TreeStore"""
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self._idstore.clear()
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# Return if no selection
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if selection == None:
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return
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# Otherwise show selection, possibly with annotations.
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id_list = list(selection[self._dimension])
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idlist = list(selection[self._dimension])
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if self._annotation[self._dimension] != None:
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annlist = annotations.get_dim_annotations(self._dimension,
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self._annotation[self._dimension],
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idlist)
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for id, ann in zip(idlist, annlist):
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self._idstore.append((id, ann))
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else:
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for e in idlist:
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self._idstore.append((e, None))
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##
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## Private interface
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##
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def _update_annotations_menu(self):
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"""Updates the annotations menu with the available annotations for the
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current dim."""
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dim_h = annotations.get_dim_handler(self._dimension)
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if not dim_h:
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self._menu_ann.set_sensitive(False)
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else:
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annotations_menu = gtk.Menu()
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self._menu_ann.set_sensitive(True)
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dh = annotations.get_dim_handler(self._dimension)
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ann_names = dh.get_annotation_names()
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for ann in ann_names:
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item = gtk.MenuItem(ann)
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item.connect('activate', self._on_annotation_activated, ann)
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annotations_menu.append(item)
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item.show()
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self._menu_ann.set_submenu(annotations_menu)
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def import_annotation_file(self):
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"""Pops up a file dialog and ask the user to select the annotation
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file to be loaded. Only one file can be selected. The file is loaded
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into a annotations.AnnotationDictHandler object"""
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dialog = gtk.FileChooserDialog('Load annotations')
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dialog.set_action(gtk.FILE_CHOOSER_ACTION_OPEN)
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dialog.add_buttons(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
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gtk.STOCK_OPEN, gtk.RESPONSE_OK)
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dialog.set_select_multiple(True)
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retval = dialog.run()
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if retval in [gtk.RESPONSE_CANCEL, gtk.RESPONSE_DELETE_EVENT]:
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pass
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elif retval == gtk.RESPONSE_OK:
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for filename in dialog.get_filenames():
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annotations.read_annotations_file(filename)
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else:
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print "unknown; ", retval
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dialog.destroy()
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##
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## GTK Callbacks
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##
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def _popup_menu(self, *rest):
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self._update_annotations_menu()
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self._menu.popup(None, None, None, 0, 0)
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def _on_annotation_activated(self, menuitem, annotation):
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self.set_annotation(annotation)
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def _button_pressed(self, widget, event):
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if event.button == 3:
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self._update_annotations_menu()
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self._menu.popup(None, None, None, event.button, event.time)
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def _on_export_list(self, menuitem):
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print "export stuff"
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def _on_import_list(self, menuitem):
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self.import_annotation_file()
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class SelectionListController:
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def __init__(self, seltree, idlist_controller):
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self._seltree = seltree
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self._sel_stores = {}
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self._detail_cols = []
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self._dimension = None
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self._idlist_controller = idlist_controller
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self._details_on = False
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# Selection column
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renderer = gtk.CellRendererText()
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sel_column = gtk.TreeViewColumn('Selection', renderer, text=0)
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seltree.insert_column(sel_column, 0)
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# Detail columns
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cols = [('In CS', 3), ('All', 4), ('Rank', 5)]
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for name, store_col in cols:
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self._detail_cols.append(gtk.TreeViewColumn(name, renderer, text=store_col))
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# Signals
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seltree.connect('row-activated', self._on_row_activated)
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seltree.connect('cursor-changed', self._on_cursor_changed)
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seltree.connect('button-press-event', self._on_button_pressed)
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seltree.drag_dest_set(gtk.DEST_DEFAULT_ALL,
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[("GTK_TREE_MODEL_ROW", gtk.TARGET_SAME_APP, 7)],
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gtk.gdk.ACTION_LINK)
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seltree.connect('drag-data-received', self._drag_data_received)
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# Selections context menu
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self._seltree_menu = SimpleMenu()
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self._seltree_menu.add_simple_item('Sort by selection',
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self._on_seltree_sort)
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self._seltree_menu.add_simple_item('Show details',
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self._enable_details, True)
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self._seltree_menu.add_simple_item('Hide details',
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self._enable_details, False)
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#
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# Public interface
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#
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def activate(self):
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self._seltree.set_cursor((0,))
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def set_project(self, project):
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"""Dependency injection."""
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self.project = project
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project.add_selection_observer(self)
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def set_dimlist_controller(self, dimlist_controller):
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"""Dependency injection of the dimension list controller."""
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self._dimlist_controller = dimlist_controller
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def set_dimension(self, dim):
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"""Set the current dimension, changing the model of the treeview
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to match dim. After this the current dimension of the identifier list
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is updated."""
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self._ensure_selection_store(dim)
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self._seltree.set_model(self._sel_stores[dim])
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self._idlist_controller.set_dimension(dim)
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self._dimension = dim
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def selection_changed(self, dimname, selection):
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"""Callback function from Project."""
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for dim in selection.dims():
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self._ensure_selection_store(dim)
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store = self._sel_stores[dim]
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if not self._get_current_selection_iter(selection, dim):
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n = len(selection[dim])
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values = (selection.title, selection, dim, n, n, 0)
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store.insert_after(None, None, values)
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else:
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# update size of current selection
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for row in store:
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if row[1]==selection:
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row[3] = row[4] = len(selection[dim])
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path = self._seltree.get_cursor()
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if path and self._sel_stores.has_key(self._dimension):
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it = self._sel_stores[self._dimension].get_iter(path[0])
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sel = self._sel_stores[self._dimension].get_value(it, 1)
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self._idlist_controller.set_selection(sel)
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def add_dataset(self, dataset):
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"""Converts a CategoryDataset to Selection objects and adds it to
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the selection tree. The name of the dataset will be the parent
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node in the tree, and the identifers along the first axis will
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be added as the names of the subselections."""
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dim_name = dataset.get_dim_name(0)
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self._ensure_selection_store(dim_name)
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store = self._sel_stores[dim_name]
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di = self._get_dataset_iter(dataset)
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if not di:
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n_tot = dataset.shape[0]
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selection = self.project.get_selection().get(dim_name)
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ds_idents = dataset.get_identifiers(dim_name)
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n_cs = len(selection.intersection(ds_idents))
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values = (dataset.get_name(), dataset, dim_name, n_cs, n_tot, 2)
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i = store.insert_after(None, None, values)
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for selection in dataset.as_selections():
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n_sel = len(selection[dim_name])
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values = (selection.title, selection, dim_name, 0, n_sel, 0)
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store.insert_after(i, None, values)
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#
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# Private interface
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#
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def _add_selection_store(self, dim):
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"""Add a new gtk.TreeStore for the selections on a dimension."""
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# Create new store
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# Two types of lines, one for CategoryDatasets and one for
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# Selections. The elements are title, link to dataset or selection,
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# name of dimension, num. members in selection, num. in
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# intersection with current selection and the rank of selection.
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store = gtk.TreeStore(gobject.TYPE_STRING,
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gobject.TYPE_PYOBJECT,
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gobject.TYPE_STRING,
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gobject.TYPE_INT,
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gobject.TYPE_INT,
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gobject.TYPE_FLOAT)
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# Set selection store for this dimension
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self._sel_stores[dim] = store
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def _ensure_selection_store(self, dim):
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"""Ensure that the object has a gtk.TreeStore for the given dimension"""
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# Do not overwrite existing stores
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if self._sel_stores.has_key(dim):
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return
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self._add_selection_store(dim)
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def _get_dataset_iter(self, ds):
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"""Returns the iterator to the selection tree row containing a
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given dataset."""
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store = self._sel_stores[ds.get_dim_name(0)]
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i = store.get_iter_first()
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while i:
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if store.get_value(i, 1) == ds:
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return i
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i = store.iter_next(i)
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return None
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def _get_current_selection_iter(self, selection, dimension):
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if not self._sel_stores.has_key(dimension):
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return None
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store = self._sel_stores[dimension]
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i = store.get_iter_first()
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while i:
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if store.get_value(i, 1) == selection:
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if store.get_value(i, 2) == dimension:
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return i
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i = store.iter_next(i)
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return None
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def _sort_selections(self, dataset):
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"""Ranks selections by intersection with current selection.
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Ranks determined by the hypergeometric distribution.
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"""
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dim_name = dataset.get_dim_name(0)
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sel_store = self._sel_stores[dim_name]
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selection_obj = self.project.get_selection()
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current_selection = selection_obj.get(dim_name)
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if current_selection==None: return
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pvals = hypergeom.gene_hypergeo_test(current_selection, dataset)
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for row in sel_store:
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if row[1]==dataset:
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for child in row.iterchildren():
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name = child[0]
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child[3] = pvals[name][0]
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child[4] = pvals[name][1]
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child[5] = pvals[name][2]
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sel_store.set_sort_column_id(5, gtk.SORT_ASCENDING)
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#
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# GTK callbacks
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#
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def _enable_details(self, widget, bool):
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if self._details_on == bool : return
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self._details_on = bool
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if bool==True:
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for col in self._detail_cols:
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self._seltree.insert_column(col, -1)
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else:
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for col in self._detail_cols:
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self._seltree.remove_column(col)
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def _drag_data_received(self, widget, drag_context, x, y,
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selection, info, timestamp):
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treestore, path = selection.tree_get_row_drag_data()
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i = treestore.get_iter(path)
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obj = treestore.get_value(i, 2)
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if isinstance(obj, dataset.CategoryDataset):
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self.add_dataset(obj)
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self._dimlist_controller.set_dimension(obj.get_dim_name(0))
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widget.emit_stop_by_name('drag-data-received')
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def _on_cursor_changed(self, widget):
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"Show the list of identifier strings."
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store = self._sel_stores[self._dimension]
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p = self._seltree.get_cursor()[0]
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i = store.get_iter(p)
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obj = store.get_value(i, 1)
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if isinstance(obj, dataset.Selection):
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self._idlist_controller.set_selection(obj)
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else:
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self._idlist_controller.set_selection(None)
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def _on_row_activated(self, widget, path, column):
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store = self._sel_stores[self._dimension]
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i = store.get_iter(path)
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obj = store.get_value(i, 1)
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if isinstance(obj, dataset.Dataset):
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seltree = self._seltree
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if seltree.row_expanded(path):
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seltree.collapse_row(path)
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else:
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seltree.expand_row(path, True)
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elif isinstance(obj, dataset.Selection):
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self.project.set_selection(self._dimension,
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obj[self._dimension])
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def _on_button_pressed(self, widget, event):
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"""Button press callbak."""
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if event.button == 3:
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self._seltree_menu.popup(None, None, None, event.button, event.time)
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def _on_seltree_sort(self, menuitem):
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"""Sort selection tree if row is category dataset."""
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store = self._sel_stores[self._dimension]
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p = self._seltree.get_cursor()[0]
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i = store.get_iter(p)
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obj = store.get_value(i, 1)
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if isinstance(obj, dataset.CategoryDataset):
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self._sort_selections(obj)
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class DimListController:
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def __init__(self, dimlist, seltree_controller):
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self._current_dim = None
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self._seltree_controller = seltree_controller
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## dimstore is a list of all dimensions in the application
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self.dimstore = gtk.ListStore(gobject.TYPE_STRING)
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# filter for hiding dims prefixed with underscore
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self.dimstore_filter = self.dimstore.filter_new()
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self.dimstore_filter.set_visible_func(self._dimension_filter)
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## The widgets we are controlling
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self.dimlist = dimlist
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## Set up dimensions list
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dimlist.set_model(self.dimstore_filter)
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renderer = gtk.CellRendererText()
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dim_column = gtk.TreeViewColumn('Dimension', renderer, text=0)
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dimlist.insert_column(dim_column, 0)
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# Signals
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dimlist.connect('row-activated', self._dim_row_activated)
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dimlist.connect('cursor-changed', self._dim_cursor_changed)
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dimlist.connect('button-press-event', self._dimlist_button_pressed)
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# Set up dimension context menu
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self._dimlist_menu = SimpleMenu()
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self._dimlist_menu.add_simple_item('Hide', self._on_dim_hide)
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self._dimlist_menu.add_simple_item('Show all', self._on_dim_show)
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##
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## Public interface
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##
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def set_project(self, project):
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"""Dependency injection."""
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self.project = project
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self.dim_names = project.dim_names
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self.update_dims()
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project.add_dataset_observer(self)
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def get_dimension(self, dim):
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"""Returns the iterator to the dimension with the given name, or
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None if not found."""
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i = self.dimstore.get_iter_first()
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while i:
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if self.dimstore.get_value(i, 0) == dim:
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return i
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i = self.dimstore.iter_next(i)
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return None
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def set_dimension(self, dimname):
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"""Sets the current dimension."""
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self._current_dim = dimname
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dim = self.get_dimension(self._current_dim)
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path = self.dimstore.get_path(dim)
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if self.dimlist.get_cursor()[0] != path:
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self.dimlist.set_cursor(self.dimstore.get_path(dim))
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self._seltree_controller.set_dimension(dimname)
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def dataset_changed(self):
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"""Callback function from Project."""
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self.update_dims()
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def update_dims(self):
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"""Update the list of dimensions shown"""
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for dim in self.dim_names:
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if not self.get_dimension(dim):
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self.dimstore.insert_after(None, (dim,))
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#
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# Private interface
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#
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def _dimension_filter(self, store, row):
|
|
"""Filters out dimensions with underscore prefix."""
|
|
visible = False
|
|
name = store.get_value(row, 0)
|
|
if name != None:
|
|
visible = name[0]!="_"
|
|
return visible
|
|
|
|
#
|
|
# GTK Callbacks.
|
|
#
|
|
def _on_dim_hide(self, menuitem):
|
|
"""Menu item callback function which hides underscore prefixed
|
|
dimensions."""
|
|
self.dimstore_filter.refilter()
|
|
self.dimlist.set_model(self.dimstore_filter)
|
|
|
|
def _on_dim_show(self, menuitem):
|
|
"""Menu item callback function that shows underscore prefixed
|
|
dimension names."""
|
|
self.dimlist.set_model(self.dimstore)
|
|
|
|
def _dim_cursor_changed(self, widget):
|
|
cursor = self.dimlist.get_cursor()[0]
|
|
i = self.dimlist.get_model().get_iter(cursor)
|
|
row = self.dimlist.get_model().get_value(i, 0)
|
|
self.set_dimension(row)
|
|
self._seltree_controller.activate()
|
|
|
|
def _dim_row_activated(self, widget, path, column):
|
|
self._seltree_controller.set_dimension(dim)
|
|
|
|
def _dimlist_button_pressed(self, widget, event):
|
|
if event.button == 3:
|
|
self._dimlist_menu.popup(None, None, None, event.button, event.time)
|
|
|