import pygtk import gtk import gtk.gdk import gtk.glade import gnome import gnome.ui import gobject import scipy import logger, dataset, main import annotations from lib import hypergeom class SimpleMenu(gtk.Menu): def __init__(self): gtk.Menu.__init__(self) def add_simple_item(self, title, function, *args): item = gtk.MenuItem(title) item.connect('activate', function, *args) self.append(item) item.show() class IdListController: """Controller class for the identifier list.""" def __init__(self, idlist): self._idlist = idlist self._idlist.get_selection().set_mode(gtk.SELECTION_MULTIPLE) self._idlist.set_rubber_banding(True) # dimname: current_annotation_name self._annotation = {} # current dimension self._dimension = None # id, annotation self._idstore = gtk.ListStore(gobject.TYPE_STRING, gobject.TYPE_STRING) self._idstore.set_sort_func(0, self._numeric_compare) # Annotation tree column self._annotation_column = None ## Set up identifier list idlist.set_model(self._idstore) renderer = gtk.CellRendererText() dim_column = gtk.TreeViewColumn('Identifiers', renderer, text=0) dim_column.set_sort_indicator(True) dim_column.set_sort_column_id(0) dim_column.set_sort_order(gtk.SORT_ASCENDING) idlist.insert_column(dim_column, 0) idlist.connect('button-press-event', self._button_pressed) ## Enable dropping idlist.drag_dest_set(gtk.DEST_DEFAULT_ALL, [("GTK_TREE_MODEL_ROW", gtk.TARGET_SAME_APP, 7)], gtk.gdk.ACTION_LINK) idlist.connect('drag-data-received', self._drag_data_received) ## Set up identifier list context menu menu = self._menu = SimpleMenu() menu.add_simple_item('Import...', self._on_import_list) menu.add_simple_item('Export...', self._on_export_list) menu.add_simple_item('Add to selection', self._on_make_selection) item = gtk.MenuItem('Show annotations') menu.append(item) item.show() self._menu_ann = item ## ## Public interface ## def set_dimension(self, dimname): """Set dimension""" if dimname == self._dimension: return self._dimension = dimname self.set_annotation(self._annotation.get(dimname, None)) if not self._annotation.has_key(dimname): self._annotation[dimname] = None def set_annotation(self, annotation): """Set the displayed annotation to annotation. If annotation is None, the annotation column is hidden. Otherwise the annotation column is shown and filled with values from the given annotation field.""" if annotation == None: if self._annotation_column != None: self._idlist.remove_column(self._annotation_column) self._annotation_column = None else: idlist = [x[0] for x in self._idstore] annlist = annotations.get_dim_annotations(self._dimension, annotation, idlist) for i, x in enumerate(self._idstore): x[1] = annlist[i] if self._annotation_column == None: renderer = gtk.CellRendererText() col = gtk.TreeViewColumn(annotation, renderer, text=1) col.set_sort_indicator(True) col.set_sort_column_id(1) col.set_sort_order(gtk.SORT_ASCENDING) self._idlist.append_column(col) self._annotation_column = col self._annotation_column.set_title(annotation) self._annotation[self._dimension] = annotation def set_selection(self, selection): """Set the selection to be displayed. The selection is not stored, the values are copied into the TreeStore""" self._idstore.clear() # Return if no selection if selection == None: return # Otherwise show selection, possibly with annotations. #id_list = list(selection[self._dimension]) idlist = list(selection[self._dimension]) if self._annotation[self._dimension] != None: annlist = annotations.get_dim_annotations(self._dimension, self._annotation[self._dimension], idlist) for id, ann in zip(idlist, annlist): self._idstore.append((id, ann)) else: for e in idlist: self._idstore.append((e, None)) ## ## Private interface ## def _update_annotations_menu(self): """Updates the annotations menu with the available annotations for the current dim.""" dim_h = annotations.get_dim_handler(self._dimension) if not dim_h: self._menu_ann.set_sensitive(False) else: annotations_menu = gtk.Menu() self._menu_ann.set_sensitive(True) dh = annotations.get_dim_handler(self._dimension) ann_names = dh.get_annotation_names() for ann in ann_names: item = gtk.MenuItem(ann) item.connect('activate', self._on_annotation_activated, ann) annotations_menu.append(item) item.show() self._menu_ann.set_submenu(annotations_menu) def import_annotation_file(self): """Pops up a file dialog and ask the user to select the annotation file to be loaded. Only one file can be selected. The file is loaded into a annotations.AnnotationDictHandler object""" dialog = gtk.FileChooserDialog('Load annotations') dialog.set_action(gtk.FILE_CHOOSER_ACTION_OPEN) dialog.add_buttons(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_OPEN, gtk.RESPONSE_OK) dialog.set_select_multiple(True) dialog.set_current_folder(main.project.anndir) retval = dialog.run() if retval in [gtk.RESPONSE_CANCEL, gtk.RESPONSE_DELETE_EVENT]: pass elif retval == gtk.RESPONSE_OK: for filename in dialog.get_filenames(): annotations.read_annotations_file(filename) else: print "unknown; ", retval dialog.destroy() def export_annotations(self): """Pops up a file dialog and ask the user to select a file to save the currently displayed annotations to. """ dialog = gtk.FileChooserDialog('Load annotations') dialog.set_current_folder(main.project.exportdir) dialog.set_action(gtk.FILE_CHOOSER_ACTION_SAVE) dialog.add_buttons(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_SAVE, gtk.RESPONSE_OK) retval = dialog.run() if retval in [gtk.RESPONSE_CANCEL, gtk.RESPONSE_DELETE_EVENT]: pass elif retval == gtk.RESPONSE_OK: filename = dialog.get_filename() fd = open(filename, 'w') dim = self._dimension print >> fd, "%s\t%s" % (dim, self._annotation[dim]) for id, value in self._idstore: print >> fd, "%s\t%s" % (id, value) fd.close() else: print "unknown; ", retval dialog.destroy() def set_rank(self, ds): print "Set rank." ra = scipy.sum(ds.asarray(), 1) ranks = {} dim = ds.get_dim_name()[0] for key, value in ds[dim].items(): ranks[key] = ra[value] ann_h = annotations.get_dim_handler(self._dimension) if ann_h is None: ann_h = annotations.DictAnnotationHandler() annotations.set_dim_handler(self._dimension, ann_h) ann_h.add_annotations('Rank', ranks) ## ## GTK Callbacks ## def _numeric_compare(self, treemodel, iter1, iter2): column = treemodel.get_sort_column_id()[0] item1 = treemodel.get_value(iter1, column) item2 = treemodel.get_value(iter2, column) try: item1 = float(item1) item2 = float(item2) except: logger.log("notice", "Could not convert to float: %s, %s" %(item1, item2)) return cmp(item1, item2) def _popup_menu(self, *rest): self._update_annotations_menu() self._menu.popup(None, None, None, 0, 0) def _on_annotation_activated(self, menuitem, annotation): self.set_annotation(annotation) def _button_pressed(self, widget, event): if event.button == 3: self._update_annotations_menu() self._menu.popup(None, None, None, event.button, event.time) return True def _on_export_list(self, menuitem): self.export_annotations() def _on_import_list(self, menuitem): self.import_annotation_file() def _on_make_selection(self, menuitem): selection = self._idlist.get_selection() model, paths = selection.get_selected_rows() if paths==None: return iters = [self._idstore.get_iter(p) for p in paths] ids = [self._idstore.get_value(i, 0) for i in iters] main.projectview.set_selection(self._dimension, ids) def _drag_data_received(self, widget, drag_context, x, y, selection, info, timestamp): treestore, path = selection.tree_get_row_drag_data() i = treestore.get_iter(path) obj = treestore.get_value(i, 2) if isinstance(obj, dataset.Dataset): if self._dimension in obj.get_dim_name(): self.set_rank(obj) widget.emit_stop_by_name('drag-data-received') class SelectionListController: def __init__(self, seltree, idlist_controller): self._seltree = seltree self._sel_stores = {} self._detail_cols = [] self._dimension = None self._idlist_controller = idlist_controller self._details_on = False # Selection column renderer = gtk.CellRendererText() sel_column = gtk.TreeViewColumn('Selection', renderer, text=0) sel_column.set_resizable(True) sel_column.set_max_width(200) seltree.insert_column(sel_column, 0) # Detail columns cols = [('In CS', 3), ('All', 4), ('Rank', 5)] for name, store_col_num in cols: col = gtk.TreeViewColumn(name, renderer, text=store_col_num) col.set_sort_indicator(True) col.set_sort_column_id(store_col_num) col.set_sort_order(gtk.SORT_ASCENDING) self._detail_cols.append(col) # Signals seltree.connect('row-activated', self._on_row_activated) seltree.connect('cursor-changed', self._on_cursor_changed) seltree.connect('button-press-event', self._on_button_pressed) seltree.drag_dest_set(gtk.DEST_DEFAULT_ALL, [("GTK_TREE_MODEL_ROW", gtk.TARGET_SAME_APP, 7)], gtk.gdk.ACTION_LINK) seltree.connect('drag-data-received', self._drag_data_received) # Selections context menu self._seltree_menu = SimpleMenu() self._seltree_menu.add_simple_item('Sort by selection', self._on_seltree_sort) self._seltree_menu.add_simple_item('Show details', self._enable_details, True) self._seltree_menu.add_simple_item('Hide details', self._enable_details, False) # # Public interface # def activate(self): self._seltree.set_cursor((0,)) def set_projectview(self, projectview): """Dependency injection.""" main.projectview.add_selection_observer(self) def set_dimlist_controller(self, dimlist_controller): """Dependency injection of the dimension list controller.""" self._dimlist_controller = dimlist_controller def set_dimension(self, dim): """Set the current dimension, changing the model of the treeview to match dim. After this the current dimension of the identifier list is updated.""" self._ensure_selection_store(dim) self._seltree.set_model(self._sel_stores[dim]) self._idlist_controller.set_dimension(dim) self._dimension = dim def selection_changed(self, dimname, selection): """Callback function from Project.""" for dim in selection.dims(): self._ensure_selection_store(dim) store = self._sel_stores[dim] if not self._get_current_selection_iter(selection, dim): n = len(selection[dim]) values = (selection.title, selection, dim, n, n, 0) store.insert_after(None, None, values) else: # update size of current selection for row in store: if row[1]==selection: row[3] = row[4] = len(selection[dim]) path = self._seltree.get_cursor() if path and self._sel_stores.has_key(self._dimension): it = self._sel_stores[self._dimension].get_iter(path[0]) sel = self._sel_stores[self._dimension].get_value(it, 1) self._idlist_controller.set_selection(sel) def add_dataset(self, dataset): """Converts a CategoryDataset to Selection objects and adds it to the selection tree. The name of the dataset will be the parent node in the tree, and the identifers along the first axis will be added as the names of the subselections.""" dim_name = dataset.get_dim_name(0) self._ensure_selection_store(dim_name) store = self._sel_stores[dim_name] di = self._get_dataset_iter(dataset) if not di: n_tot = dataset.shape[0] selection = main.projectview.get_selection().get(dim_name) ds_idents = dataset.get_identifiers(dim_name) n_cs = len(selection.intersection(ds_idents)) values = (dataset.get_name(), dataset, dim_name, n_cs, n_tot, 2) i = store.insert_after(None, None, values) for selection in dataset.as_selections(): n_sel = len(selection[dim_name]) values = (selection.title, selection, dim_name, 0, n_sel, 0) store.insert_after(i, None, values) # # Private interface # def _add_selection_store(self, dim): """Add a new gtk.TreeStore for the selections on a dimension.""" # Create new store # Two types of lines, one for CategoryDatasets and one for # Selections. The elements are title, link to dataset or selection, # name of dimension, num. members in selection, num. in # intersection with current selection and the rank of selection. store = gtk.TreeStore(gobject.TYPE_STRING, gobject.TYPE_PYOBJECT, gobject.TYPE_STRING, gobject.TYPE_INT, gobject.TYPE_INT, gobject.TYPE_FLOAT) # Set selection store for this dimension self._sel_stores[dim] = store def _ensure_selection_store(self, dim): """Ensure that the object has a gtk.TreeStore for the given dimension""" # Do not overwrite existing stores if self._sel_stores.has_key(dim): return self._add_selection_store(dim) def _get_dataset_iter(self, ds): """Returns the iterator to the selection tree row containing a given dataset.""" store = self._sel_stores[ds.get_dim_name(0)] i = store.get_iter_first() while i: if store.get_value(i, 1) == ds: return i i = store.iter_next(i) return None def _get_current_selection_iter(self, selection, dimension): if not self._sel_stores.has_key(dimension): return None store = self._sel_stores[dimension] i = store.get_iter_first() while i: if store.get_value(i, 1) == selection: if store.get_value(i, 2) == dimension: return i i = store.iter_next(i) return None def _sort_selections(self, dataset): """Ranks selections by intersection with current selection. Ranks determined by the hypergeometric distribution. """ dim_name = dataset.get_dim_name(0) sel_store = self._sel_stores[dim_name] selection_obj = main.projectview.get_selection() current_selection = selection_obj.get(dim_name) if current_selection==None: return pvals = hypergeom.gene_hypergeo_test(current_selection, dataset) for row in sel_store: if row[1]==dataset: for child in row.iterchildren(): name = child[0] child[3] = pvals[name][0] child[4] = pvals[name][1] child[5] = pvals[name][2] sel_store.set_sort_column_id(5, gtk.SORT_ASCENDING) # # GTK callbacks # def _enable_details(self, widget, bool): if self._details_on == bool : return self._details_on = bool if bool==True: for col in self._detail_cols: self._seltree.insert_column(col, -1) else: for col in self._detail_cols: self._seltree.remove_column(col) def _drag_data_received(self, widget, drag_context, x, y, selection, info, timestamp): treestore, path = selection.tree_get_row_drag_data() i = treestore.get_iter(path) obj = treestore.get_value(i, 2) if isinstance(obj, dataset.CategoryDataset): self.add_dataset(obj) self._dimlist_controller.set_dimension(obj.get_dim_name(0)) widget.emit_stop_by_name('drag-data-received') def _on_cursor_changed(self, widget): "Show the list of identifier strings." store = self._sel_stores[self._dimension] p = self._seltree.get_cursor()[0] i = store.get_iter(p) obj = store.get_value(i, 1) if isinstance(obj, dataset.Selection): self._idlist_controller.set_selection(obj) else: self._idlist_controller.set_selection(None) def _on_row_activated(self, widget, path, column): store = self._sel_stores[self._dimension] i = store.get_iter(path) obj = store.get_value(i, 1) if isinstance(obj, dataset.Dataset): seltree = self._seltree if seltree.row_expanded(path): seltree.collapse_row(path) else: seltree.expand_row(path, True) elif isinstance(obj, dataset.Selection): main.projectview.set_selection(self._dimension, obj[self._dimension]) def _on_button_pressed(self, widget, event): """Button press callbak.""" if event.button == 3: self._seltree_menu.popup(None, None, None, event.button, event.time) def _on_seltree_sort(self, menuitem): """Sort selection tree if row is category dataset.""" store = self._sel_stores[self._dimension] p = self._seltree.get_cursor()[0] i = store.get_iter(p) obj = store.get_value(i, 1) if isinstance(obj, dataset.CategoryDataset): self._sort_selections(obj) class DimListController: def __init__(self, dimlist, seltree_controller): self._current_dim = None self._seltree_controller = seltree_controller self.show_hidden = False ## dimstore is a list of all dimensions in the application self.dimstore = gtk.ListStore(gobject.TYPE_STRING) # filter for hiding dims prefixed with underscore self.dimstore_filter = self.dimstore.filter_new() self.dimstore_filter.set_visible_func(self._dimension_filter) ## The widgets we are controlling self.dimlist = dimlist ## Set up dimensions list dimlist.set_model(self.dimstore_filter) renderer = gtk.CellRendererText() dim_column = gtk.TreeViewColumn('Dimension', renderer, text=0) dimlist.insert_column(dim_column, 0) # Signals dimlist.connect('row-activated', self._dim_row_activated) dimlist.connect('cursor-changed', self._dim_cursor_changed) dimlist.connect('button-press-event', self._dimlist_button_pressed) # Set up dimension context menu self._dimlist_menu = SimpleMenu() self._dimlist_menu.add_simple_item('Hide', self._on_dim_hide) self._dimlist_menu.add_simple_item('Show all', self._on_dim_show) ## ## Public interface ## def set_projectview(self, projectview): """Dependency injection.""" self.dim_names = projectview.dim_names self.update_dims() projectview.add_dataset_observer(self) def get_dimension(self, dim): """Returns the iterator to the dimension with the given name, or None if not found.""" i = self.dimstore_filter.get_iter_first() while i: if self.dimstore_filter.get_value(i, 0) == dim: return i i = self.dimstore_filter.iter_next(i) return None def set_dimension(self, dimname): """Sets the current dimension.""" self._current_dim = dimname dim = self.get_dimension(self._current_dim) path = self.dimstore_filter.get_path(dim) if self.dimlist.get_cursor()[0] != path: self.dimlist.set_cursor(self.dimstore_filter.get_path(dim)) self._seltree_controller.set_dimension(dimname) def dataset_changed(self): """Callback function from Project.""" self.update_dims() def update_dims(self): """Update the list of dimensions shown""" for dim in self.dim_names: if not self.get_dimension(dim): self.dimstore.insert_after(None, (dim,)) self.dimstore_filter.refilter() # # Private interface # def _dimension_filter(self, store, row): """Filters out dimensions with underscore prefix.""" if self.show_hidden: return True 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.show_hidden = False self.dimstore_filter.refilter() def _on_dim_show(self, menuitem): """Menu item callback function that shows underscore prefixed dimension names.""" self.show_hidden = True self.dimstore_filter.refilter() def _dim_cursor_changed(self, widget): cursor = self.dimlist.get_cursor()[0] i = self.dimstore_filter.get_iter(cursor) row = self.dimstore_filter.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) pass def _dimlist_button_pressed(self, widget, event): if event.button == 3: self._dimlist_menu.popup(None, None, None, event.button, event.time)