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zmapWindowNavigatorMenus.c 20.27 KiB
/* File: zmapWindowNavigatorMenus.c
* Author: Roy Storey (rds@sanger.ac.uk)
* Copyright (c) 2006-2010: Genome Research Ltd.
*-------------------------------------------------------------------
* ZMap is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
* or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
*-------------------------------------------------------------------
* This file is part of the ZMap genome database package
* originally written by:
*
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
* Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Jun 29 16:57 2009 (rds)
* Created: Wed Oct 18 08:21:15 2006 (rds)
* CVS info: $Id: zmapWindowNavigatorMenus.c,v 1.26 2010-03-04 15:13:13 mh17 Exp $
*-------------------------------------------------------------------
*/
#include <zmapWindowNavigator_P.h>
#include <ZMap/zmapUtils.h>
#include <zmapWindowContainerFeatureSet_I.h>
#define FILTER_DATA_KEY "ZMapWindowNavigatorFilterData"
#define FILTER_CANCEL_DATA_KEY "ZMapWindowNavigatorFilterCancelData"
static void navigatorBumpMenuCB(int menu_item_id, gpointer callback_data);
static void navigatorColumnMenuCB(int menu_item_id, gpointer callback_data);
static GHashTable *access_navigator_context_to_item(gpointer user_data);
static GHashTable *access_window_context_to_item(gpointer user_data);
static GtkWidget *zmapWindowNavigatorNewToplevel(char *title);
static void destroyFilterCB(GtkWidget *widget, gpointer user_data);
static void filter_checkbox_toggled_cb(GtkWidget *checkbox, gpointer user_data);
static void makeFilterPanel(ZMapWindowNavigator navigator, GtkWidget *parent);
static void cancel_destroy_cb(GtkWidget *widget, gpointer user_data);
static void apply_destroy_cb(GtkWidget *widget, gpointer user_data);
static void zmapWindowNavigatorLocusFilterEditorCreate(ZMapWindowNavigator navigator);
static gboolean searchLocusSetCB(FooCanvasItem *item, gpointer user_data)
{
GQuark locus_name = GPOINTER_TO_UINT(user_data);
ZMapFeatureAny feature_any = NULL;
gboolean match = FALSE;
feature_any = zmapWindowItemGetFeatureAny(item);
zMapAssert(feature_any);
switch(feature_any->struct_type)
{
case ZMAPFEATURE_STRUCT_FEATURE:
{
ZMapFeature feature = (ZMapFeature)feature_any;#ifdef THIS_LOCUS_STUFF_IS_A_PAIN
/* quick fix to zmapWindowNavigatorShowSameNameList... */
if(locus_name == feature_any->original_id)
match = TRUE;
#endif /* THIS_LOCUS_STUFF_IS_A_PAIN */
/* Having just (locus_name == feature->locus_id) resulted in duplicates... */
/* Added (feature->locus_id != feature->original_id) to fix RT # 64287 */
if((locus_name == feature->locus_id)
&& (feature->locus_id != feature->original_id))
match = TRUE;
}
break;
default:
break;
}
return match;
}
void zmapWindowNavigatorGoToLocusExtents(ZMapWindowNavigator navigate, FooCanvasItem *item)
{
ZMapWindow window = NULL;
ZMapFeature feature = NULL;
ZMapWindowFToIPredFuncCB callback = NULL ;
GList *result = NULL, *feature_list;
GQuark locus_quark = 0;
char *wild_card = "*";
feature = zmapWindowItemGetFeature(item);
zMapAssert(feature);
window = navigate->current_window;
callback = searchLocusSetCB;
locus_quark = g_quark_from_string(wild_card);
if((result = zmapWindowFToIFindItemSetFull(window->context_to_item,
feature->parent->parent->parent->unique_id,
feature->parent->parent->unique_id,
locus_quark, // feature->parent->unique_id,
wild_card, wild_card, locus_quark,
callback, GUINT_TO_POINTER(feature->original_id))))
{
int start, end;
if((feature_list = zmapWindowItemListToFeatureList(result)))
{
/* x coords are HACKED!!!! */
if(zMapFeatureGetFeatureListExtent(feature_list, &start, &end))
zmapWindowZoomToWorldPosition(window, TRUE, 0.0, start, 100.0, end);
g_list_free(feature_list);
}
}
else
{
#ifdef TEMPORARY_AVOID_ISSUE_HERE
zMapAssertNotReached();
#endif /* TEMPORARY_AVOID_ISSUE_HERE */
}
return ;
}
/* This has the wrong name! it only works for finding variants! */
void zmapWindowNavigatorShowSameNameList(ZMapWindowNavigator navigate, FooCanvasItem *item)
{
ZMapWindow window = NULL;
ZMapFeature feature = NULL;
GQuark locus_quark = 0;
char *wild_card = "*";
feature = zmapWindowItemGetFeature(item);
zMapAssert(feature);
window = navigate->current_window;
#define USING_SET_SEARCH_DATA_METHOD
#ifndef USING_SET_SEARCH_DATA_METHOD
ZMapWindowFToIPredFuncCB callback = NULL ;
GList *result = NULL;
#ifdef RDS_PROBLEMATIC_CODE
/* Is it right to use window->context_to_item here??? */
if(!(result = zmapWindowFToIFindSameNameItems(window->context_to_item,
ZMAPSTRAND_NONE, ZMAPFRAME_NONE,
feature)))
{
#endif
/* Here we going to search for transcripts in any feature set in
* the _main_ window which have a locus set which == feature->original_id
* i.e. feature->original_id == the locus name
*/
callback = searchLocusSetCB;
locus_quark = g_quark_from_string(wild_card);
/* we use the wildcard to get all features... slow?? */
result = zmapWindowFToIFindItemSetFull(window->context_to_item,
feature->parent->parent->parent->unique_id,
feature->parent->parent->unique_id,
locus_quark, /* feature->parent->unique_id, */
wild_card, wild_card, locus_quark,
callback, GUINT_TO_POINTER(feature->original_id));
#ifdef RDS_PROBLEMATIC_CODE
}
#endif
if(result)
{
gboolean zoom_to_item = FALSE;
/* We have to access the window->context_to_item in the
* WindowList and it does that with a callback. It must
* be the same window! */
zmapWindowListWindowCreate(window, item,
(char *)(g_quark_to_string(feature->original_id)),
access_window_context_to_item, window,
NULL, NULL,
zoom_to_item);
g_list_free(result); /* clean up list. */
}
#else /* USING_SET_SEARCH_DATA_METHOD */
{
ZMapWindowFToISetSearchData search_data;
gboolean zoom_to_item = FALSE;
locus_quark = g_quark_from_string(wild_card);
search_data = zmapWindowFToISetSearchCreateFull(zmapWindowFToIFindItemSetFull, NULL,
feature->parent->parent->parent->unique_id,
feature->parent->parent->unique_id,
locus_quark, /* feature->parent->unique_id, */
locus_quark,
wild_card, /* strand */
wild_card, /* frame */
searchLocusSetCB,
GUINT_TO_POINTER(feature->original_id), NULL);
zmapWindowListWindowCreate(window, item,
(char *)(g_quark_to_string(feature->original_id)),
access_window_context_to_item, window,
(ZMapWindowListSearchHashFunc)zmapWindowFToISetSearchPerform, search_data,
(GDestroyNotify)zmapWindowFToISetSearchDestroy, zoom_to_item);
}
#endif /* USING_SET_SEARCH_DATA_METHOD */
return ;
}
static void popUpVariantList(int menu_item_id, gpointer callback_data)
{
NavigateMenuCBData menu_data = (NavigateMenuCBData)callback_data ;
switch (menu_item_id)
{
case 1:
zmapWindowNavigatorShowSameNameList(menu_data->navigate, menu_data->item);
break;
case 2:
zmapWindowNavigatorLocusFilterEditorCreate(menu_data->navigate);
break;
case 3:
g_list_free(menu_data->navigate->hide_filter);
menu_data->navigate->hide_filter = NULL;
zmapWindowNavigatorLocusRedraw(menu_data->navigate);
break;
default:
break;
}
return ;
}
ZMapGUIMenuItem zmapWindowNavigatorMakeMenuLocusOps(int *start_index_inout,
ZMapGUIMenuItemCallbackFunc callback_func,
gpointer callback_data)
{
static ZMapGUIMenuItemStruct menu[] =
{
{ZMAPGUI_MENU_NORMAL, "Show Variants List", 1, popUpVariantList, NULL},
{ZMAPGUI_MENU_NONE, NULL, 0, NULL, NULL}
};
zMapGUIPopulateMenu(menu, start_index_inout, callback_func, callback_data);
return menu;
}
ZMapGUIMenuItem zmapWindowNavigatorMakeMenuLocusColumnOps(int *start_index_inout,
ZMapGUIMenuItemCallbackFunc callback_func,
gpointer callback_data)
{
static ZMapGUIMenuItemStruct menu[] =
{
{ZMAPGUI_MENU_NORMAL, "Filter Loci", 2, popUpVariantList, NULL},
{ZMAPGUI_MENU_NORMAL, "Show All Loci", 3, popUpVariantList, NULL},
{ZMAPGUI_MENU_NONE, NULL, 0, NULL, NULL}
};
zMapGUIPopulateMenu(menu, start_index_inout, callback_func, callback_data);
return menu;
}
ZMapGUIMenuItem zmapWindowNavigatorMakeMenuColumnOps(int *start_index_inout,
ZMapGUIMenuItemCallbackFunc callback_func,
gpointer callback_data)
{ static ZMapGUIMenuItemStruct menu[] =
{
{ZMAPGUI_MENU_NORMAL, "Show Feature List", 1, navigatorColumnMenuCB, NULL},
{ZMAPGUI_MENU_NORMAL, "Feature Search Window", 2, navigatorColumnMenuCB, NULL},
{ZMAPGUI_MENU_NONE, NULL, 0, NULL, NULL}
} ;
zMapGUIPopulateMenu(menu, start_index_inout, callback_func, callback_data) ;
return menu ;
}
ZMapGUIMenuItem zmapWindowNavigatorMakeMenuBump(int *start_index_inout,
ZMapGUIMenuItemCallbackFunc callback_func,
gpointer callback_data, ZMapStyleBumpMode curr_bump)
{
static ZMapGUIMenuItemStruct menu[] =
{
{ZMAPGUI_MENU_TOGGLE, "Column Bump|UnBump", ZMAPBUMP_NAVIGATOR, navigatorBumpMenuCB, NULL},
{ZMAPGUI_MENU_NORMAL, "Column Hide", ZMAPWINDOWCOLUMN_HIDE, NULL, NULL},
{ZMAPGUI_MENU_NONE, NULL, 0, NULL, NULL}
} ;
ZMapGUIMenuItem item ;
/* Set the initial toggle button correctly....make sure this stays in step with the array above.
* NOTE logic, this button is either "no bump" or "Name + No Bump", the latter should be
* selectable whatever.... */
item = &(menu[0]) ;
if (curr_bump != ZMAPBUMP_UNBUMP)
{
item->type = ZMAPGUI_MENU_TOGGLEACTIVE ;
item->id = ZMAPBUMP_UNBUMP ;
}
else
{
item->type = ZMAPGUI_MENU_TOGGLE ;
item->id = ZMAPBUMP_NAVIGATOR ;
}
zMapGUIPopulateMenu(menu, start_index_inout, callback_func, callback_data) ;
return menu ;
}
static void navigatorBumpMenuCB(int menu_item_id, gpointer callback_data)
{
NavigateMenuCBData menu_data = (NavigateMenuCBData)callback_data ;
ZMapStyleBumpMode bump_type = (ZMapStyleBumpMode)menu_item_id ;
FooCanvasItem *style_item ;
/* This will only toggle the bumping */
style_item = menu_data->item ;
if(!ZMAP_IS_CONTAINER_GROUP(style_item))
style_item = (FooCanvasItem *)zmapWindowContainerCanvasItemGetContainer(style_item);
if(bump_type == ZMAPBUMP_NAVIGATOR)
{
bump_type = ZMAPBUMP_ALTERNATING;
}
zmapWindowColumnBump(style_item, bump_type) ;
zmapWindowNavigatorPositioning(menu_data->navigate);
g_free(menu_data) ;
return ;
}
static void navigatorColumnMenuCB(int menu_item_id, gpointer callback_data)
{
NavigateMenuCBData menu_data = (NavigateMenuCBData)callback_data ;
switch (menu_item_id)
{
case 1:
{
ZMapFeatureAny feature ;
ZMapWindowContainerFeatureSet container;
ZMapWindowFToISetSearchData search_data;
FooCanvasItem *set_item = menu_data->item;
gboolean zoom_to_item = FALSE;
feature = zmapWindowItemGetFeatureAny(menu_data->item);
if(feature->struct_type == ZMAPFEATURE_STRUCT_FEATURE)
{
/* a small hack for the time being... */
set_item = FOO_CANVAS_ITEM(zmapWindowContainerCanvasItemGetContainer(menu_data->item));
feature = (ZMapFeatureAny)(feature->parent);
}
container = (ZMapWindowContainerFeatureSet)set_item;
search_data = zmapWindowFToISetSearchCreate(zmapWindowFToIFindItemSetFull, NULL,
feature->parent->parent->unique_id,
feature->parent->unique_id,
feature->unique_id,
g_quark_from_string("*"),
zMapFeatureStrand2Str(container->strand),
zMapFeatureFrame2Str(container->frame));
zmapWindowListWindowCreate(menu_data->navigate->current_window,
NULL,
(char *)g_quark_to_string(feature->original_id),
access_navigator_context_to_item,
menu_data->navigate,
(ZMapWindowListSearchHashFunc)zmapWindowFToISetSearchPerform, search_data,
(GDestroyNotify)zmapWindowFToISetSearchDestroy, zoom_to_item) ;
break ;
}
case 2:
zmapWindowCreateSearchWindow(menu_data->navigate->current_window,
access_navigator_context_to_item,
menu_data->navigate,
menu_data->item) ;
break ;
case 5:
zmapWindowCreateSequenceSearchWindow(menu_data->navigate->current_window, menu_data->item, ZMAPSEQUENCE_DNA) ;
break ;
case 6:
zmapWindowCreateSequenceSearchWindow(menu_data->navigate->current_window, menu_data->item, ZMAPSEQUENCE_PEPTIDE) ;
break ;
default:
zMapAssert("Coding error, unrecognised menu item number.") ;
break ;
}
g_free(menu_data) ;
return ;
}
static GHashTable *access_navigator_context_to_item(gpointer user_data)
{
ZMapWindowNavigator navigator = (ZMapWindowNavigator)user_data;
GHashTable *context_to_item;
context_to_item = navigator->ftoi_hash;
return context_to_item;
}
static GHashTable *access_window_context_to_item(gpointer user_data)
{
ZMapWindow window = (ZMapWindow)user_data;
GHashTable *context_to_item;
context_to_item = window->context_to_item;
return context_to_item;
}
static GtkWidget *zmapWindowNavigatorNewToplevel(char *title)
{
GtkWidget *window;
GtkWindow *gtk_window;
window = gtk_window_new(GTK_WINDOW_TOPLEVEL);
gtk_window = GTK_WINDOW(window);
/* Set it up graphically nice */
gtk_window_set_title(gtk_window, title) ;
gtk_window_set_default_size(gtk_window, -1, -1);
gtk_container_border_width(GTK_CONTAINER(window), 5) ;
return window;
}
static void destroyFilterCB(GtkWidget *widget, gpointer user_data)
{
GList *copied_list;
if((copied_list = g_object_get_data(G_OBJECT(widget), FILTER_CANCEL_DATA_KEY)))
g_list_free(copied_list);
return ;
}
static void filter_checkbox_toggled_cb(GtkWidget *checkbox, gpointer user_data)
{
ZMapWindowNavigator navigator = (ZMapWindowNavigator)user_data;
GList *in_hide_list;
char *filter = NULL;
gboolean button_pressed;
button_pressed = gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(checkbox));
filter = g_object_get_data(G_OBJECT(checkbox), FILTER_DATA_KEY);
zMapAssert(filter != NULL);
if((in_hide_list = g_list_find(navigator->hide_filter, filter)))
{
if(!button_pressed)
navigator->hide_filter = g_list_remove_all(navigator->hide_filter, filter);
}
else if(button_pressed)
{
navigator->hide_filter = g_list_append(navigator->hide_filter, filter); }
else if(!button_pressed)
{
g_warning("Turning filter '%s' off, but it's not in the list.", filter);
}
return ;
}
static void makeFilterPanel(ZMapWindowNavigator navigator, GtkWidget *parent)
{
int list_length;
if((list_length = g_list_length(navigator->available_filters)) > 0 &&
GTK_IS_CONTAINER(parent))
{
GList *tmp;
tmp = navigator->available_filters;
do
{
GtkWidget *checkbox_with_label;
GList *filter_list;
char *filter;
gboolean filter_active = FALSE;
filter = (char *)(tmp->data);
checkbox_with_label = gtk_check_button_new_with_label(filter);
g_object_set_data(G_OBJECT(checkbox_with_label), FILTER_DATA_KEY, filter);
if((filter_list = g_list_find(navigator->hide_filter, filter)))
filter_active = TRUE;
g_object_set(G_OBJECT(checkbox_with_label),
"active", filter_active,
NULL);
g_signal_connect(G_OBJECT(checkbox_with_label), "toggled",
G_CALLBACK(filter_checkbox_toggled_cb), navigator);
if(GTK_IS_BOX(parent))
gtk_box_pack_start(GTK_BOX(parent), checkbox_with_label, FALSE, FALSE, 0);
else
gtk_container_add(GTK_CONTAINER(parent), checkbox_with_label);
}
while((tmp = g_list_next(tmp)));
}
return ;
}
static void cancel_destroy_cb(GtkWidget *widget, gpointer user_data)
{
ZMapWindowNavigator navigator = (ZMapWindowNavigator)user_data;
GtkWidget *toplevel;
if((toplevel = zMapGUIFindTopLevel(widget)))
{
GList *tmp;
/* logic here is just to swap the pointers between the navigator and
* the toplevel g_object_set_data version... */
tmp = navigator->hide_filter;
navigator->hide_filter = g_object_get_data(G_OBJECT(toplevel), FILTER_CANCEL_DATA_KEY);
/* Hope this works... It should, we're not destroying yet... */
g_object_set_data(G_OBJECT(toplevel), FILTER_CANCEL_DATA_KEY, tmp);
/* The destroy cb will liberate the list for us... */
gtk_widget_destroy(toplevel);
}
return ;
}
static void apply_destroy_cb(GtkWidget *widget, gpointer user_data)
{
ZMapWindowNavigator navigator = (ZMapWindowNavigator)user_data;
GtkWidget *toplevel;
/* request a redraw of the navigator... */
zmapWindowNavigatorLocusRedraw(navigator);
/* Get the toplevel to destroy */
if((toplevel = zMapGUIFindTopLevel(widget)))
{
gtk_widget_destroy(toplevel);
}
return ;
}
static void zmapWindowNavigatorLocusFilterEditorCreate(ZMapWindowNavigator navigator)
{
GtkWidget
*toplevel = NULL,
*vbox_1,
*vbox_2,
*frame,
*label,
*button_box,
*cancel_button,
*apply_button;
toplevel = zmapWindowNavigatorNewToplevel("ZMap - Filter Loci By Name");
vbox_1 = gtk_vbox_new(FALSE, 0);
gtk_container_add(GTK_CONTAINER(toplevel), vbox_1);
frame = gtk_frame_new("Filter");
gtk_box_pack_start(GTK_BOX(vbox_1), frame, TRUE, TRUE, 5);
vbox_2 = gtk_vbox_new(FALSE, 0);
gtk_container_add(GTK_CONTAINER(frame), vbox_2);
label = gtk_label_new("This simple dialog controls the filtering\n"
"system used when drawing the Loci in the\n"
"navigator.");
gtk_box_pack_start(GTK_BOX(vbox_2), label, FALSE, FALSE, 5);
makeFilterPanel(navigator, vbox_2);
label = gtk_label_new("[Selected loci prefixes will not be shown\n"
"in the navigator.]");
gtk_box_pack_start(GTK_BOX(vbox_2), label, FALSE, FALSE, 5);
{
GList *copied_list = NULL;
copied_list = g_list_copy(navigator->hide_filter);
/* This gets liberated in destroy */
g_object_set_data(G_OBJECT(toplevel), FILTER_CANCEL_DATA_KEY, copied_list);
g_signal_connect(G_OBJECT(toplevel), "destroy",
G_CALLBACK(destroyFilterCB), navigator);
}
button_box = gtk_hbutton_box_new();
cancel_button = gtk_button_new_with_label("Cancel");
gtk_box_pack_start(GTK_BOX(button_box), cancel_button, FALSE, FALSE, 5);
g_signal_connect(G_OBJECT(cancel_button), "clicked",
G_CALLBACK(cancel_destroy_cb), navigator);
apply_button = gtk_button_new_with_label("Apply");
gtk_box_pack_end(GTK_BOX(button_box), apply_button, FALSE, FALSE, 5);
g_signal_connect(G_OBJECT(apply_button), "clicked",
G_CALLBACK(apply_destroy_cb), navigator);
gtk_box_pack_end(GTK_BOX(vbox_1), button_box, FALSE, FALSE, 0);
gtk_widget_show_all(toplevel);
return ;
}