diff --git a/src/include/ZMap/zmapStyle.h b/src/include/ZMap/zmapStyle.h
index 09c44a6d3d366fc878b023571728c3442a84158d..ebd1080a0c47c612888e75558df2fb6b420ce18c 100755
--- a/src/include/ZMap/zmapStyle.h
+++ b/src/include/ZMap/zmapStyle.h
@@ -6,12 +6,12 @@
* 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.
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jan 26 08:42 2010 (edgrif)
* Created: Mon Feb 26 09:28:26 2007 (edgrif)
- * CVS info: $Id: zmapStyle.h,v 1.47 2010-01-26 12:03:23 edgrif Exp $
+ * CVS info: $Id: zmapStyle.h,v 1.48 2010-03-01 11:39:40 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_STYLE_H
@@ -89,7 +89,7 @@
/* ... frame sensitivity */
#define ZMAPSTYLE_PROPERTY_FRAME_MODE "frame-mode"
/* ... deferred loading */
-#define ZMAPSTYLE_PROPERTY_DEFERRED "deferred"
+#define ZMAPSTYLE_PROPERTY_DEFERRED "deferred"
#define ZMAPSTYLE_PROPERTY_LOADED "loaded"
/* graph properties. */
@@ -121,14 +121,14 @@
/* Assembly path properties */
#define ZMAPSTYLE_PROPERTY_ASSEMBLY_PATH_NON_COLOURS "non-assembly-colours"
-/*
+/*
* The following are a series of enums that define various properties of a style.
* NOTE that it is imperative that each enum type has as it's first member
* a ZMAP_xxxx_INVALID element whose value is zero to allow simple testing of the
* form
* if (element)
* do_something ;
- * */
+ * */
#define ZMAP_STYLE_MODE_LIST(_) \
_(ZMAPSTYLE_MODE_INVALID, , "invalid" , "invalid mode " , "") \
@@ -175,7 +175,8 @@ _(ZMAPBUMP_ALL, , "all", "Bump All",
_(ZMAPBUMP_NAME, , "name", "Name", "A sub-column for features with the same name.") \
_(ZMAPBUMP_NAME_INTERLEAVE, , "name-interleave", "Name Interleave", "All features with same name in a single sub-column but several names interleaved in each sub-column, the most compact display.") \
_(ZMAPBUMP_NAME_NO_INTERLEAVE, , "name-no-interleave", "Name No Interleave", "Display as for Interleave but no interleaving of different names.") \
-_(ZMAPBUMP_NAME_COLINEAR, , "name-colinear", "Name No Interleave & Colinear", "As for No Interleave but for alignments only colinear shown.") \
+_(ZMAPBUMP_NAME_COLINEAR, , "name-colinear", "Name & Colinear", "As for Name but colinear alignments shown.") \
+_(ZMAPBUMP_NAME_INTERLEAVE_COLINEAR, , "name-colinear-interleave", "Name Interleave & Colinear", "As for Name & Colinear but interleaved, the most compact display.") \
_(ZMAPBUMP_NAME_BEST_ENDS, , "name-best-ends", "Name and Best 5'& 3' Matches", "As for No Interleave but for alignments sorted by 5' and 3' best/biggest matches, one sub_column per match.")
@@ -402,7 +403,7 @@ double zMapStyleGetMinScore(ZMapFeatureTypeStyle style) ;
gboolean zMapStyleGetShowWhenEmpty(ZMapFeatureTypeStyle style);
gboolean zMapStyleGetColours(ZMapFeatureTypeStyle style, ZMapStyleColourTarget target, ZMapStyleColourType type,
GdkColor **fill, GdkColor **draw, GdkColor **border) ;
-gboolean zMapStyleGetColoursDefault(ZMapFeatureTypeStyle style,
+gboolean zMapStyleGetColoursDefault(ZMapFeatureTypeStyle style,
GdkColor **background, GdkColor **foreground, GdkColor **outline);
char *zMapStyleGetDescription(ZMapFeatureTypeStyle style) ;
double zMapStyleGetWidth(ZMapFeatureTypeStyle style) ;
@@ -439,9 +440,9 @@ void zMapStyleSetWidth(ZMapFeatureTypeStyle style, double width) ;
gboolean zMapStyleIsDrawable(ZMapFeatureTypeStyle style, GError **error) ;
gboolean zMapStyleMakeDrawable(ZMapFeatureTypeStyle style) ;
-gboolean zMapStyleGetColoursCDSDefault(ZMapFeatureTypeStyle style,
+gboolean zMapStyleGetColoursCDSDefault(ZMapFeatureTypeStyle style,
GdkColor **background, GdkColor **foreground, GdkColor **outline);
-gboolean zMapStyleGetColoursGlyphDefault(ZMapFeatureTypeStyle style,
+gboolean zMapStyleGetColoursGlyphDefault(ZMapFeatureTypeStyle style,
GdkColor **background, GdkColor **foreground, GdkColor **outline);
gboolean zMapStyleIsColour(ZMapFeatureTypeStyle style, ZMapStyleDrawContext colour_context) ;
gboolean zMapStyleIsBackgroundColour(ZMapFeatureTypeStyle style) ;
@@ -493,7 +494,7 @@ void zMapFeatureTypeDestroy(ZMapFeatureTypeStyle type) ;
ZMapFeatureTypeStyle zMapStyleGetPredefined(char *style_name) ;
gboolean zMapFeatureTypeSetAugment(GData **current, GData **new) ;
-void zMapStyleInitBumpMode(ZMapFeatureTypeStyle style,
+void zMapStyleInitBumpMode(ZMapFeatureTypeStyle style,
ZMapStyleBumpMode default_bump_mode, ZMapStyleBumpMode curr_bump_mode) ;
ZMapStyleBumpMode zMapStyleResetBumpMode(ZMapFeatureTypeStyle style) ;
diff --git a/src/zmapWindow/zmapWindowColBump.c b/src/zmapWindow/zmapWindowColBump.c
index 76b8562d84e49cd2fde9b56b4d673bd2aa11c24c..38a539160980c5c2b820518391bf0803f68a5f6d 100755
--- a/src/zmapWindow/zmapWindowColBump.c
+++ b/src/zmapWindow/zmapWindowColBump.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Feb 15 11:54 2010 (edgrif)
* Created: Tue Sep 4 10:52:09 2007 (edgrif)
- * CVS info: $Id: zmapWindowColBump.c,v 1.64 2010-02-26 13:34:51 mh17 Exp $
+ * CVS info: $Id: zmapWindowColBump.c,v 1.65 2010-03-01 11:39:40 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -402,6 +402,17 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
else
zMapAssertNotReached();
+
+ historic_bump_mode = zmapWindowContainerFeatureSetGetBumpMode(container) ;
+ if (bump_mode == ZMAPBUMP_INVALID) // this is set to 'rebump' the columns
+ bump_mode = historic_bump_mode ;
+
+ // if bumping from one mode to another just clear up with am unbump first, it's tidier this way
+ // mh17: ideally i'd prefer to have a separate unbump function, can hack it out later?
+ if(historic_bump_mode > ZMAPBUMP_UNBUMP && historic_bump_mode != bump_mode && bump_mode != ZMAPBUMP_UNBUMP)
+ zmapWindowColumnBumpRange(bump_item,ZMAPBUMP_UNBUMP,compress_mode);
+
+
window = container->window ;
column_features = (FooCanvasGroup *)zmapWindowContainerGetFeatures((ZMapWindowContainerGroup)container) ;
@@ -418,11 +429,6 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
/* Need to know if mark is set for limiting feature display for several modes/feature types. */
mark_set = zmapWindowMarkIsSet(window->mark) ;
- /* We need this to know whether to remove and add Gaps */
- historic_bump_mode = zmapWindowContainerFeatureSetGetBumpMode(container) ;
-
- if (bump_mode == ZMAPBUMP_INVALID)
- bump_mode = historic_bump_mode ;
bump_properties.container = container ;
bump_properties.window = window ;
@@ -695,7 +701,7 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
/* TRY JUST ADDING GAPS IF A MARK IS SET */
- if (mark_set && bump_mode != ZMAPBUMP_NAME_INTERLEAVE)
+ if (mark_set && bump_mode != ZMAPBUMP_NAME_INTERLEAVE)
{
/* NOTE THERE IS AN ISSUE HERE...WE SHOULD ADD COLINEAR STUFF FOR ALIGN FEATURES
* THIS IS NOT EXPLICIT IN THE CODE WHICH IS NOT CORRECT....NEED TO THINK THIS
@@ -719,11 +725,16 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
g_list_foreach(complex.bumpcol_list, NEWaddMultiBackgrounds, container) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
- g_list_foreach(complex.bumpcol_list, collection_add_colinear_cb, &complex);
+ // g_list_foreach(complex.bumpcol_list, collection_add_colinear_cb, &complex);
- zMapPrintTimer(NULL, "added inter align bars etc.") ;
}
+ if (mark_set && bump_mode == ZMAPBUMP_NAME_COLINEAR)
+ {
+ g_list_foreach(complex.bumpcol_list, collection_add_colinear_cb, &complex);
+
+ }
+ zMapPrintTimer(NULL, "added inter align bars etc.") ;
}
/* Clear up. */
diff --git a/src/zmapWindow/zmapWindowMenus.c b/src/zmapWindow/zmapWindowMenus.c
index 5d4c9a535b4f354193d4f2ebcaccf83c1d6247d6..cbd192b8bb7ab04bdad641453c9566c2170a994c 100755
--- a/src/zmapWindow/zmapWindowMenus.c
+++ b/src/zmapWindow/zmapWindowMenus.c
@@ -6,12 +6,12 @@
* 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.
@@ -25,11 +25,11 @@
* Description: Code implementing the menus for sequence display.
*
* Exported functions: ZMap/zmapWindows.h
- *
+ *
* HISTORY:
* Last edited: Feb 10 11:58 2010 (edgrif)
* Created: Thu Mar 10 07:56:27 2005 (edgrif)
- * CVS info: $Id: zmapWindowMenus.c,v 1.68 2010-02-10 11:59:21 edgrif Exp $
+ * CVS info: $Id: zmapWindowMenus.c,v 1.69 2010-03-01 11:39:40 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -92,11 +92,11 @@ enum
enum {
- ZMAPNAV_SPLIT_FIRST_LAST_EXON,
+ ZMAPNAV_SPLIT_FIRST_LAST_EXON,
ZMAPNAV_SPLIT_FLE_WITH_OVERVIEW,
- ZMAPNAV_FIRST,
- ZMAPNAV_PREV,
- ZMAPNAV_NEXT,
+ ZMAPNAV_FIRST,
+ ZMAPNAV_PREV,
+ ZMAPNAV_NEXT,
ZMAPNAV_LAST
};
@@ -132,8 +132,8 @@ static void insertSubMenus(GString *branch_point_string,
ZMapGUIMenuItem sub_menus,
ZMapGUIMenuItem item,
GArray **items_array);
-static ZMapFeatureContextExecuteStatus alignBlockMenusDataListForeach(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus alignBlockMenusDataListForeach(GQuark key,
+ gpointer data,
gpointer user_data,
char **error_out);
@@ -142,26 +142,26 @@ static ZMapFeatureContextExecuteStatus alignBlockMenusDataListForeach(GQuark key
/* Set of makeMenuXXXX functions to create common subsections of menus. If you add to this
* you should make sure you understand how to specify menu paths in the item factory style.
* If you get it wrong then the menus will be scr*wed up.....
- *
+ *
* The functions are defined in pairs: one to define the menu, one to handle the callback
* actions, this is to emphasise that their indexes must be kept in step !
- *
+ *
* NOTE HOW THE MENUS ARE DECLARED STATIC IN THE VARIOUS ROUTINES TO MAKE SURE THEY STAY
* AROUND...OTHERWISE WE WILL HAVE TO KEEP ALLOCATING/DEALLOCATING THEM.....
- *
+ *
* and this is also the weakness of the system, there is duplication in the code because
* the menus in each function must persist after the function has exitted. This isn't
* worth fixing now as we will be moving on to the better gtk UI scheme later.
- *
+ *
*/
/* Probably it would be wise to pass in the callback function, the start index for the item
* identifier and perhaps the callback data......
- *
- * There is some mucky stuff for setting buttons etc but it's a bit unavoidable....
- *
+ *
+ * There is some mucky stuff for setting buttons etc but it's a bit unavoidable....
+ *
* */
ZMapGUIMenuItem zmapWindowMakeMenuBump(int *start_index_inout,
ZMapGUIMenuItemCallbackFunc callback_func,
@@ -177,11 +177,13 @@ ZMapGUIMenuItem zmapWindowMakeMenuBump(int *start_index_inout,
{ZMAPGUI_MENU_NORMAL, "Column Configure/Configure This Column", ZMAPWINDOWCOLUMN_CONFIGURE, configureMenuCB, NULL},
{ZMAPGUI_MENU_NORMAL, "Column Configure/Configure All Columns", ZMAPWINDOWCOLUMN_CONFIGURE_ALL, configureMenuCB, NULL},
{ZMAPGUI_MENU_BRANCH, MORE_OPTS, 0, NULL, NULL},
+ {ZMAPGUI_MENU_RADIO, NULL, ZMAPBUMP_NAME, bumpMenuCB, NULL},
{ZMAPGUI_MENU_RADIO, NULL, ZMAPBUMP_NAME_INTERLEAVE, bumpMenuCB, NULL},
- {ZMAPGUI_MENU_RADIO, NULL, ZMAPBUMP_NAME_NO_INTERLEAVE, bumpMenuCB, NULL},
{ZMAPGUI_MENU_RADIO, NULL, ZMAPBUMP_NAME_COLINEAR, bumpMenuCB, NULL},
+ {ZMAPGUI_MENU_RADIO, NULL, ZMAPBUMP_NAME_NO_INTERLEAVE, bumpMenuCB, NULL},
+// may be some logical problems doing this
+// {ZMAPGUI_MENU_RADIO, NULL, ZMAPBUMP_NAME_INTERLEAVE_COLINEAR, bumpMenuCB, NULL},
{ZMAPGUI_MENU_RADIO, NULL, ZMAPBUMP_NAME_BEST_ENDS, bumpMenuCB, NULL},
- {ZMAPGUI_MENU_RADIO, NULL, ZMAPBUMP_NAME, bumpMenuCB, NULL},
{ZMAPGUI_MENU_RADIO, NULL, ZMAPBUMP_OVERLAP, bumpMenuCB, NULL},
{ZMAPGUI_MENU_RADIO, NULL, ZMAPBUMP_START_POSITION, bumpMenuCB, NULL},
{ZMAPGUI_MENU_RADIO, NULL, ZMAPBUMP_ALTERNATING, bumpMenuCB, NULL},
@@ -538,7 +540,7 @@ ZMapGUIMenuItem zmapWindowMakeMenuTranscriptTools(int *start_index_inout,
return menu ;
}
-static void transcriptNavMenuCB(int menu_item_id, gpointer callback_data)
+static void transcriptNavMenuCB(int menu_item_id, gpointer callback_data)
{
ItemMenuCBData menu_data = (ItemMenuCBData)callback_data;
ZMapWindow window = NULL;
@@ -568,7 +570,7 @@ static void transcriptNavMenuCB(int menu_item_id, gpointer callback_data)
g_array_append_val(patterns, split_style);
/*
*/
- split.split_patterns = patterns;
+ split.split_patterns = patterns;
(*(window->caller_cbs->splitToPattern))(window, window->app_data, &split);
}
@@ -586,7 +588,7 @@ static void transcriptNavMenuCB(int menu_item_id, gpointer callback_data)
split_style.orientation = GTK_ORIENTATION_HORIZONTAL;
g_array_append_val(patterns, split_style);
- split.split_patterns = patterns;
+ split.split_patterns = patterns;
(*(window->caller_cbs->splitToPattern))(window, window->app_data, &split);
}
@@ -725,7 +727,7 @@ static void compressMenuCB(int menu_item_id, gpointer callback_data)
g_free(menu_data) ;
return ;
-
+
}
@@ -779,7 +781,7 @@ static void unbumpAllCB(int menu_item_id, gpointer callback_data)
}
/* Bump a column and reposition the other columns.
- *
+ *
* NOTE that this function may be called for an individual feature OR a column and
* needs to deal with both.
*/
@@ -807,7 +809,7 @@ static void bumpMenuCB(int menu_item_id, gpointer callback_data)
}
/* Bump a column and reposition the other columns.
- *
+ *
* NOTE that this function may be called for an individual feature OR a column and
* needs to deal with both.
*/
@@ -823,11 +825,11 @@ static void bumpToggleMenuCB(int menu_item_id, gpointer callback_data)
ZMapWindowContainerFeatureSet container;
ZMapStyleBumpMode curr_bump_mode, bump_mode ;
ZMapWindowCompressMode compress_mode ;
-
+
container = (ZMapWindowContainerFeatureSet)column_group;
curr_bump_mode = zmapWindowContainerFeatureSetGetBumpMode(container);
-
+
if (curr_bump_mode != ZMAPBUMP_UNBUMP)
bump_mode = ZMAPBUMP_UNBUMP ;
else
@@ -837,9 +839,9 @@ static void bumpToggleMenuCB(int menu_item_id, gpointer callback_data)
compress_mode = ZMAPWINDOW_COMPRESS_MARK ;
else
compress_mode = ZMAPWINDOW_COMPRESS_ALL ;
-
+
zmapWindowColumnBumpRange(FOO_CANVAS_ITEM(column_group), bump_mode, compress_mode) ;
-
+
zmapWindowFullReposition(menu_data->window) ;
}
@@ -910,7 +912,7 @@ static void dumpMenuCB(int menu_item_id, gpointer callback_data)
dumpFASTA(menu_data->window, ZMAPFASTA_SEQTYPE_DNA, sequence, seq_name, seq_len, "DNA", NULL) ;
else
zMapShowMsg(ZMAP_MSG_WARNING, "%s", "Context contains no DNA.") ;
-
+
break ;
}
case 2:
@@ -1171,7 +1173,7 @@ static void blixemMenuCB(int menu_item_id, gpointer callback_data)
/* this needs to be a general function... */
-static FooCanvasGroup *menuDataItemToColumn(FooCanvasItem *item)
+static FooCanvasGroup *menuDataItemToColumn(FooCanvasItem *item)
{
ZMapWindowContainerGroup container;
FooCanvasGroup *column_group = NULL;
@@ -1260,7 +1262,7 @@ static void dumpFeatures(ZMapWindow window, ZMapSpan region_span, ZMapFeatureAny
if (error)
{
zMapShowMsg(ZMAP_MSG_WARNING, "%s %s", error_prefix, error->message) ;
-
+
g_error_free(error) ;
}
}
@@ -1326,7 +1328,7 @@ static void dumpContext(ZMapWindow window)
* This is an attempt to make dynamic menus... Only really worth it
* for the align & block menus. With others a static struct, as above,
- * is much more preferable.
+ * is much more preferable.
*/
@@ -1348,11 +1350,11 @@ static void insertSubMenus(GString *branch_point_string,
item->name = g_strdup(branch_point_string->str); /* memory leak */
- *items_array = g_array_append_val(*items_array, *item);
+ *items_array = g_array_append_val(*items_array, *item);
}
-
- branch_point_string = g_string_erase(branch_point_string,
- branch_length,
+
+ branch_point_string = g_string_erase(branch_point_string,
+ branch_length,
branch_point_string->len - branch_length);
sub_menus++; /* move on */
}
@@ -1361,8 +1363,8 @@ static void insertSubMenus(GString *branch_point_string,
}
-static ZMapFeatureContextExecuteStatus alignBlockMenusDataListForeach(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus alignBlockMenusDataListForeach(GQuark key,
+ gpointer data,
gpointer user_data,
char **error_out)
{
@@ -1385,14 +1387,14 @@ static ZMapFeatureContextExecuteStatus alignBlockMenusDataListForeach(GQuark key
{
case ZMAPFEATURE_STRUCT_ALIGN:
item_name = g_string_sized_new(100);
- g_string_printf(item_name, "%s%sAlign %s",
+ g_string_printf(item_name, "%s%sAlign %s",
(stem ? stem : ""),
(stem ? "/" : ""),
g_quark_to_string( feature_any->original_id ));
item->name = g_strdup(item_name->str); /* memory leak */
item->type = ZMAPGUI_MENU_BRANCH;
- *items_array = g_array_append_val(*items_array, *item);
+ *items_array = g_array_append_val(*items_array, *item);
align_items = all_data->each_align_items;
while(align_items && align_items->name != NULL)
@@ -1411,7 +1413,7 @@ static ZMapFeatureContextExecuteStatus alignBlockMenusDataListForeach(GQuark key
break;
case ZMAPFEATURE_STRUCT_BLOCK:
item_name = g_string_sized_new(100);
- g_string_printf(item_name, "%s%sAlign %s/Block %s",
+ g_string_printf(item_name, "%s%sAlign %s/Block %s",
(stem ? stem : ""),
(stem ? "/" : ""),
g_quark_to_string( feature_any->parent->original_id ),
@@ -1419,7 +1421,7 @@ static ZMapFeatureContextExecuteStatus alignBlockMenusDataListForeach(GQuark key
item->name = g_strdup(item_name->str); /* memory leak */
item->type = ZMAPGUI_MENU_BRANCH;
- *items_array = g_array_append_val(*items_array, *item);
+ *items_array = g_array_append_val(*items_array, *item);
block_items = all_data->each_block_items;
while(block_items && block_items->name != NULL)
@@ -1454,10 +1456,10 @@ static ZMapFeatureContextExecuteStatus alignBlockMenusDataListForeach(GQuark key
}
-void zMapWindowMenuAlignBlockSubMenus(ZMapWindow window,
- ZMapGUIMenuItem each_align,
- ZMapGUIMenuItem each_block,
- char *root,
+void zMapWindowMenuAlignBlockSubMenus(ZMapWindow window,
+ ZMapGUIMenuItem each_align,
+ ZMapGUIMenuItem each_block,
+ char *root,
GArray **items_array_out)
{
zMapAssert(window);
@@ -1468,10 +1470,10 @@ void zMapWindowMenuAlignBlockSubMenus(ZMapWindow window,
data.stem = root;
data.array = items_array_out;
- zMapFeatureContextExecute((ZMapFeatureAny)(window->feature_context),
- ZMAPFEATURE_STRUCT_BLOCK,
+ zMapFeatureContextExecute((ZMapFeatureAny)(window->feature_context),
+ ZMAPFEATURE_STRUCT_BLOCK,
alignBlockMenusDataListForeach,
&data);
-
+
return ;
}