From 7c9c2c5abb1620849e878590afdf6c4c4b9da605 Mon Sep 17 00:00:00 2001
From: rds <rds>
Date: Fri, 13 Feb 2009 10:39:21 +0000
Subject: [PATCH] implementing feature in RT ticket #95467
---
src/zmapWindow/zmapWindow.c | 51 +++++++++++++++++++++++-
src/zmapWindow/zmapWindowFeature.c | 14 +++++--
src/zmapWindow/zmapWindowMenus.c | 62 ++++++++++++++++++++++++------
3 files changed, 110 insertions(+), 17 deletions(-)
diff --git a/src/zmapWindow/zmapWindow.c b/src/zmapWindow/zmapWindow.c
index d227ad235..308b0f120 100755
--- a/src/zmapWindow/zmapWindow.c
+++ b/src/zmapWindow/zmapWindow.c
@@ -26,9 +26,9 @@
*
* Exported functions: See ZMap/zmapWindow.h
* HISTORY:
- * Last edited: Feb 12 16:13 2009 (edgrif)
+ * Last edited: Feb 13 10:19 2009 (rds)
* Created: Thu Jul 24 14:36:27 2003 (edgrif)
- * CVS info: $Id: zmapWindow.c,v 1.270 2009-02-12 16:14:01 edgrif Exp $
+ * CVS info: $Id: zmapWindow.c,v 1.271 2009-02-13 10:39:21 rds Exp $
*-------------------------------------------------------------------
*/
@@ -3692,7 +3692,54 @@ static gboolean keyboardEvent(ZMapWindow window, GdkEventKey *key_event)
break ;
}
+ case GDK_a:
+ case GDK_A:
+ {
+ ZMapWindowCallbackCommandAlignStruct align;
+ ZMapWindowCallbacks window_callbacks_G = zmapWindowGetCBs();
+ ZMapFeature feature;
+ gboolean column = FALSE;
+ FooCanvasItem *focus_item ;
+
+ if ((focus_item = zmapWindowFocusGetHotItem(window->focus)))
+ focus_item = zmapWindowItemGetTrueItem(focus_item) ;
+ else
+ focus_item = FOO_CANVAS_ITEM(zmapWindowFocusGetHotColumn(window->focus)) ;
+
+ feature = g_object_get_data(G_OBJECT(focus_item), ITEM_FEATURE_DATA) ;
+ zMapAssert(feature) ; /* something badly wrong if no feature. */
+
+ if(feature->struct_type == ZMAPFEATURE_STRUCT_FEATURESET)
+ {
+ /* need to fix implicit dec here! */
+ feature = zMap_g_hash_table_nth(((ZMapFeatureSet)feature)->features, 0);
+ column = TRUE;
+ }
+
+ if(feature->type == ZMAPSTYLE_MODE_ALIGNMENT)
+ {
+ align.cmd = ZMAPWINDOW_CMD_SHOWALIGN ;
+ align.feature = feature ;
+ align.obey_protein_featuresets = FALSE;
+ align.obey_dna_featuresets = FALSE;
+ align.single_feature = FALSE;
+
+ if(key_event->keyval == GDK_A)
+ {
+ if(feature->feature.homol.type == ZMAPHOMOL_X_HOMOL ||
+ feature->feature.homol.type == ZMAPHOMOL_TX_HOMOL)
+ align.obey_protein_featuresets = TRUE;
+ else if(feature->feature.homol.type == ZMAPHOMOL_N_HOMOL)
+ align.obey_dna_featuresets = TRUE;
+ }
+ if((!column) && (key_event->state & GDK_CONTROL_MASK))
+ align.single_feature = TRUE;
+
+ (*(window_callbacks_G->command))(window, window->app_data, &align) ;
+ }
+ }
+ break;
case GDK_b:
case GDK_B:
{
diff --git a/src/zmapWindow/zmapWindowFeature.c b/src/zmapWindow/zmapWindowFeature.c
index 1eff4f462..e632e0726 100755
--- a/src/zmapWindow/zmapWindowFeature.c
+++ b/src/zmapWindow/zmapWindowFeature.c
@@ -28,9 +28,9 @@
*
* Exported functions: See zmapWindow_P.h
* HISTORY:
- * Last edited: Feb 11 11:41 2009 (rds)
+ * Last edited: Feb 13 09:23 2009 (rds)
* Created: Mon Jan 9 10:25:40 2006 (edgrif)
- * CVS info: $Id: zmapWindowFeature.c,v 1.154 2009-02-11 15:14:38 rds Exp $
+ * CVS info: $Id: zmapWindowFeature.c,v 1.155 2009-02-13 10:39:21 rds Exp $
*-------------------------------------------------------------------
*/
@@ -1690,9 +1690,15 @@ void zmapMakeItemMenu(GdkEventButton *button_event, ZMapWindow window, FooCanvas
menu_sets = g_list_append(menu_sets, makeMenuPfetchOps(NULL, NULL, menu_data)) ;
if (feature->feature.homol.type == ZMAPHOMOL_X_HOMOL)
- menu_sets = g_list_append(menu_sets, zmapWindowMakeMenuProteinHomol(NULL, NULL, menu_data)) ;
+ {
+ menu_sets = g_list_append(menu_sets, zmapWindowMakeMenuProteinHomolFeature(NULL, NULL, menu_data)) ;
+ menu_sets = g_list_append(menu_sets, zmapWindowMakeMenuProteinHomol(NULL, NULL, menu_data)) ;
+ }
else
- menu_sets = g_list_append(menu_sets, zmapWindowMakeMenuDNAHomol(NULL, NULL, menu_data)) ;
+ {
+ menu_sets = g_list_append(menu_sets, zmapWindowMakeMenuDNAHomolFeature(NULL, NULL, menu_data)) ;
+ menu_sets = g_list_append(menu_sets, zmapWindowMakeMenuDNAHomol(NULL, NULL, menu_data)) ;
+ }
}
/* DNA/Peptide ops. */
diff --git a/src/zmapWindow/zmapWindowMenus.c b/src/zmapWindow/zmapWindowMenus.c
index 1ba73a2e5..ec5a58852 100755
--- a/src/zmapWindow/zmapWindowMenus.c
+++ b/src/zmapWindow/zmapWindowMenus.c
@@ -27,9 +27,9 @@
* Exported functions: ZMap/zmapWindows.h
*
* HISTORY:
- * Last edited: Feb 9 12:27 2009 (rds)
+ * Last edited: Feb 13 10:35 2009 (rds)
* Created: Thu Mar 10 07:56:27 2005 (edgrif)
- * CVS info: $Id: zmapWindowMenus.c,v 1.55 2009-02-09 14:55:08 rds Exp $
+ * CVS info: $Id: zmapWindowMenus.c,v 1.56 2009-02-13 10:39:21 rds Exp $
*-------------------------------------------------------------------
*/
@@ -64,6 +64,12 @@
#define DEVELOPER_STR "Developer"
+#define BLIXEM_MENU_STR "Blixem "
+#define BLIXEM_DNA_STR "DNA Alignment"
+#define BLIXEM_DNAS_STR BLIXEM_DNA_STR "s"
+#define BLIXEM_AA_STR "Protein Alignment"
+#define BLIXEM_AAS_STR BLIXEM_AA_STR "s"
+
/* Choose which way a transcripts dna is dumped... */
enum
@@ -986,7 +992,6 @@ static void developerMenuCB(int menu_item_id, gpointer callback_data)
}
-
/* JAMES HAS MADE THE POINT THAT ANNOTATORS ONLY EVER USE THE "JUST THIS TYPE" OPTION, SO
* I'VE COMMENTED OUT THE TWO MENU OPTIONS AND REPLACED THEM WITH ONE.... */
ZMapGUIMenuItem zmapWindowMakeMenuDNAHomol(int *start_index_inout,
@@ -995,9 +1000,9 @@ ZMapGUIMenuItem zmapWindowMakeMenuDNAHomol(int *start_index_inout,
{
static ZMapGUIMenuItemStruct menu[] =
{
- {ZMAPGUI_MENU_NORMAL, "Blixem (DNA alignments) [this column]", 2, blixemMenuCB, NULL},
- {ZMAPGUI_MENU_NORMAL, "Blixem (DNA alignments) [all columns]", 1, blixemMenuCB, NULL},
- {ZMAPGUI_MENU_NONE, NULL, 0, NULL, NULL}
+ {ZMAPGUI_MENU_NORMAL, BLIXEM_MENU_STR BLIXEM_DNAS_STR, 1, blixemMenuCB, NULL, "a"},
+ {ZMAPGUI_MENU_NORMAL, BLIXEM_MENU_STR BLIXEM_DNAS_STR " - All Columns", 2, blixemMenuCB, NULL, "<shift>A"},
+ {ZMAPGUI_MENU_NONE, NULL, 0, NULL, NULL}
} ;
@@ -1006,15 +1011,46 @@ ZMapGUIMenuItem zmapWindowMakeMenuDNAHomol(int *start_index_inout,
return menu ;
}
+ZMapGUIMenuItem zmapWindowMakeMenuDNAHomolFeature(int *start_index_inout,
+ ZMapGUIMenuItemCallbackFunc callback_func,
+ gpointer callback_data)
+{
+ static ZMapGUIMenuItemStruct menu[] =
+ {
+ {ZMAPGUI_MENU_NORMAL, BLIXEM_MENU_STR BLIXEM_DNA_STR " - Feature", 3, blixemMenuCB, NULL, "<Ctrl>A"},
+ {ZMAPGUI_MENU_NONE, NULL, 0, NULL, NULL}
+ } ;
+
+
+ zMapGUIPopulateMenu(menu, start_index_inout, callback_func, callback_data) ;
+
+ return menu ;
+}
+
+ZMapGUIMenuItem zmapWindowMakeMenuProteinHomolFeature(int *start_index_inout,
+ ZMapGUIMenuItemCallbackFunc callback_func,
+ gpointer callback_data)
+{
+ static ZMapGUIMenuItemStruct menu[] =
+ {
+ {ZMAPGUI_MENU_NORMAL, BLIXEM_MENU_STR BLIXEM_AA_STR "", 3, blixemMenuCB, NULL, "<Ctrl>A"},
+ {ZMAPGUI_MENU_NONE, NULL, 0, NULL, NULL}
+ } ;
+
+ zMapGUIPopulateMenu(menu, start_index_inout, callback_func, callback_data) ;
+
+ return menu ;
+}
+
ZMapGUIMenuItem zmapWindowMakeMenuProteinHomol(int *start_index_inout,
ZMapGUIMenuItemCallbackFunc callback_func,
gpointer callback_data)
{
static ZMapGUIMenuItemStruct menu[] =
{
- {ZMAPGUI_MENU_NORMAL, "Blixem (Protein alignments) [this column]", 4, blixemMenuCB, NULL},
- {ZMAPGUI_MENU_NORMAL, "Blixem (Protein alignments) [all columns]", 3, blixemMenuCB, NULL},
- {ZMAPGUI_MENU_NONE, NULL, 0, NULL, NULL}
+ {ZMAPGUI_MENU_NORMAL, BLIXEM_MENU_STR BLIXEM_AAS_STR, 4, blixemMenuCB, NULL, "a"},
+ {ZMAPGUI_MENU_NORMAL, BLIXEM_MENU_STR BLIXEM_AAS_STR " - All Columns", 5, blixemMenuCB, NULL, "<shift>A"},
+ {ZMAPGUI_MENU_NONE, NULL, 0, NULL, NULL}
} ;
zMapGUIPopulateMenu(menu, start_index_inout, callback_func, callback_data) ;
@@ -1044,15 +1080,19 @@ static void blixemMenuCB(int menu_item_id, gpointer callback_data)
align.feature = feature ;
align.obey_protein_featuresets = FALSE;
align.obey_dna_featuresets = FALSE;
+ align.single_feature = FALSE;
switch(menu_item_id)
{
- case 1:
+ case 2:
align.obey_dna_featuresets = TRUE;
break;
- case 3:
+ case 5:
align.obey_protein_featuresets = TRUE;
break;
+ case 3:
+ align.single_feature = TRUE;
+ break;
default:
break;
}
--
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