From 31c0852ceae01850cc545b995962d960f7ce4133 Mon Sep 17 00:00:00 2001
From: mh17 <mh17>
Date: Mon, 15 Mar 2010 11:00:39 +0000
Subject: [PATCH] implemented delayed server
---
src/include/ZMap/zmapBase.h | 12 +-
src/include/ZMap/zmapServerProtocol.h | 24 +-
src/include/ZMap/zmapStyle.h | 4 +-
src/zmapFeature/zmapStyle.c | 380 +++++----
src/zmapFeature/zmapStyle_I.h | 10 +-
src/zmapFeature/zmapStyle_P.h | 8 +-
src/zmapServer/pipe/pipeServer.c | 89 ++-
src/zmapServer/zmapServerProtocolHandler.c | 64 +-
src/zmapUtils/zmapBase.c | 70 +-
src/zmapUtils/zmapGUITreeView.c | 3 +-
src/zmapUtils/zmapGUITreeView_I.h | 7 +-
src/zmapView/zmapView.c | 870 +++++++++++----------
src/zmapView/zmapViewUtils.c | 434 ++++------
src/zmapView/zmapView_P.h | 138 ++--
src/zmapWindow/zmapWindowDNAList.c | 3 +-
15 files changed, 1052 insertions(+), 1064 deletions(-)
diff --git a/src/include/ZMap/zmapBase.h b/src/include/ZMap/zmapBase.h
index d138cb20e..e58d5c87e 100755
--- a/src/include/ZMap/zmapBase.h
+++ b/src/include/ZMap/zmapBase.h
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Nov 13 10:54 2008 (edgrif)
* Created: Thu Jun 12 12:09:39 2008 (rds)
- * CVS info: $Id: zmapBase.h,v 1.5 2010-03-04 15:14:48 mh17 Exp $
+ * CVS info: $Id: zmapBase.h,v 1.6 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -55,11 +55,11 @@
/* Used as retrieval key for source object for object copy code. */
#define ZMAPBASECOPY_PARAMDATA_KEY "ZMap_Base_Copy_Key"
-
-#define ZMAP_PARAM_STATIC (G_PARAM_STATIC_NAME | G_PARAM_STATIC_NICK | G_PARAM_STATIC_BLURB)
-#define ZMAP_PARAM_STATIC_RW (ZMAP_PARAM_STATIC | G_PARAM_READWRITE)
-#define ZMAP_PARAM_STATIC_RO (ZMAP_PARAM_STATIC | G_PARAM_READABLE)
-#define ZMAP_PARAM_STATIC_WO (ZMAP_PARAM_STATIC | G_PARAM_WRITABLE)
+#define ZMAP_PARAM_STATIC_STRINGS (G_PARAM_STATIC_NAME | G_PARAM_STATIC_NICK | G_PARAM_STATIC_BLURB)
+//(GLIB supposedly defines the above as G_..., but it's not there)
+#define ZMAP_PARAM_STATIC_RW (ZMAP_PARAM_STATIC_STRINGS | G_PARAM_READWRITE)
+#define ZMAP_PARAM_STATIC_RO (ZMAP_PARAM_STATIC_STRINGS | G_PARAM_READABLE)
+#define ZMAP_PARAM_STATIC_WO (ZMAP_PARAM_STATIC_STRINGS | G_PARAM_WRITABLE)
/*
diff --git a/src/include/ZMap/zmapServerProtocol.h b/src/include/ZMap/zmapServerProtocol.h
index 7a0fa187f..795a5afee 100755
--- a/src/include/ZMap/zmapServerProtocol.h
+++ b/src/include/ZMap/zmapServerProtocol.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.
@@ -22,14 +22,14 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk,
*
- * Description: Interface for creating requests and passing them from
+ * Description: Interface for creating requests and passing them from
* the master thread to slave threads. Requests are via
* structs that give all the information/fields for the request/reply.
- *
+ *
* HISTORY:
* Last edited: Jan 14 09:49 2010 (edgrif)
* Created: Wed Feb 2 11:47:16 2005 (edgrif)
- * CVS info: $Id: zmapServerProtocol.h,v 1.31 2010-03-04 15:15:13 mh17 Exp $
+ * CVS info: $Id: zmapServerProtocol.h,v 1.32 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_PROTOCOL_H
@@ -57,7 +57,7 @@ extern gboolean zmap_server_styles_debug_G;
_(ZMAP_SERVERREQ_FEATURES, , "features", "features", "Get the context features.") \
_(ZMAP_SERVERREQ_SEQUENCE, , "sequence", "sequence", "Get the context sequence.") \
_(ZMAP_SERVERREQ_GETSEQUENCE, , "getsequence", "getsequence", "Get an arbitrary (named) sequence.") \
- _(ZMAP_SERVERREQ_TERMINATE, , "terminate", "terminate", "Close and destroy the connection.")
+ _(ZMAP_SERVERREQ_TERMINATE, , "terminate", "terminate", "Close and destroy the connection.")
ZMAP_DEFINE_ENUM(ZMapServerReqType, ZMAP_SERVER_REQ_LIST) ;
@@ -76,7 +76,7 @@ ZMAP_DEFINE_ENUM(ZMapServerResponseType, ZMAP_SERVER_RESPONSE_LIST) ;
-/*
+/*
* ALL request/response structs must replicate the generic ZMapServerReqAnyStruct
* so that they can all be treated as the canonical ZMapServerReqAny.
*/
@@ -229,6 +229,14 @@ typedef struct
} ZMapServerReqGetSequenceStruct, *ZMapServerReqGetSequence ;
+typedef struct
+{
+ ZMapServerReqType type ;
+ ZMapServerResponseType response ;
+
+} ZMapServerReqTerminateStruct, *ZMapServerReqTerminate ;
+
+
/* Use if you want to include any possible struct in a struct of your own. */
typedef union
{
@@ -240,6 +248,8 @@ typedef union
ZMapServerReqStylesStruct get_styles ;
ZMapServerReqNewContextStruct get_context ;
ZMapServerReqGetFeaturesStruct get_features ;
+ ZMapServerReqGetSequenceStruct get_sequence;
+ ZMapServerReqTerminateStruct terminate;
} ZMapServerReqUnion ;
diff --git a/src/include/ZMap/zmapStyle.h b/src/include/ZMap/zmapStyle.h
index 46b79c325..747f27f71 100755
--- a/src/include/ZMap/zmapStyle.h
+++ b/src/include/ZMap/zmapStyle.h
@@ -28,13 +28,13 @@
* HISTORY:
* Last edited: Jan 26 08:42 2010 (edgrif)
* Created: Mon Feb 26 09:28:26 2007 (edgrif)
- * CVS info: $Id: zmapStyle.h,v 1.49 2010-03-04 15:15:15 mh17 Exp $
+ * CVS info: $Id: zmapStyle.h,v 1.50 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_STYLE_H
#define ZMAP_STYLE_H
-
+#include <glib.h>
#include <glib-object.h>
#include <gtk/gtk.h>
#include <ZMap/zmapEnum.h>
diff --git a/src/zmapFeature/zmapStyle.c b/src/zmapFeature/zmapStyle.c
index f0ac1e6b1..0a351dc73 100755
--- a/src/zmapFeature/zmapStyle.c
+++ b/src/zmapFeature/zmapStyle.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.
@@ -30,25 +30,25 @@
* HISTORY:
* Last edited: Jul 29 09:27 2009 (edgrif)
* Created: Mon Feb 26 09:12:18 2007 (edgrif)
- * CVS info: $Id: zmapStyle.c,v 1.40 2010-03-04 15:10:31 mh17 Exp $
+ * CVS info: $Id: zmapStyle.c,v 1.41 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
#include <string.h>
#include <ZMap/zmapUtils.h>
-#include <zmapStyle_P.h>
+#include <zmapStyle_I.h>
-/*
+/*
* PLEASE READ THIS......
- *
+ *
* The g_object/paramspec stuff all needs redoing so that it's table driven
* otherwise we will all go mad.....it is way too error prone......
- *
+ *
* but it needs to be done carefully, we need the "set" flags to support
* inheritance....and they g_object copy/set/get code in glib all expects
* paramspecs etc so it's not straight forward...
- *
+ *
*/
@@ -154,13 +154,13 @@ static void set_implied_mode(ZMapFeatureTypeStyle style, guint param_id);
static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_class);
static void zmap_feature_type_style_init (ZMapFeatureTypeStyle style);
-static void zmap_feature_type_style_set_property(GObject *gobject,
- guint param_id,
- const GValue *value,
+static void zmap_feature_type_style_set_property(GObject *gobject,
+ guint param_id,
+ const GValue *value,
GParamSpec *pspec);
-static void zmap_feature_type_style_get_property(GObject *gobject,
- guint param_id,
- GValue *value,
+static void zmap_feature_type_style_get_property(GObject *gobject,
+ guint param_id,
+ GValue *value,
GParamSpec *pspec);
static void zmap_feature_type_style_dispose (GObject *object);
static void zmap_feature_type_style_finalize(GObject *object);
@@ -200,16 +200,16 @@ static ZMapBaseClass style_parent_class_G = NULL ;
/*!
* The Style is now a GObject, this function returns the class "type" of the
* style in the GObject sense.
- *
+ *
* @return GType The Style GObject type.
* */
GType zMapFeatureTypeStyleGetType(void)
{
static GType type = 0;
-
- if (type == 0)
+
+ if (type == 0)
{
- static const GTypeInfo info =
+ static const GTypeInfo info =
{
sizeof (zmapFeatureTypeStyleClass),
(GBaseInitFunc) NULL,
@@ -222,12 +222,12 @@ GType zMapFeatureTypeStyleGetType(void)
(GInstanceInitFunc) zmap_feature_type_style_init,
NULL
};
-
- type = g_type_register_static (ZMAP_TYPE_BASE,
- "ZMapFeatureTypeStyle",
+
+ type = g_type_register_static (ZMAP_TYPE_BASE,
+ "ZMapFeatureTypeStyle",
&info, (GTypeFlags)0);
}
-
+
return type;
}
@@ -251,7 +251,7 @@ ZMapFeatureTypeStyle zMapStyleCreate(char *name, char *description)
num_params++ ;
if (description && *description)
- {
+ {
g_value_init(&(params[1].value), G_TYPE_STRING) ;
params[1].name = "description" ;
g_value_set_string(&(params[1].value), description) ;
@@ -316,7 +316,7 @@ gboolean zMapStyleCCopy(ZMapFeatureTypeStyle src, ZMapFeatureTypeStyle *dest_out
* This is just like g_object_get() except that it returns a boolean
* to indicate success or failure. Note that if you supply several
* properties you will need to look in the logs to see which one failed.
- *
+ *
* @param style The style.
* @param first_property_name The start of the property name/variable pointers list
* (see g_object_get() for format of list).
@@ -331,7 +331,7 @@ gboolean zMapStyleGet(ZMapFeatureTypeStyle style, char *first_property_name, ...
* in this variable BUT we must init it to FALSE because if g_object_get() detects an error
* it will return _before_ our get function is run. */
g_object_set_data(G_OBJECT(style), ZMAPSTYLE_OBJ_RC, GINT_TO_POINTER(result)) ;
-
+
va_start(args1, first_property_name) ;
G_VA_COPY(args2, args1) ;
@@ -350,7 +350,7 @@ gboolean zMapStyleGet(ZMapFeatureTypeStyle style, char *first_property_name, ...
* This is just like g_object_set() except that it returns a boolean
* to indicate success or failure. Note that if you supply several
* properties you will need to look in the logs to see which one failed.
- *
+ *
* @param style The style.
* @param first_property_name The start of the property name/variable list
* (see g_object_set() for format of list).
@@ -365,7 +365,7 @@ gboolean zMapStyleSet(ZMapFeatureTypeStyle style, char *first_property_name, ...
* in this variable BUT we must init it to FALSE because if g_object_set() detects an error
* it will return _before_ our set function is run. */
g_object_set_data(G_OBJECT(style), ZMAPSTYLE_OBJ_RC, GINT_TO_POINTER(result)) ;
-
+
va_start(args1, first_property_name) ;
G_VA_COPY(args2, args1) ;
@@ -385,16 +385,16 @@ gboolean zMapStyleSet(ZMapFeatureTypeStyle style, char *first_property_name, ...
/* I see no easy way to do this with the "get" methodology of g_object_get(). Nor
* do I see a good way to make use of g_object stuff to help....
- *
+ *
* NOTE that property_name for all properties colours is simply the property
- * name, e.g. "min_mag".
+ * name, e.g. "min_mag".
*
* Colours have subparts however so the subpart must be specified in the form:
- *
+ *
* "<type> <context>", e.g. "normal draw"
*
* and then the function returns TRUE/FALSE to show if that particular colour is set.
- *
+ *
* */
gboolean zMapStyleIsPropertySet(ZMapFeatureTypeStyle style, char *property_name, char *property_subpart)
{
@@ -479,13 +479,13 @@ gboolean zMapStyleIsPropertySet(ZMapFeatureTypeStyle style, char *property_name,
{
if (style->fields_set.bump_fixed)
is_set = TRUE ;
- break;
+ break;
}
case STYLE_PROP_BUMP_SPACING:
{
if (style->fields_set.bump_spacing)
is_set = TRUE ;
- break;
+ break;
}
case STYLE_PROP_FRAME_MODE:
{
@@ -515,11 +515,11 @@ gboolean zMapStyleIsPropertySet(ZMapFeatureTypeStyle style, char *property_name,
{
if (style->fields_set.score_mode)
is_set = TRUE ;
- break;
+ break;
}
case STYLE_PROP_GFF_SOURCE:
{
- if (style->fields_set.gff_source)
+ if (style->fields_set.gff_source)
is_set = TRUE ;
break;
@@ -658,13 +658,13 @@ gboolean zMapStyleIsPropertySet(ZMapFeatureTypeStyle style, char *property_name,
is_set = TRUE ;
break;
}
-
+
case STYLE_PROP_ALIGNMENT_INCOMPLETE_GLYPH_COLOURS:
{
is_set = isColourSet(style, pspec->param_id, property_subpart) ;
break;
}
-
+
case STYLE_PROP_TRANSCRIPT_CDS_COLOURS:
{
is_set = isColourSet(style, pspec->param_id, property_subpart) ;
@@ -770,7 +770,7 @@ void zMapStyleDestroy(ZMapFeatureTypeStyle style)
/*!
* Does a case <i>insensitive</i> comparison of the style name and
* the supplied name, return TRUE if they are the same.
- *
+ *
* @param style The style.
* @param name The name to be compared..
* @return gboolean TRUE if the names are the same.
@@ -832,7 +832,7 @@ gboolean zMapStyleIsTrueFeature(ZMapFeatureTypeStyle style)
/* Checks a style to see if it contains the minimum necessary to be drawn,
* we need this function because we no longer allow defaults because we
* we want to do inheritance.
- *
+ *
* Function returns FALSE if there style is not valid and the GError says
* what the problem was.
* */
@@ -848,11 +848,11 @@ gboolean zMapStyleIsDrawable(ZMapFeatureTypeStyle style, GError **error)
domain = g_quark_from_string("ZmapStyle") ;
/* These are the absolute basic requirements without which we can't display something.... */
- if (valid && (style->original_id == ZMAPFEATURE_NULLQUARK || style->unique_id == ZMAPFEATURE_NULLQUARK))
+ if (valid && (style->original_id == ZMAPSTYLE_NULLQUARK || style->unique_id == ZMAPSTYLE_NULLQUARK))
{
valid = FALSE ;
code = 1 ;
- message = g_strdup_printf("Bad style ids, original: %d, unique: %d.",
+ message = g_strdup_printf("Bad style ids, original: %d, unique: %d.",
style->original_id, style->unique_id) ;
}
@@ -1164,7 +1164,7 @@ gboolean zMapStyleHasMode(ZMapFeatureTypeStyle style)
ZMapStyleMode zMapStyleGetMode(ZMapFeatureTypeStyle style)
{
ZMapStyleMode mode ;
-
+
g_object_get(style,
ZMAPSTYLE_PROPERTY_MODE, &mode,
NULL) ;
@@ -1444,9 +1444,9 @@ GdkColor *zMapStyleGetColour(ZMapFeatureTypeStyle style, ZMapStyleDrawContext co
/* I NOW THINK THIS FUNCTION IS REDUNDANT.... mh17: not true it has a new lease of life */
/* As for zMapStyleGetColours() but defaults colours that are not set in the style according
* to the style mode e.g. rules may be different for Transcript as opposed to Basic mode.
- *
+ *
* */
-gboolean zMapStyleGetColoursDefault(ZMapFeatureTypeStyle style,
+gboolean zMapStyleGetColoursDefault(ZMapFeatureTypeStyle style,
GdkColor **background, GdkColor **foreground, GdkColor **outline)
{
gboolean result = FALSE ;
@@ -1503,7 +1503,7 @@ gboolean zMapStyleGetColoursDefault(ZMapFeatureTypeStyle style,
// function not called...
/* This function looks for cds colours but defaults to the styles normal colours if there are none. */
-gboolean zMapStyleGetColoursCDSDefault(ZMapFeatureTypeStyle style,
+gboolean zMapStyleGetColoursCDSDefault(ZMapFeatureTypeStyle style,
GdkColor **background, GdkColor **foreground, GdkColor **outline)
{
gboolean result = FALSE ;
@@ -1561,7 +1561,7 @@ gboolean zMapStyleGetColoursCDSDefault(ZMapFeatureTypeStyle style,
/* This function looks for alignmemnt_incomplete_glyph colours but defaults to the styles normal colours if there are none. */
-gboolean zMapStyleGetColoursGlyphDefault(ZMapFeatureTypeStyle style,
+gboolean zMapStyleGetColoursGlyphDefault(ZMapFeatureTypeStyle style,
GdkColor **background, GdkColor **foreground, GdkColor **outline)
{
gboolean result = FALSE ;
@@ -1597,7 +1597,7 @@ gboolean zMapStyleGetColoursGlyphDefault(ZMapFeatureTypeStyle style,
}
// these default to some odd values!, we prefer to default to previous hard coded values
// currently only called from homology glyphs, in case we used these for free glyphs return false to allow other defaults
-#if MH17_DONT_USE
+#if MH17_DONT_USE
else
{
GdkColor *fill, *draw, *border ;
@@ -1739,7 +1739,7 @@ void zMapStyleGetGappedAligns(ZMapFeatureTypeStyle style, gboolean *parse_gaps,
void zMapStyleSetJoinAligns(ZMapFeatureTypeStyle style, unsigned int between_align_error)
{
zMapAssert(style);
-
+
if(style->mode == ZMAPSTYLE_MODE_ALIGNMENT)
{
style->mode_data.alignment.between_align_error = between_align_error ;
@@ -1995,7 +1995,7 @@ ZMapStyleGlyphType zMapStyleGlyphType(ZMapFeatureTypeStyle style)
-/*
+/*
* ZMapStyle package only functions.
*/
@@ -2014,7 +2014,7 @@ gboolean zmapStyleIsValid(ZMapFeatureTypeStyle style)
-/*
+/*
* Internal functions.
*/
@@ -2053,7 +2053,7 @@ static gboolean setColours(ZMapStyleColour colour, char *border, char *draw, cha
colour->fill = tmp_colour.fill ;
}
}
-
+
return status ;
}
@@ -2094,10 +2094,10 @@ static ZMapFeatureTypeStyle styleCreate(guint n_parameters, GParameter *paramete
* the mode_data union in the get/set_property functions... */
/* Without this, the copy of styles runs through each of the
- * properties doing a get_property. While doing this the
+ * properties doing a get_property. While doing this the
* code would access style.mode_data.text.font regardless
* of the style->mode, which could actually be an alignment
- * and mean that style.mode_data.text.font was completely
+ * and mean that style.mode_data.text.font was completely
* invalid as we've filled style.mode_data.alignment.parse_gaps
* etc... */
static void set_implied_mode(ZMapFeatureTypeStyle style, guint param_id)
@@ -2149,7 +2149,7 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
{
GObjectClass *gobject_class;
ZMapBaseClass zmap_class;
-
+
gobject_class = (GObjectClass *)style_class;
zmap_class = ZMAP_BASE_CLASS(style_class);
@@ -2171,14 +2171,14 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
g_object_class_install_property(gobject_class,
STYLE_PROP_ORIGINAL_ID,
g_param_spec_uint(ZMAPSTYLE_PROPERTY_ORIGINAL_ID, "original-id",
- "original id",
- 0, G_MAXUINT, 0,
+ "original id",
+ 0, G_MAXUINT, 0,
ZMAP_PARAM_STATIC_RO));
g_object_class_install_property(gobject_class,
STYLE_PROP_UNIQUE_ID,
g_param_spec_uint(ZMAPSTYLE_PROPERTY_UNIQUE_ID, "unique-id",
- "unique id",
- 0, G_MAXUINT, 0,
+ "unique id",
+ 0, G_MAXUINT, 0,
ZMAP_PARAM_STATIC_RO));
@@ -2186,8 +2186,8 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
g_object_class_install_property(gobject_class,
STYLE_PROP_PARENT_STYLE,
g_param_spec_uint(ZMAPSTYLE_PROPERTY_PARENT_STYLE, "parent-style",
- "Parent style unique id",
- 0, G_MAXUINT, 0,
+ "Parent style unique id",
+ 0, G_MAXUINT, 0,
ZMAP_PARAM_STATIC_RW));
/* description */
g_object_class_install_property(gobject_class,
@@ -2199,10 +2199,10 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
/* Mode */
g_object_class_install_property(gobject_class,
STYLE_PROP_MODE,
- g_param_spec_uint(ZMAPSTYLE_PROPERTY_MODE, "mode", "mode",
- ZMAPSTYLE_MODE_INVALID,
- ZMAPSTYLE_MODE_META,
- ZMAPSTYLE_MODE_INVALID,
+ g_param_spec_uint(ZMAPSTYLE_PROPERTY_MODE, "mode", "mode",
+ ZMAPSTYLE_MODE_INVALID,
+ ZMAPSTYLE_MODE_META,
+ ZMAPSTYLE_MODE_INVALID,
ZMAP_PARAM_STATIC_RW));
/* Colours... */
@@ -2240,10 +2240,10 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
g_object_class_install_property(gobject_class,
STYLE_PROP_COLUMN_DISPLAY_MODE,
g_param_spec_uint(ZMAPSTYLE_PROPERTY_DISPLAY_MODE, "display-mode",
- "Display mode",
- ZMAPSTYLE_COLDISPLAY_INVALID,
- ZMAPSTYLE_COLDISPLAY_SHOW,
- ZMAPSTYLE_COLDISPLAY_INVALID,
+ "Display mode",
+ ZMAPSTYLE_COLDISPLAY_INVALID,
+ ZMAPSTYLE_COLDISPLAY_SHOW,
+ ZMAPSTYLE_COLDISPLAY_INVALID,
ZMAP_PARAM_STATIC_RW));
@@ -2251,19 +2251,19 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
g_object_class_install_property(gobject_class,
STYLE_PROP_BUMP_MODE,
g_param_spec_uint(ZMAPSTYLE_PROPERTY_BUMP_MODE, "bump-mode",
- "The Bump Mode",
- ZMAPBUMP_INVALID,
- ZMAPBUMP_END,
- ZMAPBUMP_INVALID,
+ "The Bump Mode",
+ ZMAPBUMP_INVALID,
+ ZMAPBUMP_END,
+ ZMAPBUMP_INVALID,
ZMAP_PARAM_STATIC_RW));
/* bump default */
g_object_class_install_property(gobject_class,
STYLE_PROP_BUMP_DEFAULT,
g_param_spec_uint(ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE, "default-bump-mode",
- "The Default Bump Mode",
- ZMAPBUMP_INVALID,
- ZMAPBUMP_END,
- ZMAPBUMP_INVALID,
+ "The Default Bump Mode",
+ ZMAPBUMP_INVALID,
+ ZMAPBUMP_END,
+ ZMAPBUMP_INVALID,
ZMAP_PARAM_STATIC_RW));
/* bump fixed */
g_object_class_install_property(gobject_class,
@@ -2275,8 +2275,8 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
g_object_class_install_property(gobject_class,
STYLE_PROP_BUMP_SPACING,
g_param_spec_double(ZMAPSTYLE_PROPERTY_BUMP_SPACING, "bump-spacing",
- "space between columns in bumped columns",
- -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
+ "space between columns in bumped columns",
+ -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
ZMAP_PARAM_STATIC_RW));
/* Frame mode */
@@ -2284,8 +2284,8 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
STYLE_PROP_FRAME_MODE,
g_param_spec_uint(ZMAPSTYLE_PROPERTY_FRAME_MODE, "3 frame display mode",
"Defines frame sensitive display in 3 frame mode.",
- ZMAPSTYLE_3_FRAME_INVALID,
- ZMAPSTYLE_3_FRAME_ONLY_1,
+ ZMAPSTYLE_3_FRAME_INVALID,
+ ZMAPSTYLE_3_FRAME_ONLY_1,
ZMAPSTYLE_3_FRAME_INVALID,
ZMAP_PARAM_STATIC_RW));
@@ -2294,23 +2294,23 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
g_object_class_install_property(gobject_class,
STYLE_PROP_MIN_MAG,
g_param_spec_double(ZMAPSTYLE_PROPERTY_MIN_MAG, "min-mag",
- "minimum magnification",
- -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
+ "minimum magnification",
+ -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
ZMAP_PARAM_STATIC_RW));
/* max mag */
g_object_class_install_property(gobject_class,
STYLE_PROP_MAX_MAG,
g_param_spec_double(ZMAPSTYLE_PROPERTY_MAX_MAG, "max-mag",
- "maximum magnification",
- -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
+ "maximum magnification",
+ -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
ZMAP_PARAM_STATIC_RW));
/* width */
g_object_class_install_property(gobject_class,
STYLE_PROP_WIDTH,
g_param_spec_double(ZMAPSTYLE_PROPERTY_WIDTH, "width",
- "Width",
- -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
+ "Width",
+ -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
ZMAP_PARAM_STATIC_RW));
/* score mode */
g_object_class_install_property(gobject_class,
@@ -2325,15 +2325,15 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
g_object_class_install_property(gobject_class,
STYLE_PROP_MIN_SCORE,
g_param_spec_double(ZMAPSTYLE_PROPERTY_MIN_SCORE, "min-score",
- "minimum score",
- -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
+ "minimum score",
+ -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
ZMAP_PARAM_STATIC_RW));
/* max score */
g_object_class_install_property(gobject_class,
STYLE_PROP_MAX_SCORE,
g_param_spec_double(ZMAPSTYLE_PROPERTY_MAX_SCORE, "max-score",
- "maximum score",
- -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
+ "maximum score",
+ -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
ZMAP_PARAM_STATIC_RW));
/* gff_source */
g_object_class_install_property(gobject_class,
@@ -2409,8 +2409,8 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
g_object_class_install_property(gobject_class,
STYLE_PROP_GRAPH_BASELINE,
g_param_spec_double(ZMAPSTYLE_PROPERTY_GRAPH_BASELINE, "graph baseline",
- "Sets the baseline for graph values.",
- -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
+ "Sets the baseline for graph values.",
+ -G_MAXDOUBLE, G_MAXDOUBLE, 0.0,
ZMAP_PARAM_STATIC_RW));
@@ -2423,14 +2423,14 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
ZMAPSTYLE_GLYPH_MARKER,
ZMAPSTYLE_GLYPH_INVALID,
ZMAP_PARAM_STATIC_RW));
-
+
g_object_class_install_property(gobject_class,
STYLE_PROP_GLYPH_TYPE,
g_param_spec_uint(ZMAPSTYLE_PROPERTY_GLYPH_TYPE, "glyph-type",
"Type of glyph to show.",
- ZMAPSTYLE_GLYPH_TYPE_INVALID,
- ZMAPSTYLE_GLYPH_TYPE_CIRCLE,
- ZMAPSTYLE_GLYPH_TYPE_DIAMOND,
+ ZMAPSTYLE_GLYPH_TYPE_INVALID,
+ ZMAPSTYLE_GLYPH_TYPE_CIRCLE,
+ ZMAPSTYLE_GLYPH_TYPE_DIAMOND,
ZMAP_PARAM_STATIC_RW)) ;
/* Parse out gap data from data source, selectable because data can be very large. */
@@ -2477,9 +2477,9 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
STYLE_PROP_ALIGNMENT_BLIXEM,
g_param_spec_uint(ZMAPSTYLE_PROPERTY_ALIGNMENT_BLIXEM, "Blixemable alignments",
"Use blixem to view sequence of alignments ?",
- ZMAPSTYLE_BLIXEM_INVALID,
- ZMAPSTYLE_BLIXEM_X,
- ZMAPSTYLE_BLIXEM_INVALID,
+ ZMAPSTYLE_BLIXEM_INVALID,
+ ZMAPSTYLE_BLIXEM_X,
+ ZMAPSTYLE_BLIXEM_INVALID,
ZMAP_PARAM_STATIC_RW)) ;
/* These three colours are used to join HSP's with colour lines to show colinearity. */
@@ -2499,9 +2499,9 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
STYLE_PROP_ALIGNMENT_INCOMPLETE_GLYPH,
g_param_spec_uint(ZMAPSTYLE_PROPERTY_ALIGNMENT_INCOMPLETE_GLYPH, "colinear alignment glyph type",
"Type of glyph to show when alignments are incomplete.",
- ZMAPSTYLE_GLYPH_TYPE_INVALID,
- ZMAPSTYLE_GLYPH_TYPE_CIRCLE,
- ZMAPSTYLE_GLYPH_TYPE_DIAMOND,
+ ZMAPSTYLE_GLYPH_TYPE_INVALID,
+ ZMAPSTYLE_GLYPH_TYPE_CIRCLE,
+ ZMAPSTYLE_GLYPH_TYPE_DIAMOND,
ZMAP_PARAM_STATIC_RW)) ;
g_object_class_install_property(gobject_class,
@@ -2537,7 +2537,7 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
"Font to draw text with.",
"", ZMAP_PARAM_STATIC_RW));
-
+
gobject_class->dispose = zmap_feature_type_style_dispose;
gobject_class->finalize = zmap_feature_type_style_finalize;
@@ -2557,17 +2557,17 @@ static void zmap_feature_type_style_init(ZMapFeatureTypeStyle style)
/* This function is called both for straight SETTING of object properties and for COPYING
* of objects. During a copy, the "get_property" routine of one object is called to retrieve
* a value and the "set_property" routine of the new object is called to set that value.
- *
+ *
* For copies, the original style is stored on the style so we can retrieve it and do
* a "deep" copy because bizarrely gobjects interface does not give you access to the
* original style !
- *
+ *
* We return a status code in the property ZMAPSTYLE_OBJ_RC so that callers can detect
* whether this function succeeded or not.
* */
-static void zmap_feature_type_style_set_property(GObject *gobject,
- guint param_id,
- const GValue *value,
+static void zmap_feature_type_style_set_property(GObject *gobject,
+ guint param_id,
+ const GValue *value,
GParamSpec *pspec)
{
ZMapFeatureTypeStyle style, copy_style = NULL ;
@@ -2710,7 +2710,7 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
break;
}
-
+
case STYLE_PROP_BUMP_MODE:
{
SETMODEFIELD(style, copy_style, value, ZMapStyleBumpMode, fields_set.curr_bump_mode, curr_bump_mode, result) ;
@@ -2739,7 +2739,7 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
style->bump_spacing = g_value_get_double(value) ;
style->fields_set.bump_spacing = TRUE ;
}
- break;
+ break;
}
case STYLE_PROP_FRAME_MODE:
@@ -2798,7 +2798,7 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
style->fields_set.score_mode = TRUE ;
}
- break;
+ break;
}
case STYLE_PROP_MIN_SCORE:
{
@@ -2925,7 +2925,7 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
{
case STYLE_PROP_GRAPH_MODE:
{
- SETMODEFIELD(style, copy_style, value, ZMapStyleGraphMode,
+ SETMODEFIELD(style, copy_style, value, ZMapStyleGraphMode,
mode_data.graph.fields_set.mode, mode_data.graph.mode, result) ;
break ;
}
@@ -2934,14 +2934,14 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
if (!copy_style || copy_style->mode_data.graph.fields_set.baseline)
{
double baseline ;
-
+
/* Test value returned ?? */
baseline = g_value_get_double(value) ;
-
+
style->mode_data.graph.baseline = baseline ;
style->mode_data.graph.fields_set.baseline = TRUE ;
}
- break;
+ break;
}
default:
@@ -2971,7 +2971,7 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
{
case STYLE_PROP_GLYPH_MODE:
{
- SETMODEFIELD(style, copy_style, value, ZMapStyleGlyphMode,
+ SETMODEFIELD(style, copy_style, value, ZMapStyleGlyphMode,
mode_data.glyph.fields_set.mode, mode_data.glyph.mode, result) ;
break ;
}
@@ -3022,14 +3022,14 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
{
SETBOOLFIELD(style, copy_style, value, mode_data.alignment.fields_set.parse_gaps,
mode_data.alignment.state.parse_gaps) ;
-
+
break;
}
case STYLE_PROP_ALIGNMENT_SHOW_GAPS:
{
SETBOOLFIELD(style, copy_style, value, mode_data.alignment.fields_set.show_gaps,
mode_data.alignment.state.show_gaps) ;
-
+
break;
}
case STYLE_PROP_ALIGNMENT_BETWEEN_ERROR:
@@ -3037,53 +3037,53 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
if (!copy_style || copy_style->mode_data.alignment.fields_set.between_align_error)
{
unsigned int error ;
-
+
error = g_value_get_uint(value) ;
-
+
style->mode_data.alignment.between_align_error = error ;
style->mode_data.alignment.fields_set.between_align_error = TRUE ;
}
- break;
+ break;
}
case STYLE_PROP_ALIGNMENT_ALLOW_MISALIGN:
{
SETBOOLFIELD(style, copy_style, value,
- mode_data.alignment.fields_set.allow_misalign,
+ mode_data.alignment.fields_set.allow_misalign,
mode_data.alignment.state.allow_misalign) ;
-
+
break ;
}
case STYLE_PROP_ALIGNMENT_PFETCHABLE:
{
SETBOOLFIELD(style, copy_style, value,
- mode_data.alignment.fields_set.pfetchable,
+ mode_data.alignment.fields_set.pfetchable,
mode_data.alignment.state.pfetchable) ;
-
+
break ;
}
case STYLE_PROP_ALIGNMENT_BLIXEM:
{
SETMODEFIELD(style, copy_style, value, ZMapStyleBlixemType,
- mode_data.alignment.fields_set.blixem, mode_data.alignment.blixem_type,
+ mode_data.alignment.fields_set.blixem, mode_data.alignment.blixem_type,
result) ;
-
+
break ;
}
case STYLE_PROP_ALIGNMENT_PERFECT_COLOURS:
case STYLE_PROP_ALIGNMENT_COLINEAR_COLOURS:
case STYLE_PROP_ALIGNMENT_NONCOLINEAR_COLOURS:
- case STYLE_PROP_ALIGNMENT_INCOMPLETE_GLYPH_COLOURS:
+ case STYLE_PROP_ALIGNMENT_INCOMPLETE_GLYPH_COLOURS:
{
result = parseColours(style, copy_style, param_id, (GValue *)value) ;
-
+
break;
}
case STYLE_PROP_ALIGNMENT_INCOMPLETE_GLYPH:
{
SETMODEFIELD(style, copy_style, value, ZMapStyleGlyphType,
- mode_data.alignment.fields_set.incomplete_glyph, mode_data.alignment.incomplete_glyph_type,
+ mode_data.alignment.fields_set.incomplete_glyph, mode_data.alignment.incomplete_glyph_type,
result) ;
-
+
break;
}
default:
@@ -3121,7 +3121,7 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
default:
G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
result = FALSE ;
-
+
break;
}
}
@@ -3153,7 +3153,7 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
default:
G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
result = FALSE ;
-
+
break;
}
}
@@ -3184,9 +3184,9 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
if (!copy_style || copy_style->mode_data.text.fields_set.font)
{
char *font_name ;
-
+
font_name = g_value_dup_string(value) ;
-
+
style->mode_data.text.font = font_name;
style->mode_data.text.fields_set.font = 1;
}
@@ -3209,7 +3209,7 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
result = FALSE ;
break;
}
-
+
}
@@ -3226,14 +3226,14 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
* Note that the get might be called as part of a style copy in which case the gobject
* code will try to set _all_ properties so we have to deal with this for the mode
* specific properties by ignoring inappropriate ones.
- *
+ *
* We return a status code in the property ZMAPSTYLE_OBJ_RC so that callers can detect
* whether this function succeeded or not.
- *
+ *
* this function pays no attention to the field_set data...is this correct ???? */
-static void zmap_feature_type_style_get_property(GObject *gobject,
- guint param_id,
- GValue *value,
+static void zmap_feature_type_style_get_property(GObject *gobject,
+ guint param_id,
+ GValue *value,
GParamSpec *pspec)
{
ZMapFeatureTypeStyle style;
@@ -3317,7 +3317,7 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
case STYLE_PROP_FRAME2_COLOURS:
case STYLE_PROP_REV_COLOURS:
{
- /* We allocate memory here to hold the colour string, it's g_object_get caller's
+ /* We allocate memory here to hold the colour string, it's g_object_get caller's
* responsibility to g_free the string... */
ZMapStyleFullColour this_colour = NULL ;
GString *colour_string = NULL ;
@@ -3347,7 +3347,7 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
formatColours(colour_string, "normal", &(this_colour->normal)) ;
formatColours(colour_string, "selected", &(this_colour->selected)) ;
-
+
if (colour_string->len)
g_value_set_string(value, g_string_free(colour_string, FALSE)) ;
else
@@ -3362,7 +3362,7 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
case STYLE_PROP_MIN_SCORE:
{
if (style->fields_set.min_score)
- g_value_set_double(value, style->min_score);
+ g_value_set_double(value, style->min_score);
else
result = FALSE ;
@@ -3411,7 +3411,7 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
else
result = FALSE ;
- break;
+ break;
}
case STYLE_PROP_FRAME_MODE:
{
@@ -3456,11 +3456,11 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
else
result = FALSE ;
- break;
+ break;
}
case STYLE_PROP_GFF_SOURCE:
{
- if (style->fields_set.gff_source)
+ if (style->fields_set.gff_source)
g_value_set_string(value, g_quark_to_string(style->gff_source));
else
result = FALSE ;
@@ -3588,7 +3588,7 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
case STYLE_PROP_GRAPH_BASELINE:
{
if (style->mode_data.graph.fields_set.baseline)
- g_value_set_double(value, style->mode_data.graph.baseline) ;
+ g_value_set_double(value, style->mode_data.graph.baseline) ;
else
result = FALSE ;
@@ -3609,6 +3609,7 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
case STYLE_PROP_GLYPH_MODE:
+ case STYLE_PROP_GLYPH_TYPE:
{
/* Handle all glyph specific options. */
@@ -3630,9 +3631,16 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
g_value_set_uint(value, style->mode_data.glyph.mode);
else
result = FALSE ;
-
- break ;
- }
+ }
+ break ;
+ case STYLE_PROP_GLYPH_TYPE:
+ {
+ if (style->mode_data.glyph.fields_set.type)
+ g_value_set_uint(value, style->mode_data.glyph.type);
+ else
+ result = FALSE ;
+ }
+ break;
default:
{
G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
@@ -3641,18 +3649,8 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
}
}
}
-
break ;
}
- case STYLE_PROP_GLYPH_TYPE:
- {
- if (style->mode_data.glyph.fields_set.type)
- g_value_set_uint(value, style->mode_data.glyph.type);
- else
- result = FALSE ;
-
- break;
- }
case STYLE_PROP_ALIGNMENT_PARSE_GAPS:
@@ -3735,19 +3733,19 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
break;
}
-
+
case STYLE_PROP_ALIGNMENT_PERFECT_COLOURS:
case STYLE_PROP_ALIGNMENT_COLINEAR_COLOURS:
case STYLE_PROP_ALIGNMENT_NONCOLINEAR_COLOURS:
case STYLE_PROP_ALIGNMENT_INCOMPLETE_GLYPH_COLOURS:
{
- /* We allocate memory here to hold the colour string, it's g_object_get caller's
+ /* We allocate memory here to hold the colour string, it's g_object_get caller's
* responsibility to g_free the string... */
ZMapStyleFullColour this_colour = NULL ;
GString *colour_string = NULL ;
-
+
colour_string = g_string_sized_new(500) ;
-
+
switch(param_id)
{
case STYLE_PROP_ALIGNMENT_PERFECT_COLOURS:
@@ -3765,10 +3763,10 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
default:
break;
}
-
+
formatColours(colour_string, "normal", &(this_colour->normal)) ;
formatColours(colour_string, "selected", &(this_colour->selected)) ;
-
+
if (colour_string->len)
g_value_set_string(value, g_string_free(colour_string, FALSE)) ;
else
@@ -3776,7 +3774,7 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
g_string_free(colour_string, TRUE) ;
result = FALSE ;
}
-
+
break;
}
case STYLE_PROP_ALIGNMENT_INCOMPLETE_GLYPH:
@@ -3815,13 +3813,13 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
}
else
{
- /* We allocate memory here to hold the colour string, it's g_object_get caller's
+ /* We allocate memory here to hold the colour string, it's g_object_get caller's
* responsibility to g_free the string... */
ZMapStyleFullColour this_colour = NULL ;
GString *colour_string = NULL ;
-
+
colour_string = g_string_sized_new(500) ;
-
+
switch(param_id)
{
case STYLE_PROP_TRANSCRIPT_CDS_COLOURS:
@@ -3831,10 +3829,10 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
break;
}
-
+
formatColours(colour_string, "normal", &(this_colour->normal)) ;
formatColours(colour_string, "selected", &(this_colour->selected)) ;
-
+
if (colour_string->len)
g_value_set_string(value, g_string_free(colour_string, FALSE)) ;
else
@@ -3861,13 +3859,13 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
}
else
{
- /* We allocate memory here to hold the colour string, it's g_object_get caller's
+ /* We allocate memory here to hold the colour string, it's g_object_get caller's
* responsibility to g_free the string... */
ZMapStyleFullColour this_colour = NULL ;
GString *colour_string = NULL ;
-
+
colour_string = g_string_sized_new(500) ;
-
+
switch(param_id)
{
case STYLE_PROP_ASSEMBLY_PATH_NON_COLOURS:
@@ -3877,10 +3875,10 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
break;
}
-
+
formatColours(colour_string, "normal", &(this_colour->normal)) ;
formatColours(colour_string, "selected", &(this_colour->selected)) ;
-
+
if (colour_string->len)
g_value_set_string(value, g_string_free(colour_string, FALSE)) ;
else
@@ -3943,7 +3941,7 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
/* Now set the result so we can return it to the user. */
g_object_set_data(G_OBJECT(style), ZMAPSTYLE_OBJ_RC, GINT_TO_POINTER(result)) ;
-
+
return ;
}
@@ -3977,18 +3975,18 @@ static void zmap_feature_type_style_finalize(GObject *object)
/* Parse out colour triplets from a colour keyword-value line.
- *
+ *
* The line format is:
- *
- * NNN_colours = <normal | selected> <fill | draw | border> <colour> ;
- *
+ *
+ * NNN_colours = <normal | selected> <fill | draw | border> <colour> ;
+ *
* the colour spec may be repeated up to 6 times to specify fill, draw or border colours
* for normal or selected features. Each triplet is separated by a ";".
- *
+ *
* NOTE that in the triplet, the colour specifier may consist of more than one word
* (e.g. "dark slate gray") so the g_strsplit_set() is done into just three fields
* and all text in the last field is stored as the colour specifier.
- *
+ *
* */
static gboolean parseColours(ZMapFeatureTypeStyle style, ZMapFeatureTypeStyle copy_style,
guint param_id, GValue *value)
@@ -4084,7 +4082,7 @@ static gboolean parseColours(ZMapFeatureTypeStyle style, ZMapFeatureTypeStyle co
zMapAssertNotReached() ;
break;
}
-
+
switch (type)
{
case ZMAPSTYLE_COLOURTYPE_NORMAL:
@@ -4161,7 +4159,7 @@ static gboolean isColourSet(ZMapFeatureTypeStyle style, int param_id, char *subp
char *dummy_colour = NULL ;
full_colour = g_strdup_printf("%s dummy_colour", subpart) ;
-
+
if ((full_colour = g_strstrip(full_colour))
&& (col_spec = g_strsplit_set(full_colour, " \t", 3))
&& validSplit(col_spec, &type, &context, &dummy_colour))
@@ -4242,13 +4240,13 @@ static gboolean isColourSet(ZMapFeatureTypeStyle style, int param_id, char *subp
/* strings should be a NULL terminated array of three string pointers, the
* contents of the three strings must be:
- *
+ *
* first string: "normal" or "selected"
- *
+ *
* second string: "fill" or "draw" or "border"
- *
+ *
* third string: A colour spec in X11 rgb format (not validated by this routine)
- *
+ *
*/
static gboolean validSplit(char **strings,
ZMapStyleColourType *type_out, ZMapStyleDrawContext *context_out, char **colour_out)
diff --git a/src/zmapFeature/zmapStyle_I.h b/src/zmapFeature/zmapStyle_I.h
index 84f5ad1b5..4ed62bed9 100755
--- a/src/zmapFeature/zmapStyle_I.h
+++ b/src/zmapFeature/zmapStyle_I.h
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jul 29 09:43 2009 (edgrif)
* Created: Mon Feb 26 09:13:30 2007 (edgrif)
- * CVS info: $Id: zmapStyle_I.h,v 1.16 2010-03-04 15:10:33 mh17 Exp $
+ * CVS info: $Id: zmapStyle_I.h,v 1.17 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -36,9 +36,6 @@
#define __ZMAP_STYLE_I_H__
-/* TEMP....WHILE I MOVE STYLE STUFF IN HERE.... */
-#include <ZMap/zmapFeature.h>
-
#include <ZMap/zmapStyle.h>
#include <zmapBase_I.h>
@@ -48,12 +45,15 @@
* the get method is called for the original style and the set method for the new style. */
#define ZMAPSTYLE_OBJ_COPY "ZMap_Style_Copy"
-/* We need out get/set routines to signal whether they succeeded, this must be done via setting
+/* We need our get/set routines to signal whether they succeeded, this must be done via setting
* user data on the style itself because there is nothing in the GObject interface that allows
* us to signal this. */
#define ZMAPSTYLE_OBJ_RC "ZMap_Style_RC"
+/* We use GQuarks to give each feature a unique id, the documentation doesn't say, but you
+ * can surmise from the code that zero is not a valid quark. */
+enum {ZMAPSTYLE_NULLQUARK = 0} ;
diff --git a/src/zmapFeature/zmapStyle_P.h b/src/zmapFeature/zmapStyle_P.h
index b90691d04..5484b356d 100755
--- a/src/zmapFeature/zmapStyle_P.h
+++ b/src/zmapFeature/zmapStyle_P.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.
@@ -28,12 +28,14 @@
* HISTORY:
* Last edited: Jun 13 17:33 2008 (rds)
* Created: Mon Feb 26 09:13:30 2007 (edgrif)
- * CVS info: $Id: zmapStyle_P.h,v 1.14 2010-03-04 15:10:34 mh17 Exp $
+ * CVS info: $Id: zmapStyle_P.h,v 1.15 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_STYLE_P_H
#define ZMAP_STYLE_P_H
+// mh17: file not used
+
#define STYLES_ARE_G_OBJECTS
#include <zmapStyle_I.h>
diff --git a/src/zmapServer/pipe/pipeServer.c b/src/zmapServer/pipe/pipeServer.c
index acb2a45eb..f493e984e 100755
--- a/src/zmapServer/pipe/pipeServer.c
+++ b/src/zmapServer/pipe/pipeServer.c
@@ -7,12 +7,12 @@
* 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.
@@ -23,7 +23,7 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
*
- * Description: These functions provide code to read the output of a script
+ * Description: These functions provide code to read the output of a script
* as though it were a server according to the interface defined
* for accessing servers. The aim is to allow ZMap to request
* arbritary data from external sources as defined in the config files.
@@ -34,13 +34,13 @@
* HISTORY:
* Last edited: Jan 14 10:10 2010 (edgrif)
* Created: 2009-11-26 12:02:40 (mh17)
- * CVS info: $Id: pipeServer.c,v 1.19 2010-03-04 15:10:48 mh17 Exp $
+ * CVS info: $Id: pipeServer.c,v 1.20 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
/* WARNING, THIS DOES NOT COPE WITH MULTIPLE ALIGNS/BLOCKS AS IT STANDS, TO DO THAT REQUIRES
- * WORK BOTH ON THE GFF PARSER CODE (TO ACCEPT ALIGN/BLOCK ID/COORDS AND ON THIS CODE TO
+ * WORK BOTH ON THE GFF PARSER CODE (TO ACCEPT ALIGN/BLOCK ID/COORDS AND ON THIS CODE TO
* GENERALISE IT MORE TO DEAL WITH BLOCKS...I'LL DO THAT NEXT....EG */
@@ -61,7 +61,7 @@ typedef struct
{
ZMapServerResponseType result ;
PipeServer server ;
- ZMapGFFParser parser
+ ZMapGFFParser parser
GString * gff_line ;
} GetFeaturesStruct, *GetFeatures ;
#endif
@@ -69,7 +69,7 @@ typedef struct
static gboolean globalInit(void) ;
static gboolean createConnection(void **server_out,
- ZMapURL url, char *format,
+ ZMapURL url, char *format,
char *version_str, int timeout) ;
static gboolean pipe_server_spawn(PipeServer server,GError **error);
@@ -131,7 +131,7 @@ void pipeGetServerFuncs(ZMapServerFuncs pipe_funcs)
}
-/*
+/*
* Although these routines are static they form the external interface to the pipe server.
*/
@@ -155,7 +155,7 @@ static void getConfiguration(PipeServer server)
char *tmp_string = NULL;
/* default script directory to use */
- if(zMapConfigIniContextGetString(context, ZMAPSTANZA_APP_CONFIG, ZMAPSTANZA_APP_CONFIG,
+ if(zMapConfigIniContextGetString(context, ZMAPSTANZA_APP_CONFIG, ZMAPSTANZA_APP_CONFIG,
ZMAPSTANZA_APP_SCRIPTS, &tmp_string))
{
server->script_dir = tmp_string;
@@ -166,7 +166,7 @@ static void getConfiguration(PipeServer server)
}
/* default directory to use */
- if(zMapConfigIniContextGetString(context, ZMAPSTANZA_APP_CONFIG, ZMAPSTANZA_APP_CONFIG,
+ if(zMapConfigIniContextGetString(context, ZMAPSTANZA_APP_CONFIG, ZMAPSTANZA_APP_CONFIG,
ZMAPSTANZA_APP_DATA, &tmp_string))
{
server->data_dir = tmp_string;
@@ -188,10 +188,10 @@ static void getConfiguration(PipeServer server)
* where <host> is null and <path> begins with a /
* For now we will assume that "host" contains the script name and then we just ignore the other
* parameters....
- *
+ *
* */
static gboolean createConnection(void **server_out,
- ZMapURL url, char *format,
+ ZMapURL url, char *format,
char *version_str, int timeout_unused)
{
gboolean result = TRUE ;
@@ -230,11 +230,11 @@ static gboolean createConnection(void **server_out,
server->query = g_strdup_printf("%s",url->query);
else
server->query = g_strdup("");
-
+
server->protocol = PIPE_PROTOCOL_STR;
if(server->scheme == SCHEME_FILE)
server->protocol = FILE_PROTOCOL_STR;
-
+
server->zmap_start = 1;
server->zmap_end = 0; // default to all of it
@@ -244,7 +244,7 @@ static gboolean createConnection(void **server_out,
-/*
+/*
* fork and exec the script and read the output via a pipe
* no data sent to STDIN and STDERR ignored
* in case of errors or hangups eventually we will time out and an error popped up.
@@ -298,7 +298,7 @@ static gboolean pipe_server_spawn(PipeServer server,GError **error)
/*
- * read stderr from the external source and if non empty display and log some messages
+ * read stderr from the external source and if non empty display and log some messages
* use non-blocking i/o so we don't hang ???
* gets called by setErrMsg() - if the server fails we read STDERR and possibly report why
* if no failures we ignore STDERR
@@ -339,7 +339,7 @@ gchar *pipe_server_get_stderr(PipeServer server)
*(line->str + terminator_pos) = '\0' ; /* Remove terminating newline. */
msg = g_strdup(line->str);
}
-
+
g_string_free(line,TRUE);
return(msg);
}
@@ -379,7 +379,7 @@ static ZMapServerResponseType openConnection(void *server_in, gboolean sequence_
result = pipeGetHeader(server);
if(result == ZMAP_SERVERRESPONSE_OK)
{
- // always read it: have to skip over if not wanted
+ // always read it: have to skip over if not wanted
// need a flag here to say if this is a sequence server
// ignore error response as we want to report open is OK
pipeGetSequence(server);
@@ -420,7 +420,7 @@ static ZMapServerResponseType getInfo(void *server_in, ZMapServerInfo info)
/* We could parse out all the "source" fields from the gff stream but I don't have time
* to do this now. So we just return "unsupported", so if this function is called it
* will alert the caller that something has gone wrong.
- *
+ *
* */
static ZMapServerResponseType getFeatureSetNames(void *server_in,
GList **feature_sets_inout,
@@ -449,7 +449,7 @@ static ZMapServerResponseType getFeatureSetNames(void *server_in,
/* We cannot parse the styles from a gff stream, gff simply doesn't have display styles so we
* just return "unsupported", so if this function is called it will alert the caller that
* something has gone wrong.
- *
+ *
* */
static ZMapServerResponseType getStyles(void *server_in, GData **styles_out)
{
@@ -494,7 +494,7 @@ static ZMapServerResponseType getSequences(void *server_in, GList *sequences_ino
/* We don't check anything here, we could look in the data to check that it matches the context
- * I guess which is essentially what we do for the acedb server.
+ * I guess which is essentially what we do for the acedb server.
* NB: as we process a stream we cannot search backwards or forwards
*/
static ZMapServerResponseType setContext(void *server_in, ZMapFeatureContext feature_context)
@@ -555,7 +555,7 @@ static ZMapServerResponseType pipeGetHeader(PipeServer server)
if (!error)
{
/* SHOULD ABORT HERE.... */
- setErrMsg(server,
+ setErrMsg(server,
g_strdup_printf("zMapGFFParseHeader() failed with no GError for line %d: %s",
zMapGFFGetLineNumber(server->parser), server->gff_line->str)) ;
ZMAPPIPESERVER_LOG(Critical, server->protocol, server->script_path,server->query,
@@ -581,7 +581,7 @@ static ZMapServerResponseType pipeGetHeader(PipeServer server)
}
}
server->result = ZMAP_SERVERRESPONSE_REQFAIL ;
- }
+ }
break ;
}
@@ -665,7 +665,7 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
zMapGFFParserInitForFeatures(server->parser, styles, FALSE) ; // FALSE = create features
- // default to OK, previous pipeGetSequence() could have set unsupported
+ // default to OK, previous pipeGetSequence() could have set unsupported
// if no DNA was provided
server->result = ZMAP_SERVERRESPONSE_OK;
@@ -688,7 +688,7 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
GError *error = NULL ;
server->parser->state == ZMAPGFF_PARSE_BODY;
zMapFeatureDumpStdOutFeatures(feature_context, &error) ;
-
+
}
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
@@ -720,7 +720,7 @@ static void eachBlockSequence(gpointer key, gpointer data, gpointer user_data)
{
GError *error;
char *estr;
-
+
error = zMapGFFGetError(server->parser);
if(error)
estr = error->message;
@@ -728,7 +728,7 @@ static void eachBlockSequence(gpointer key, gpointer data, gpointer user_data)
estr = "No error reported";
setErrMsg(server,
g_strdup_printf("zMapGFFGetSequence() failed, error=%s",estr));
- ZMAPPIPESERVER_LOG(Warning, server->protocol,
+ ZMAPPIPESERVER_LOG(Warning, server->protocol,
server->script_path,server->query,
"%s", server->last_err_msg);
}
@@ -745,16 +745,16 @@ static void eachBlockSequence(gpointer key, gpointer data, gpointer user_data)
/* This temp style creation feels wrong, and probably is,
* but we don't have the merged in default styles in here,
* or so it seems... */
- dna_style = zMapStyleCreate(ZMAP_FIXED_STYLE_DNA_NAME,
+ dna_style = zMapStyleCreate(ZMAP_FIXED_STYLE_DNA_NAME,
ZMAP_FIXED_STYLE_DNA_NAME_TEXT);
-
+
feature = zMapFeatureDNACreateFeature(feature_block, dna_style,
sequence->sequence, sequence->length);
-
+
zMapStyleDestroy(dna_style);
}
- context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)feature_block,
+ context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)feature_block,
ZMAPFEATURE_STRUCT_CONTEXT) ;
/* I'm going to create the three frame translation up front! */
@@ -763,12 +763,12 @@ static void eachBlockSequence(gpointer key, gpointer data, gpointer user_data)
if ((zMapFeature3FrameTranslationCreateSet(feature_block, &feature_set)))
{
ZMapFeatureTypeStyle frame_style = NULL;
-
- frame_style = zMapStyleCreate(ZMAP_FIXED_STYLE_DNA_NAME,
+
+ frame_style = zMapStyleCreate(ZMAP_FIXED_STYLE_DNA_NAME,
ZMAP_FIXED_STYLE_DNA_NAME_TEXT);
-
+
zMapFeature3FrameTranslationSetCreateFeatures(feature_set, frame_style);
-
+
zMapStyleDestroy(frame_style);
}
}
@@ -827,7 +827,7 @@ static char *lastErrorMsg(void *server_in)
-static ZMapServerResponseType closeConnection(void *server_in)
+static ZMapServerResponseType closeConnection(void *server_in)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_OK ;
PipeServer server = (PipeServer)server_in ;
@@ -868,7 +868,7 @@ static ZMapServerResponseType closeConnection(void *server_in)
result = ZMAP_SERVERRESPONSE_REQFAIL ;
}
- else
+ else
{
/* this seems to be required to destroy the GIOChannel.... */
g_io_channel_unref(server->gff_stderr) ;
@@ -882,13 +882,22 @@ static ZMapServerResponseType destroyConnection(void *server_in)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_OK ;
PipeServer server = (PipeServer)server_in ;
-
+
+printf("pipeserver destroy_connection\n");
if (server->script_path)
g_free(server->script_path) ;
if (server->last_err_msg)
g_free(server->last_err_msg) ;
+ /* Clear up. -> in destroyConnection() */
+/* crashes...
+ if(server->parser)
+ zMapGFFDestroyParser(server->parser) ;
+ if(server->gff_line)
+ g_string_free(server->gff_line, TRUE) ;
+*/
+
g_free(server) ;
return result ;
@@ -1024,7 +1033,7 @@ static gboolean sequenceRequest(PipeServer server, ZMapGFFParser parser, GString
feature_block->block_to_sequence.t2) ;
zMapGFFSetFeatureClip(parser,GFF_CLIP_ALL); // mh17: needs config added to server stanza for clip type
}
-
+
first = TRUE ;
do
{
@@ -1117,7 +1126,7 @@ static void setErrMsg(PipeServer server, char *new_msg)
errmsg = pipe_server_get_stderr(server);
if(errmsg)
- {
+ {
g_free(new_msg);
new_msg = errmsg; // explain the cause of the error not the symptom
}
diff --git a/src/zmapServer/zmapServerProtocolHandler.c b/src/zmapServer/zmapServerProtocolHandler.c
index 169400dba..87b383107 100755
--- a/src/zmapServer/zmapServerProtocolHandler.c
+++ b/src/zmapServer/zmapServerProtocolHandler.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.
@@ -22,12 +22,12 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk,
*
- * Description:
+ * Description:
* Exported functions: See ZMap/zmapServerProtocol.h
* HISTORY:
* Last edited: Jan 14 10:26 2010 (edgrif)
* Created: Thu Jan 27 13:17:43 2005 (edgrif)
- * CVS info: $Id: zmapServerProtocolHandler.c,v 1.56 2010-03-04 15:10:43 mh17 Exp $
+ * CVS info: $Id: zmapServerProtocolHandler.c,v 1.57 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -106,7 +106,7 @@ static ZMapProtocolInitListStruct protocol_init_G = {PTHREAD_MUTEX_INITIALIZER,
-/*
+/*
* External Interface
*/
@@ -174,6 +174,12 @@ ZMapServerReqAny zMapServerRequestCreate(ZMapServerReqType request_type, ...)
break ;
}
+ case ZMAP_SERVERREQ_TERMINATE:
+ {
+ size = sizeof(ZMapServerReqTerminateStruct) ;
+
+ break ;
+ }
default:
{
zMapLogFatalLogicErr("switch(), unknown value: %d", request_type) ;
@@ -247,14 +253,22 @@ ZMapServerReqAny zMapServerRequestCreate(ZMapServerReqType request_type, ...)
}
case ZMAP_SERVERREQ_GETSEQUENCE:
{
- ZMapServerReqGetSequence get_sequence = (ZMapServerReqGetSequence)req_any ;
-
+ // mh17: was missing -> has never appeared?
+// ZMapServerReqGetSequence get_sequence = (ZMapServerReqGetSequence)req_any ;
+/*
get_sequence->orig_feature = va_arg(args, ZMapFeature) ;
get_sequence->sequences = va_arg(args, GList *) ;
get_sequence->flags = va_arg(args, int) ;
-
+*/
break ;
}
+ case ZMAP_SERVERREQ_TERMINATE:
+ {
+ //ZMapServerReqTerminate terminate = (ZMapServerReqTerminate)req_any ;
+
+ break;
+ }
+
default:
{
zMapLogFatalLogicErr("switch(), unknown value: %d", request_type) ;
@@ -467,7 +481,7 @@ if(*slave_data) zMapLogMessage("req %s/%s %d",server->url->protocol,server->url-
zMapAssert(g_hash_table_size(blocks) == 1) ;
block = (ZMapFeatureBlock)(zMap_g_hash_table_nth(blocks, 0)) ;
- if(!block->block_to_sequence.t2)
+ if(!block->block_to_sequence.t2)
{
// mh17: this happens before getFeatures? which is where the data gets set
// adding the if has no effect of course
@@ -627,7 +641,7 @@ static void protocolGlobalInitFunc(ZMapProtocolInitList protocols, ZMapURL url,
/* Enum -> String functions, these functions convert the enums _directly_ to strings.
- *
+ *
* The functions all have the form
* const char *zMapXXXX2ExactStr(ZMapXXXXX type)
* {
@@ -659,12 +673,12 @@ static int findProtocol(gconstpointer list_data, gconstpointer custom_data)
{
result = 1;
}
-
+
return result ;
}
-
-
+
+
/* Get a specific sequences from the server. */
static ZMapThreadReturnCode getSequence(ZMapServer server, ZMapServerReqGetSequence request, char **err_msg_out)
{
@@ -781,7 +795,7 @@ ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, ch
if (thread_rc == ZMAPTHREAD_RETURNCODE_OK)
{
/* If there's a styles file get the styles from that, otherwise get them from the source.
- * At the moment we don't merge styles from files and sources, perhaps we should...
+ * At the moment we don't merge styles from files and sources, perhaps we should...
*
* mgh: function modified to return all styles in file if style list not specified
* pipe and file servers should not need to do this as zmapView will read the file anyway
@@ -822,9 +836,9 @@ ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, ch
zMapStyleSetPrintAll(dest, styles->styles_out, "Before merge", styles_debug) ;
string = zMapOutGetStr(dest) ;
-
+
printf("%s\n", string) ;
-
+
zMapOutDestroy(dest) ;
}
@@ -843,13 +857,13 @@ ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, ch
if(styles_debug)
{
dest = zMapOutCreateStr(NULL, 0) ;
-
+
zMapStyleSetPrintAll(dest, tmp_styles, "Before inherit", styles_debug) ;
string = zMapOutGetStr(dest) ;
printf("%s\n", string) ;
-
+
zMapOutDestroy(dest) ;
}
@@ -861,13 +875,13 @@ ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, ch
if(styles_debug)
{
dest = zMapOutCreateStr(NULL, 0) ;
-
+
zMapStyleSetPrintAll(dest, tmp_styles, "After inherit", styles_debug) ;
-
+
string = zMapOutGetStr(dest) ;
-
+
printf("%s\n", string) ;
-
+
zMapOutDestroy(dest) ;
}
}
@@ -876,7 +890,7 @@ ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, ch
if(styles->response != ZMAP_SERVERRESPONSE_UNSUPPORTED)
{
-
+
/* Make sure that all the styles that are required for the feature sets were found.
* (This check should be controlled from analysing the number of feature servers or
* flags set for servers.....) */
@@ -892,7 +906,7 @@ ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, ch
{
g_free(missing_styles); /* haveRequiredStyles return == TRUE doesn't mean missing_styles == NULL */
}
-
+
/* Find out if the styles will need to have their mode set from the features.
* I'm feeling like this is a bit hacky because it's really an acedb issue. */
if (thread_rc == ZMAPTHREAD_RETURNCODE_OK
@@ -906,7 +920,7 @@ ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, ch
}
}
}
-
+
/* return the styles in the styles struct... */
styles->styles_out = tmp_styles ;
diff --git a/src/zmapUtils/zmapBase.c b/src/zmapUtils/zmapBase.c
index 9fab9aae9..2948cf61d 100755
--- a/src/zmapUtils/zmapBase.c
+++ b/src/zmapUtils/zmapBase.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.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See ZMap/zmapBase.h
* HISTORY:
* Last edited: Jan 12 11:52 2009 (rds)
* Created: Thu Jun 12 12:02:12 2008 (rds)
- * CVS info: $Id: zmapBase.c,v 1.9 2010-03-04 15:10:59 mh17 Exp $
+ * CVS info: $Id: zmapBase.c,v 1.10 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -44,13 +44,13 @@ enum
static void zmap_base_base_init (ZMapBaseClass zmap_base_class);
static void zmap_base_class_init (ZMapBaseClass zmap_base_class);
static void zmap_base_inst_init (ZMapBase zmap_base);
-static void zmap_base_set_property(GObject *gobject,
- guint param_id,
- const GValue *value,
+static void zmap_base_set_property(GObject *gobject,
+ guint param_id,
+ const GValue *value,
GParamSpec *pspec);
-static void zmap_base_get_property(GObject *gobject,
- guint param_id,
- GValue *value,
+static void zmap_base_get_property(GObject *gobject,
+ guint param_id,
+ GValue *value,
GParamSpec *pspec);
#ifdef ZMAP_BASE_NEEDS_DISPOSE_FINALIZE
static void zmap_base_dispose (GObject *object);
@@ -68,8 +68,8 @@ static void zmapBaseCopyConstructor(const GValue *src_value, GValue *dest_value)
GType zMapBaseGetType (void)
{
static GType type = 0;
-
- if (type == 0)
+
+ if (type == 0)
{
static const GTypeInfo info = {
sizeof (zmapBaseClass),
@@ -86,7 +86,7 @@ GType zMapBaseGetType (void)
type = g_type_register_static (G_TYPE_OBJECT, "ZMapBase", &info, (GTypeFlags)0);
}
-
+
return type;
}
@@ -141,7 +141,7 @@ gboolean zMapBaseDebug(GObject *gobject)
static void zmap_base_base_init (ZMapBaseClass zmap_base_class)
{
- zmap_base_class->copy_set_property = NULL;
+ zmap_base_class->copy_set_property = NULL; // mh17: this is for derived classes not zmapBase
zmap_base_class->value_copy = zmapBaseCopyConstructor;
@@ -151,7 +151,7 @@ static void zmap_base_base_init (ZMapBaseClass zmap_base_class)
static void zmap_base_class_init (ZMapBaseClass zmap_base_class)
{
GObjectClass *gobject_class;
-
+
gobject_class = (GObjectClass *)zmap_base_class;
gobject_class->set_property = zmap_base_set_property;
@@ -180,9 +180,9 @@ static void zmap_base_inst_init (ZMapBase zmap_base)
return ;
}
-static void zmap_base_set_property(GObject *gobject,
- guint param_id,
- const GValue *value,
+static void zmap_base_set_property(GObject *gobject,
+ guint param_id,
+ const GValue *value,
GParamSpec *pspec)
{
ZMapBase base;
@@ -204,9 +204,9 @@ static void zmap_base_set_property(GObject *gobject,
return ;
}
-static void zmap_base_get_property(GObject *gobject,
- guint param_id,
- GValue *value,
+static void zmap_base_get_property(GObject *gobject,
+ guint param_id,
+ GValue *value,
GParamSpec *pspec)
{
ZMapBase base;
@@ -279,7 +279,7 @@ static gboolean zmapBaseCopy(ZMapBase src, ZMapBase *dest_out, gboolean copy_by_
if(dest_out)
{
gobject_type = G_TYPE_FROM_INSTANCE(src);
-
+
if(copy_by_reference)
{
GTypeValueTable *value_table;
@@ -303,16 +303,16 @@ static gboolean zmapBaseCopy(ZMapBase src, ZMapBase *dest_out, gboolean copy_by_
{
g_value_init(&src_value, gobject_type);
g_value_init(&dest_value, gobject_type);
-
+
g_value_set_object(&src_value, src);
-
+
if((done = zmapBaseCopyValue(&src_value, &dest_value, value_copy_func)))
{
/* return it to caller */
dest = g_value_get_object(&dest_value);
*dest_out = dest;
}
-
+
g_value_unset(&src_value);
g_value_unset(&dest_value);
}
@@ -327,7 +327,7 @@ static gboolean zmapBaseCopy(ZMapBase src, ZMapBase *dest_out, gboolean copy_by_
*
* @param The original GValue
* @param The new GValue
- * @param The function to use to copy the GValue from
+ * @param The function to use to copy the GValue from
* origin to new.
*
* @return How successful copying was. TRUE == Success
@@ -339,7 +339,7 @@ static gboolean zmapBaseCopyValue(const GValue *src_value, GValue *dest_value, Z
g_return_val_if_fail (G_IS_VALUE (src_value), FALSE);
g_return_val_if_fail (G_IS_VALUE (dest_value), FALSE);
g_return_val_if_fail (g_value_type_compatible (G_VALUE_TYPE (src_value), G_VALUE_TYPE (dest_value)), FALSE);
-
+
if (value_copy && src_value != dest_value)
{
GType dest_type = G_VALUE_TYPE (dest_value);
@@ -348,12 +348,12 @@ static gboolean zmapBaseCopyValue(const GValue *src_value, GValue *dest_value, Z
/* make sure dest_value's value is free()d */
if (value_table->value_free)
value_table->value_free (dest_value);
-
+
/* setup and copy */
#ifdef RDS_INIT_PROBLEM
g_value_init(dest_value, dest_type);
- /*
- * value_meminit (dest_value, dest_type);
+ /*
+ * value_meminit (dest_value, dest_type);
* g_value_copy() uses value_meminit here, but that's static so
* I used g_value_init(), but that does some sanity checks. The
* solution is to reimplement value_meminit, which has the warning
@@ -377,10 +377,10 @@ static gboolean zmapBaseCopyValue(const GValue *src_value, GValue *dest_value, Z
* \brief Copy all data from one ZMapBase, or derived, object to
* another. This involves _creating_ a new ZMapBase (g_object_new()),
* getting properties from the original one and setting them on the
- * new one. This avoids duplicating this code throughout any objects
+ * new one. This avoids duplicating this code throughout any objects
* we need to do this with.
*
- * This function is called by zmapBaseCopyValue in the line
+ * This function is called by zmapBaseCopyValue in the line
* value_copy(src_value, dest_value);
*
* @param The original GValue
@@ -427,15 +427,15 @@ static void zmapBaseCopyConstructor(const GValue *src_value, GValue *dest_value)
* Also the copy_set_property method can have the same signature as get/set_prop */
guint param_id = current->param_id;
GValue value = { 0, };
-
+
g_value_init(&value, current_type);
-
+
gobject_class = g_type_class_peek(current->owner_type);
zmap_class = ZMAP_BASE_CLASS(gobject_class);
if((redirect = g_param_spec_get_redirect_target(current)))
current = redirect;
-
+
#ifdef COPY_CONSTRUCT_DEBUG
printf("Copy Constructor %s\n", name);
#endif
diff --git a/src/zmapUtils/zmapGUITreeView.c b/src/zmapUtils/zmapGUITreeView.c
index 8cb74748f..643ea668c 100755
--- a/src/zmapUtils/zmapGUITreeView.c
+++ b/src/zmapUtils/zmapGUITreeView.c
@@ -29,13 +29,14 @@
* HISTORY:
* Last edited: May 22 10:41 2009 (rds)
* Created: Thu May 22 10:00:37 2008 (rds)
- * CVS info: $Id: zmapGUITreeView.c,v 1.9 2010-03-04 15:11:10 mh17 Exp $
+ * CVS info: $Id: zmapGUITreeView.c,v 1.10 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
#include <string.h> /* memcpy() */
+#include <ZMap/zmapBase.h>
#include <ZMap/zmapUtils.h>
#include <ZMap/zmapUtilsGUI.h>
#include <zmapGUITreeView_I.h>
diff --git a/src/zmapUtils/zmapGUITreeView_I.h b/src/zmapUtils/zmapGUITreeView_I.h
index 540d60d91..35fd03911 100755
--- a/src/zmapUtils/zmapGUITreeView_I.h
+++ b/src/zmapUtils/zmapGUITreeView_I.h
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Jun 3 11:45 2008 (rds)
* Created: Thu May 22 10:49:23 2008 (rds)
- * CVS info: $Id: zmapGUITreeView_I.h,v 1.4 2010-03-04 15:11:11 mh17 Exp $
+ * CVS info: $Id: zmapGUITreeView_I.h,v 1.5 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -38,11 +38,6 @@
#include <ZMap/zmapGUITreeView.h>
-/* If we had a ZMap base class these could go in its _I.h */
-#define ZMAP_PARAM_STATIC (G_PARAM_STATIC_NAME | G_PARAM_STATIC_NICK | G_PARAM_STATIC_BLURB)
-#define ZMAP_PARAM_STATIC_RW (ZMAP_PARAM_STATIC | G_PARAM_READWRITE)
-#define ZMAP_PARAM_STATIC_RO (ZMAP_PARAM_STATIC | G_PARAM_READABLE)
-
#define DEFAULT_COLUMN_FLAGS (ZMAP_GUITREEVIEW_COLUMN_VISIBLE | ZMAP_GUITREEVIEW_COLUMN_CLICKABLE)
/*
diff --git a/src/zmapView/zmapView.c b/src/zmapView/zmapView.c
index a75b8585a..d5e1752dd 100755
--- a/src/zmapView/zmapView.c
+++ b/src/zmapView/zmapView.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.
@@ -24,12 +24,12 @@
*
* Description: Handles the getting of the feature context from sources
* and their subsequent processing.
- *
+ *
* Exported functions: See ZMap/zmapView.h
* HISTORY:
* Last edited: Mar 11 14:55 2010 (edgrif)
* Created: Thu May 13 15:28:26 2004 (edgrif)
- * CVS info: $Id: zmapView.c,v 1.181 2010-03-12 14:47:25 edgrif Exp $
+ * CVS info: $Id: zmapView.c,v 1.182 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -97,7 +97,7 @@ typedef struct
} UnsetDeferredLoadStylesStruct, *UnsetDeferredLoadStyles ;
-
+static GList *zmapViewGetIniSources(char *config_str, char **stylesfile);
static ZMapView createZMapView(GtkWidget *xremote_widget, char *view_name,
GList *sequences, void *app_data) ;
@@ -128,24 +128,26 @@ static gboolean checkStateConnections(ZMapView zmap_view) ;
static gboolean dispatchContextRequests(ZMapViewConnection view_con, ZMapServerReqAny req_any) ;
static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAny req_any) ;
-static void freeDataRequest(ZMapViewConnection view_con, ZMapServerReqAny req_any) ;
+static void freeDataRequest(ZMapServerReqAny req_any) ;
static gboolean processGetSeqRequests(ZMapViewConnection view_con, ZMapServerReqAny req_any) ;
static ZMapViewConnection createConnection(ZMapView zmap_view,
- ZMapURL url, char *format,
+ ZMapViewConnection view_con,
+ ZMapFeatureContext context,
+ char *url, char *format,
int timeout, char *version,
char *styles, char *styles_file,
- char *feature_sets, char *navigator_set_names,
- gboolean sequence_server, gboolean writeback_server,
- char *sequence, int start, int end) ;
+ GList *req_featuresets,
+ gboolean dna_requested, gboolean writeback_server,
+ gboolean terminate);
static void destroyConnection(ZMapViewConnection *view_conn) ;
static void killGUI(ZMapView zmap_view) ;
static void killConnections(ZMapView zmap_view) ;
static void resetWindows(ZMapView zmap_view) ;
static void displayDataWindows(ZMapView zmap_view,
- ZMapFeatureContext all_features,
+ ZMapFeatureContext all_features,
ZMapFeatureContext new_features, GData *new_styles,
gboolean undisplay) ;
static void killAllWindows(ZMapView zmap_view) ;
@@ -195,7 +197,7 @@ static void drawableCB(GQuark key_id, gpointer data, gpointer user_data) ;
static void addPredefined(GData **styles_inout, GHashTable **featureset_2_stylelist_inout) ;
static void styleCB(GQuark key_id, gpointer data, gpointer user_data) ;
-
+static void invoke_merge_in_names(gpointer list_data, gpointer user_data);
/* These callback routines are global because they are set just once for the lifetime of the
@@ -206,12 +208,12 @@ static ZMapViewCallbacks view_cbs_G = NULL ;
/* Callbacks back we set in the level below us, i.e. zMapWindow. */
-ZMapWindowCallbacksStruct window_cbs_G =
+ZMapWindowCallbacksStruct window_cbs_G =
{
enterCB, leaveCB,
scrollCB,
- viewFocusCB,
- viewSelectCB,
+ viewFocusCB,
+ viewSelectCB,
viewSplitToPatternCB,
setZoomStatusCB,
viewVisibilityChangeCB,
@@ -230,12 +232,12 @@ ZMapWindowCallbacksStruct window_cbs_G =
/*! @defgroup zmapview zMapView: feature context display/processing
* @{
- *
+ *
* \brief Feature Context View Handling.
- *
+ *
* zMapView routines receive requests to load, display and process
* feature contexts. Each ZMapView corresponds to a single feature context.
- *
+ *
*
* */
@@ -244,7 +246,7 @@ ZMapWindowCallbacksStruct window_cbs_G =
/*!
* This routine must be called just once before any other views routine,
* the caller must supply all of the callback routines.
- *
+ *
* @param callbacks Caller registers callback functions that view will call
* from the appropriate actions.
* @return <nothing>
@@ -290,7 +292,7 @@ void zMapViewInit(ZMapViewCallbacks callbacks)
* A view _always_ has at least one window, this window may be blank but as long as
* there is a view, there is a window. This makes the coding somewhat simpler and is
* intuitively sensible.
- *
+ *
* @param xremote_widget Widget that xremote commands for this view will be delivered to.
* @param view_container Parent widget of the view window(s)
* @param sequence Name of virtual sequence of context to be created.
@@ -362,6 +364,8 @@ void zMapViewSetupNavigator(ZMapViewWindow view_window, GtkWidget *canvas_widget
return ;
}
+
+
/* Connect a View to its databases via threads, at this point the View is blank and waiting
* to be called to load some data. */
gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
@@ -369,23 +373,17 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
gboolean result = TRUE ;
- if (zmap_view->state != ZMAPVIEW_INIT)
+ if (zmap_view->state != ZMAPVIEW_INIT) // && zmap_view->state != ZMAPVIEW_LOADED)
+
{
/* Probably we should indicate to caller what the problem was here....
* e.g. if we are resetting then say we are resetting etc.....again we need g_error here. */
zMapLogCritical("GUI: %s", "cannot connect because not in init state.") ;
- result = FALSE ;
- }
- else if (zmap_view->step_list)
- {
- zMapLogCritical("GUI: %s", "View is already executing connection requests so cannot connect.") ;
-
result = FALSE ;
}
else
{
- ZMapConfigIniContext context ;
GList *settings_list = NULL, *free_this_list = NULL;
char *stylesfile = NULL;
@@ -398,22 +396,29 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
* and load in one call but we will almost certainly need the extra states later... */
zmap_view->state = ZMAPVIEW_CONNECTING ;
- if ((context = zMapConfigIniContextProvide()))
- {
- GValue *value = NULL;
- zMapConfigIniContextIncludeBuffer(context, config_str);
+ settings_list = zmapViewGetIniSources(config_str,&stylesfile); // get the stanza structs from ZMap config
- settings_list = zMapConfigIniContextGetSources(context)
- ;
- if(zMapConfigIniContextGetValue(context,ZMAPSTANZA_APP_CONFIG,ZMAPSTANZA_APP_CONFIG ,ZMAPSTANZA_APP_STYLESFILE,&value))
- stylesfile = (char *) g_value_get_string(value);
- else
- zMapLogMessage("%s",context->error_message);
-
- zMapConfigIniContextDestroy(context);
+ // in case we have no persistent connections read the styles file
+ {
+ /* There are a number of predefined methods that we require so add these in as well
+ * as the mapping for "feature set" -> style for these. */
+ addPredefined(&(zmap_view->orig_styles), &(zmap_view->featureset_2_stylelist)) ;
- context = NULL ;
- }
+#ifdef MH17_NOT_NEEDED
+ if(stylesfile)
+ {
+ // each server will either return styles or read in the ones on styles file
+ // so no need to do this here and merge them in
+ GData *styles;
+
+ if(zMapConfigIniGetStylesFromFile(NULL,stylesfile,&styles))
+ {
+ zmap_view->orig_styles =
+ zMapStyleMergeStyles(zmap_view->orig_styles,styles,ZMAPSTYLE_MERGE_MERGE) ;
+ }
+ }
+#endif
+ }
/* Set up connections to the named servers. */
if (settings_list)
@@ -425,49 +430,21 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
current_server = (ZMapConfigSource)settings_list->data ;
- /* There are a number of predefined methods that we require so add these in as well
- * as the mapping for "feature set" -> style for these. */
- addPredefined(&(zmap_view->orig_styles), &(zmap_view->featureset_2_stylelist)) ;
-
- if(stylesfile)
- {
- GData *styles;
-
- /* do a merge of styles from the stylesfile with these predefined ones. */
- /* merge the predefined ones, if not we don't have to redefine then in the file */
- if(zMapConfigIniGetStylesFromFile(NULL,stylesfile,&styles))
- {
- zmap_view->orig_styles =
- zMapStyleMergeStyles(zmap_view->orig_styles,styles,ZMAPSTYLE_MERGE_MERGE) ;
- }
- }
-
-
- /* Create the step list that will be used to control obtaining the feature
- * context from the multiple sources. */
- zmap_view->step_list = zmapViewStepListCreate(dispatchContextRequests,
- processDataRequests,
- freeDataRequest) ;
- zmapViewStepListAddStep(zmap_view->step_list, ZMAP_SERVERREQ_CREATE, REQUEST_ONFAIL_CANCEL_THREAD) ;
- zmapViewStepListAddStep(zmap_view->step_list, ZMAP_SERVERREQ_OPEN, REQUEST_ONFAIL_CANCEL_THREAD) ;
- zmapViewStepListAddStep(zmap_view->step_list, ZMAP_SERVERREQ_GETSERVERINFO, REQUEST_ONFAIL_CANCEL_THREAD) ;
- zmapViewStepListAddStep(zmap_view->step_list, ZMAP_SERVERREQ_FEATURESETS, REQUEST_ONFAIL_CANCEL_THREAD) ;
- zmapViewStepListAddStep(zmap_view->step_list, ZMAP_SERVERREQ_STYLES, REQUEST_ONFAIL_CANCEL_THREAD) ;
- zmapViewStepListAddStep(zmap_view->step_list, ZMAP_SERVERREQ_NEWCONTEXT, REQUEST_ONFAIL_CANCEL_THREAD) ;
- zmapViewStepListAddStep(zmap_view->step_list, ZMAP_SERVERREQ_FEATURES, REQUEST_ONFAIL_CANCEL_THREAD) ;
/* Current error handling policy is to connect to servers that we can and
* report errors for those where we fail but to carry on and set up the ZMap
* as long as at least one connection succeeds. */
do
{
- int url_parse_error ;
- ZMapURL urlObj;
+
ZMapViewConnection view_con ;
-
+
current_server = (ZMapConfigSource)settings_list->data ;
-
+
+ if(current_server->delayed) // only request data when asked by otterlace
+ continue;
+
/* we have a global styles file set in [zmap] and we need to pass this to pipe and file servers
* to avoid getting an error message. We have already read the file if it's specified
* DAS servers may need this if styles not specified.
@@ -477,14 +454,6 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
if(stylesfile)
current_server->stylesfile = g_strdup(stylesfile);
-
-
- /* need to do this for all servers, or else we require the first one to have the sequence
- * (moved here from before this loop
- */
- /* Should test for dna col here as well....should unify dna and other features.... */
- if (current_server->sequence)
- zmapViewStepListAddStep(zmap_view->step_list, ZMAP_SERVERREQ_SEQUENCE, REQUEST_ONFAIL_CANCEL_THREAD) ;
/* Check for required fields from config, if not there then we can't connect. */
if (!current_server->url)
@@ -510,14 +479,14 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
continue ;
}
-
+
#ifdef NOT_REQUIRED_ATM
/* This will become redundant with step stuff..... */
else if (!checkSequenceToServerMatch(zmap_view->sequence_2_server, &tmp_seq))
{
- /* If certain sequences must only be fetched from certain servers then make sure
+ /* If certain sequences must only be fetched from certain servers zmap_viewthen make sure
* we only make those connections. */
zMapLogMessage("server %s no sequence: ignored",current_server->url);
continue ;
@@ -525,55 +494,65 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
#endif /* NOT_REQUIRED_ATM */
- /* Parse the url and create connection. */
- if (!(urlObj = url_parse(current_server->url, &url_parse_error)))
- {
- zMapLogWarning("GUI: url %s did not parse. Parse error < %s >\n",
- current_server->url,
- url_error(url_parse_error)) ;
- }
- else
{
- if ((view_con = createConnection(zmap_view, urlObj,
+ GList *req_featuresets = NULL, *tmp_navigator_sets = NULL ;
+ ZMapFeatureContext context;
+ gboolean dna_requested = FALSE;
+
+ /* req all featuresets as a list of their quark names. */
+ req_featuresets = zMapFeatureString2QuarkList(current_server->featuresets) ;
+
+ /* Check whether DNA was requested, see comments below about setting up sequence req. */
+ if ((zMap_g_list_find_quark(req_featuresets, zMapStyleCreateID(ZMAP_FIXED_STYLE_DNA_NAME))))
+ dna_requested = TRUE ;
+
+ g_list_foreach(zmap_view->window_list, invoke_merge_in_names, req_featuresets);
+
+
+ /* Navigator styles are all predefined so no need to merge into main feature sets to get the styles. */
+ if (current_server->navigatorsets)
+ {
+ tmp_navigator_sets = zmap_view->navigator_set_names = zMapFeatureString2QuarkList(current_server->navigatorsets);
+ /* We _must_ merge the set names into the navigator though. */
+ /* The navigator knows nothing of view, so saving them there isn't really useful for getting them drawn.
+ * N.B. This is zMapWindowNavigatorMergeInFeatureSetNames _not_ zMapWindowMergeInFeatureSetNames. */
+ if(zmap_view->navigator_window)
+ zMapWindowNavigatorMergeInFeatureSetNames(zmap_view->navigator_window, tmp_navigator_sets);
+ }
+
+ /* Create data specific to this step list...and set it in the connection. */
+ context = createContext(zmap_view->sequence, zmap_view->start, zmap_view->end, req_featuresets) ;
+
+ if ((view_con = createConnection(zmap_view, NULL, context,
+ current_server->url,
(char *)current_server->format,
current_server->timeout,
(char *)current_server->version,
(char *)current_server->styles_list,
- (char *)current_server->stylesfile,
- (char *)current_server->featuresets,
- (char *)current_server->navigatorsets,
- current_server->sequence,
+ (char *)stylesfile,
+ req_featuresets,
+ dna_requested, // current_server->sequence,
current_server->writeback,
- zmap_view->sequence,
- zmap_view->start,
- zmap_view->end)))
+ FALSE ))) // (has to be) current_server->delayed,
{
- /* Everything went well... replace current call */
- zmap_view->connection_list = g_list_append(zmap_view->connection_list, view_con) ;
connections++ ;
+ /* If at least one connection succeeded then we are up and running, if not then the zmap
+ * returns to the init state. */
+ zmap_view->state = ZMAPVIEW_LOADING ;
- /* THESE NEED TO GO WHEN STEP LIST STUFF IS DONE PROPERLY.... */
+ /* THESE NEED TO GO WHEN STEP LIST STUFF IS DONE PROPERLY.... */
if (current_server->sequence)
zmap_view->sequence_server = view_con ;
if (current_server->writeback)
zmap_view->writeback_server = view_con ;
-
- }
- else
- {
- zMapLogWarning("GUI: url %s looks ok (host: %s\tport: %d)"
- "but could not connect to server.",
- urlObj->url,
- urlObj->host,
- urlObj->port) ;
}
}
}
while ((settings_list = g_list_next(settings_list)));
-
+
/* Ought to return a gerror here........ */
if (!connections)
@@ -587,16 +566,7 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
}
- /* If at least one connection succeeded then we are up and running, if not then the zmap
- * returns to the init state. */
- if (result)
- {
- zmap_view->state = ZMAPVIEW_LOADING ;
-
- /* Start the connections to the sources. */
- zmapViewStepListIter(zmap_view->step_list) ;
- }
- else
+ if (!result)
{
zmap_view->state = ZMAPVIEW_INIT ;
}
@@ -729,7 +699,7 @@ void zMapViewRemoveWindow(ZMapViewWindow view_window)
/*!
* Get the views "xremote" widget, returns NULL if view is dying.
- *
+ *
* @param The ZMap View
* @return NULL or views xremote widget.
* */
@@ -748,7 +718,7 @@ GtkWidget *zMapViewGetXremote(ZMapView view)
* Get the views X window id for the "xremote" widget, this is the label
* by which the view is known to the client program. Function will
* always return the value <b>even</b> the actual widget has been destroyed.
- *
+ *
* @param The ZMap View
* @return The X Window id of the views xremote widget.
* */
@@ -765,7 +735,7 @@ unsigned long zMapViewGetXremoteXWID(ZMapView view)
* @param The ZMap View
* @param The Context to erase. Those features which
* match will be removed from this context and
- * the view's own context. They will also be
+ * the view's own context. They will also be
* removed from the display windows. Those that
* don't match will be left in this context.
* @return void
@@ -807,7 +777,7 @@ ZMapFeatureContext zmapViewMergeInContext(ZMapView view, ZMapFeatureContext cont
* @param The ZMap View
* @param The Context to draw...
*
- * @return Boolean to notify whether the context was
+ * @return Boolean to notify whether the context was
* free'd and now == NULL, FALSE only if
* diff_context is the same context as view->features
*************************************************** */
@@ -888,12 +858,12 @@ void zMapViewStats(ZMapViewWindow view_window,GString *text)
/* Reverse complement a view, this call will:
- *
+ *
* - leave the View window(s) displayed and hold onto user information such as machine/port
* sequence etc so user does not have to add the data again.
* - reverse complement the sequence context.
* - display the reversed context.
- *
+ *
* */
gboolean zMapViewReverseComplement(ZMapView zmap_view)
{
@@ -921,11 +891,11 @@ gboolean zMapViewReverseComplement(ZMapView zmap_view)
{
ZMapViewWindow view_window ;
GData *copy_styles = NULL;
-
+
view_window = list_item->data ;
-
+
copy_styles = zmap_view->orig_styles ;
-
+
zMapWindowFeatureRedraw(view_window->window, zmap_view->features,
zmap_view->orig_styles, copy_styles, TRUE) ;
}
@@ -935,7 +905,7 @@ gboolean zMapViewReverseComplement(ZMapView zmap_view)
/* Not sure if we need to do this or not.... */
/* signal our caller that we have data. */
(*(view_cbs_G->load_data))(zmap_view, zmap_view->app_data, NULL) ;
-
+
zmapViewBusy(zmap_view, FALSE);
result = TRUE ;
@@ -953,15 +923,15 @@ gboolean zMapViewGetRevCompStatus(ZMapView zmap_view)
/* Reset an existing view, this call will:
- *
+ *
* - leave the View window(s) displayed and hold onto user information such as machine/port
* sequence etc so user does not have to add the data again.
* - Free all ZMap window data that was specific to the view being loaded.
* - Kill the existing server thread(s).
- *
+ *
* After this call the ZMap will be ready for the user to try again with the existing
* machine/port/sequence or to enter data for a new sequence etc.
- *
+ *
* */
gboolean zMapViewReset(ZMapView zmap_view)
{
@@ -990,10 +960,10 @@ gboolean zMapViewReset(ZMapView zmap_view)
}
-/*
+/*
* If view_window is NULL all windows are zoomed.
- *
- *
+ *
+ *
* */
void zMapViewZoom(ZMapView zmap_view, ZMapViewWindow view_window, double zoom)
{
@@ -1089,7 +1059,7 @@ GData *zMapViewGetStyles(ZMapViewWindow view_window)
{
GData *styles = NULL ;
ZMapView view = zMapViewGetView(view_window);
-
+
if (view->state != ZMAPVIEW_DYING)
styles = view->orig_styles ;
@@ -1223,7 +1193,7 @@ void zmapViewFeatureDump(ZMapViewWindow view_window, char *file)
* NOTE: if the function returns FALSE it means the view has signalled its threads
* and is waiting for them to die, the caller should thus wait until view signals
* via the killedcallback that the view has really died before doing final clear up.
- *
+ *
* If the function returns TRUE it means that the view has been killed immediately
* because it had no threads so the caller can clear up immediately.
*/
@@ -1296,19 +1266,100 @@ char *zmapViewGetStatusAsStr(ZMapViewState state)
+
+static GList *zmapViewGetIniSources(char *config_str, char **stylesfile)
+{
+ ZMapConfigIniContext context ;
+ GList *settings_list = NULL;
+
+ if ((context = zMapConfigIniContextProvide()))
+ {
+ GValue *value = NULL;
+ if(config_str)
+ zMapConfigIniContextIncludeBuffer(context, config_str);
+
+ settings_list = zMapConfigIniContextGetSources(context);
+
+ if(stylesfile)
+ {
+ if(zMapConfigIniContextGetValue(context,ZMAPSTANZA_APP_CONFIG,ZMAPSTANZA_APP_CONFIG ,ZMAPSTANZA_APP_STYLESFILE,&value))
+ *stylesfile = (char *) g_value_get_string(value);
+ else
+ zMapLogMessage("%s",context->error_message);
+ }
+ zMapConfigIniContextDestroy(context);
+ }
+
+ return(settings_list);
+}
+
+
+// create a hash table of feature set names and thier sources
+static GHashTable *zmapViewGetFeatureSourceHash(GList *sources)
+{
+ GHashTable *hash = NULL;
+ ZMapConfigSource src;
+ gchar **features,**feats;
+
+ hash = g_hash_table_new(NULL,NULL);
+
+ // for each source extract featuresets and add a hash to the source
+ for(;sources; sources = g_list_next(sources))
+ {
+ src = sources->data;
+ if(!src->featuresets)
+ continue;
+ features = g_strsplit_set(src->featuresets,"; \t",0); // this will give null entries eg 'aaa ; bbbb' -> 5 strings
+ if(!features)
+ continue;
+
+ for(feats = features;*feats;feats++)
+ {
+ GQuark q;
+ // the data we want to lookup happens to have been quarked
+ if(**feats)
+ {
+ q = g_quark_from_string(*feats);
+ g_hash_table_insert(hash,GUINT_TO_POINTER(q), (gpointer) src);
+ }
+ }
+
+ g_strfreev(features);
+ }
+
+ return(hash);
+}
+
+#define zmapViewGetSourceFromFeatureset(hash,featurequark) (ZMapConfigSource) g_hash_table_lookup(hash,(gpointer) featurequark)
+
+
+
+
+
+
/* Loads features within block from the sets req_featuresets that lie within features_start
* to features_end. The features are fetched from the data sources and added to the existing
* view. N.B. this is asynchronous because the sources are separate threads and once
* retrieved the features are added via a gtk event. */
+ /* mh17:
+ * unlike zmapViewConnect() we request one feature set at a time from the relevant server
+ * we scan the config file and create a hash table linking feature set
+ */
void zmapViewLoadFeatures(ZMapView view, ZMapFeatureBlock block_orig, GList *req_sources,
int features_start, int features_end)
{
- ZMapViewConnection view_con ;
- ZMapServerReqAny req_any ;
ZMapFeatureContext orig_context, context ;
- ConnectionData connect_data ;
ZMapFeatureBlock block ;
GList *req_featuresets ;
+ GHashTable *hash = NULL;
+ GList * sources;
+ ZMapConfigSource server;
+ char *stylesfile;
+ gboolean requested = FALSE;
+
+ sources = zmapViewGetIniSources(NULL,&stylesfile);
+ hash = zmapViewGetFeatureSourceHash(sources);
+
orig_context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)block_orig,
ZMAPFEATURE_STRUCT_CONTEXT) ;
@@ -1327,51 +1378,49 @@ void zmapViewLoadFeatures(ZMapView view, ZMapFeatureBlock block_orig, GList *req
zMapFeatureBlockSetFeaturesCoords(block, features_start, features_end) ;
+ for(;req_sources;req_sources = g_list_next(req_sources))
+ {
+ GQuark featureset = GPOINTER_TO_INT(req_sources->data);
- /* Create the step list that will be used to control obtaining the feature
- * context from the multiple sources. */
- view->step_list = zmapViewStepListCreate(dispatchContextRequests,
- processDataRequests,
- freeDataRequest) ;
- zmapViewStepListAddStep(view->step_list, ZMAP_SERVERREQ_FEATURESETS, REQUEST_ONFAIL_CANCEL_THREAD) ;
- zmapViewStepListAddStep(view->step_list, ZMAP_SERVERREQ_STYLES, REQUEST_ONFAIL_CANCEL_THREAD) ;
- zmapViewStepListAddStep(view->step_list, ZMAP_SERVERREQ_NEWCONTEXT, REQUEST_ONFAIL_CANCEL_THREAD) ;
- zmapViewStepListAddStep(view->step_list, ZMAP_SERVERREQ_FEATURES, REQUEST_ONFAIL_CANCEL_THREAD) ;
-
-
- /* HACK...MAKE THIS DO ALL SERVERS..... */
- /* should add all servers ???? need to loop for all servers.....
- * for test just add one... */
- view_con = (ZMapViewConnection)(view->connection_list->data) ;
-
-
- /* Create data specific to this step list...and set it in the connection. */
- connect_data = g_new0(ConnectionDataStruct, 1) ;
- connect_data->curr_context = context ;
- connect_data->dynamic_loading = TRUE ;
-
- connect_data->featureset_2_stylelist = zMap_g_hashlist_create() ;
-
- view_con->request_data = connect_data ;
-
-
- zmapViewStepListAddServerReq(view->step_list, view_con, ZMAP_SERVERREQ_GETSERVERINFO, req_any) ;
-
- req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_FEATURESETS, req_featuresets, req_sources) ;
- zmapViewStepListAddServerReq(view->step_list, view_con, ZMAP_SERVERREQ_FEATURESETS, req_any) ;
-
- req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_STYLES, NULL, NULL) ;
- zmapViewStepListAddServerReq(view->step_list, view_con, ZMAP_SERVERREQ_STYLES, req_any) ;
- req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_NEWCONTEXT, context) ;
- zmapViewStepListAddServerReq(view->step_list, view_con, ZMAP_SERVERREQ_NEWCONTEXT, req_any) ;
- req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_FEATURES) ;
- zmapViewStepListAddServerReq(view->step_list, view_con, ZMAP_SERVERREQ_FEATURES, req_any) ;
-
- connect_data->last_request = ZMAP_SERVERREQ_FEATURES ;
+ // MH17: a question: we are requesting source not featuresets: is this right?
+ server = zmapViewGetSourceFromFeatureset(hash,featureset);
+ if(server)
+ {
+ GList *req_feature = NULL;
+ int existing = FALSE;
+ ZMapViewConnection view_conn = NULL;
+
+ // make a list of one feature only
+ req_feature = g_list_append(req_feature,req_sources->data);
+
+ // look for server in view->connections list
+ view_conn = NULL; // (not implemented)
+
+printf("request featureset %s from %s\n",g_quark_to_string(GPOINTER_TO_UINT(req_feature->data)),server->url);
+ // start a new server connection
+ // can optionally use an existing one -> pass in second arg
+ createConnection(view, view_conn, context, server->url,
+ (char *)server->format,
+ server->timeout,
+ (char *)server->version,
+ (char *)server->styles_list,
+ stylesfile,
+ req_feature,
+ FALSE,
+ server->writeback,
+ !existing );
+ g_list_free(req_feature);
+ requested = TRUE; // set even if create fails: wiil get unset in check connection state
+ }
+ }
- /* Start the step list. */
- zmapViewStepListIter(view->step_list) ;
+ if(requested)
+ zmapViewBusy(view, TRUE) ; // gets unset when all step lists finish
+ if(sources)
+ zMapConfigSourcesFreeList(sources);
+ if(hash)
+ g_hash_table_destroy(hash);
return ;
}
@@ -1397,7 +1446,7 @@ static gint zmapIdleCB(gpointer cb_data)
gint call_again = 0 ;
ZMapView zmap_view = (ZMapView)cb_data ;
-
+
/* Returning a value > 0 tells gtk to call zmapIdleCB again, so if checkConnections() returns
* TRUE we ask to be called again. */
if (checkStateConnections(zmap_view))
@@ -1526,7 +1575,7 @@ static void viewSelectCB(ZMapWindow window, void *caller_data, void *window_data
view_select.xml_handler = window_select->xml_handler ; /* n.b. struct copy. */
-
+
if(window_select->xml_handler.zmap_action)
{
view_select.xml_handler.handled =
@@ -1535,16 +1584,16 @@ static void viewSelectCB(ZMapWindow window, void *caller_data, void *window_data
window_select->xml_handler.xml_events,
window_select->xml_handler.start_handlers,
window_select->xml_handler.end_handlers,
- window_select->xml_handler.handler_data);
+ window_select->xml_handler.handler_data);
}
/* Pass back a ZMapViewWindow as it has both the View and the window to our caller. */
(*(view_cbs_G->select))(view_window, view_window->parent_view->app_data, &view_select) ;
-
+
window_select->xml_handler.handled = view_select.xml_handler.handled;
-
+
return ;
}
@@ -1566,7 +1615,7 @@ static void viewSplitToPatternCB(ZMapWindow window, void *caller_data, void *win
/* foreach window find feature and Do something according to pattern */
split->window_index = 0;
g_list_foreach(view_split.touched_window_list, splitMagic, window_data);
-
+
/* clean up the list */
g_list_free(view_split.touched_window_list);
@@ -1669,7 +1718,7 @@ static ZMapViewWindow addWindow(ZMapView zmap_view, GtkWidget *parent_widget)
/* add to list of windows.... */
zmap_view->window_list = g_list_append(zmap_view->window_list, view_window) ;
-
+
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
@@ -1754,8 +1803,6 @@ static void destroyZMapView(ZMapView *zmap_view_out)
g_free(zmap_view->session_data) ;
}
- if (zmap_view->step_list)
- zmapViewStepListDestroy(zmap_view->step_list) ;
killAllSpawned(zmap_view);
@@ -1769,7 +1816,7 @@ static void destroyZMapView(ZMapView *zmap_view_out)
-/*
+/*
* Connection control functions, interface to the data fetching threads.
*/
@@ -1781,7 +1828,7 @@ static void startStateConnectionChecking(ZMapView zmap_view)
#ifdef UTILISE_ALL_CPU_ON_DESKPRO203
zmap_view->idle_handle = gtk_idle_add(zmapIdleCB, (gpointer)zmap_view) ;
-#endif /* UTILISE_ALL_CPU_ON_DESKPRO203 */
+#endif /* UTILISE_ALL_CPU_ON_DESKPRO203 */
zmap_view->idle_handle = gtk_timeout_add(100, zmapIdleCB, (gpointer)zmap_view) ;
// WARNING: gtk_timeout_add is deprecated and should not be used in newly-written code. Use g_timeout_add() instead.
@@ -1811,22 +1858,21 @@ static void stopStateConnectionChecking(ZMapView zmap_view)
* then acts on it, it gets called from the ZMap idle function.
* If all threads are ok and zmap has not been killed then routine returns TRUE
* meaning it wants to be called again, otherwise FALSE.
- *
+ *
* The function monitors the View state so that when the last connection has disappeared
* and the View is dying then the View is cleaned up and the caller gets called to say
* the View is now dead.
- *
+ *
* NOTE that you cannot use a condvar here, if the connection thread signals us using a
* condvar we will probably miss it, that just doesn't work, we have to pole for changes
* and this is possible because this routine is called from the idle function of the GUI.
- *
+ *
* */
static gboolean checkStateConnections(ZMapView zmap_view)
{
- gboolean call_again = TRUE ; /* Normally we want to called continuously. */
- gboolean state_change = TRUE ; /* Has view state changed ?. */
- gboolean threads_have_died = FALSE ; /* Have any threads died ? */
-
+ gboolean call_again = TRUE ; /* Normally we want to called continuously. */
+ gboolean state_change = TRUE ; /* Has view state changed ?. */
+ gboolean has_step_list = FALSE; // any requests still active?
if (zmap_view->connection_list)
{
@@ -1841,7 +1887,8 @@ static gboolean checkStateConnections(ZMapView zmap_view)
ZMapThreadReply reply ;
void *data = NULL ;
char *err_msg = NULL ;
-
+ gboolean thread_has_died = FALSE ;
+
view_con = list_item->data ;
thread = view_con->thread ;
@@ -1866,7 +1913,7 @@ static gboolean checkStateConnections(ZMapView zmap_view)
zMapLogCritical("Source \"%s\", cannot access reply from server thread,"
" error was: %s", view_con->url, err_msg) ;
- threads_have_died = TRUE ;
+ thread_has_died = TRUE ;
}
else
{
@@ -1897,7 +1944,7 @@ static gboolean checkStateConnections(ZMapView zmap_view)
/* Recover the stepRequest from the view connection and process the data from
* the request. */
- if (!(request = zmapViewStepListFindRequest(zmap_view->step_list, req_any->type, view_con)))
+ if (!(request = zmapViewStepListFindRequest(view_con->step_list, req_any->type, view_con)))
{
zMapLogCritical("Request of type %s for connection %s not found in view %s step list !",
zMapServerReqType2ExactStr(req_any->type),
@@ -1905,10 +1952,10 @@ static gboolean checkStateConnections(ZMapView zmap_view)
zmap_view->view_name) ;
kill_connection = TRUE ;
- }
+ }
else
{
- step = request->step ;
+ step = (ZMapViewConnectionStep) view_con->step_list->current->data; //request->step ;
if (reply == ZMAPTHREAD_REPLY_REQERROR)
{
@@ -1925,8 +1972,6 @@ static gboolean checkStateConnections(ZMapView zmap_view)
zMapLogCritical(format_str, view_con->url, err_msg) ;
}
- if (step->on_fail == REQUEST_ONFAIL_CANCEL_THREAD)
- kill_connection = TRUE ;
}
else
{
@@ -1939,18 +1984,23 @@ static gboolean checkStateConnections(ZMapView zmap_view)
zmapViewGetStatusAsStr(zMapViewGetStatus(zmap_view))) ;
}
- zmapViewStepListStepProcessRequest(zmap_view->step_list, request) ;
- }
+ zmapViewStepListStepProcessRequest(view_con, request) ;
+ if(request->state != STEPLIST_FINISHED) // ie there was an error
+ reply = ZMAPTHREAD_REPLY_REQERROR;
+ }
}
-
- if (reply == ZMAPTHREAD_REPLY_REQERROR
- && (step->on_fail == REQUEST_ONFAIL_CANCEL_THREAD
- || step->on_fail == REQUEST_ONFAIL_CANCEL_STEPLIST))
- {
- /* Remove request from all steps.... */
- zmapViewStepListStepConnectionDeleteAll(zmap_view->step_list, view_con) ;
- }
+ if (reply == ZMAPTHREAD_REPLY_REQERROR)
+ {
+ if (step->on_fail == REQUEST_ONFAIL_CANCEL_THREAD
+ || step->on_fail == REQUEST_ONFAIL_CANCEL_STEPLIST)
+ {
+ /* Remove request from all steps.... */
+ zmapViewStepListDestroy(view_con) ;
+ }
+ if (step->on_fail == REQUEST_ONFAIL_CANCEL_THREAD)
+ kill_connection = TRUE ;
+ }
if (kill_connection)
{
@@ -1976,17 +2026,17 @@ static gboolean checkStateConnections(ZMapView zmap_view)
if (err_msg)
zMapWarning("%s", err_msg) ;
- threads_have_died = TRUE ;
+ thread_has_died = TRUE ;
threadDebugMsg(thread, "GUI: thread %s has died so cleaning up....\n", NULL) ;
-
+
break ;
}
case ZMAPTHREAD_REPLY_CANCELLED:
{
/* This happens when we have signalled the threads to die and they are
* replying to say that they have now died. */
- threads_have_died = TRUE ;
+ thread_has_died = TRUE ;
/* This means the thread was cancelled so we should clean up..... */
threadDebugMsg(thread, "GUI: thread %s has been cancelled so cleaning up....\n", NULL) ;
@@ -1994,7 +2044,7 @@ static gboolean checkStateConnections(ZMapView zmap_view)
break ;
}
default:
- {
+ {
zMapLogFatalLogicErr("switch(), unknown value: %d", reply) ;
break ;
@@ -2003,42 +2053,41 @@ static gboolean checkStateConnections(ZMapView zmap_view)
}
+ /* Check for more connection steps and dispatch them or clear up if finished. */
+ if ((view_con->step_list))
+ {
+ /* If there were errors then all connections may have been removed from
+ * step list or if we have finished then destroy step_list. */
+ if (zmapViewStepListIsNext(view_con->step_list))
+ {
+ zmapViewStepListIter(view_con) ;
+ has_step_list = TRUE;
+ }
+ else
+ {
+ zmapViewStepListDestroy(view_con) ;
+ }
+ }
/* If the thread has died then remove it's connection. */
- if (threads_have_died)
+ if (thread_has_died)
{
/* We are going to remove an item from the list so better move on from
* this item. */
list_item = g_list_next(list_item) ;
zmap_view->connection_list = g_list_remove(zmap_view->connection_list, view_con) ;
- /* If step list is unfinished then remove failed connection from it. */
- if (zmap_view->step_list)
- zmapViewStepListStepConnectionDeleteAll(zmap_view->step_list, view_con) ;
-
destroyConnection(&view_con) ;
}
if (err_msg)
g_free(err_msg) ;
}
- while ((list_item = g_list_next(list_item))) ;
+ while (list_item && (list_item = g_list_next(list_item))) ;
}
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- /* I don't think this is correct..... */
-
- /* Fiddly logic here as this could be combined with the following code that handles if we don't
- * have any connections any more...but not so easy as some of the code below kills the zmap so.
- * easier to do this here. */
- if (zmap_view->busy && !zmapAnyConnBusy(zmap_view->connection_list))
- zmapViewBusy(zmap_view, FALSE) ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
/* At this point if we have connections then we carry on looping looking for
* replies from the views. If there are no threads left then we need to examine
* our state and take action depending on whether we are dying or threads
@@ -2049,24 +2098,9 @@ static gboolean checkStateConnections(ZMapView zmap_view)
if (state_change)
(*(view_cbs_G->state_change))(zmap_view, zmap_view->app_data, NULL) ;
- /* Check for more connection steps and dispatch them or clear up if finished. */
- if ((zmap_view->step_list))
- {
- /* If there were errors then all connections may have been removed from
- * step list or if we have finished then destroy step_list. */
- if (zmapViewStepListAreConnections(zmap_view->step_list) && zmapViewStepListIsNext(zmap_view->step_list))
- {
- zmapViewStepListIter(zmap_view->step_list) ;
- }
- else
- {
- zmapViewStepListDestroy(zmap_view->step_list) ;
- zmap_view->step_list = NULL ;
-
- /* Try this here..... */
- zmapViewBusy(zmap_view, FALSE) ;
- }
- }
+ /* Try this here..... */
+ if(!has_step_list)
+ zmapViewBusy(zmap_view, FALSE) ;
}
else
{
@@ -2134,16 +2168,30 @@ static gboolean dispatchContextRequests(ZMapViewConnection connection, ZMapServe
break ;
}
case ZMAP_SERVERREQ_SEQUENCE:
+ // mh17: this was a cut and paste of _FEATURES
+ // it turns out that the code that fields this expects it, so what is ZMapServerReqGetSequence about?
{
- ZMapServerReqGetFeatures get_features = (ZMapServerReqGetFeatures)req_any ;
+ ZMapServerReqGetFeatures get_features = (ZMapServerReqGetFeatures)req_any ;
- get_features->context = connect_data->curr_context ;
- get_features->styles = connect_data->curr_styles ;
+ get_features->context = connect_data->curr_context ;
+ get_features->styles = connect_data->curr_styles ;
+// ZMapServerReqGetSequence get_sequence = (ZMapServerReqGetSequence)req_any ;
+/*
+ get_sequence->orig_feature = va_arg(args, ZMapFeature) ;
+ get_sequence->sequences = va_arg(args, GList *) ;
+ get_sequence->flags = va_arg(args, int) ;
+*/
break ;
}
+ case ZMAP_SERVERREQ_TERMINATE:
+ {
+ //ZMapServerReqTerminate terminate = (ZMapServerReqTerminate) req_any ;
+
+ break ;
+ }
default:
- {
+ {
zMapLogFatalLogicErr("switch(), unknown value: %d", req_any->type) ;
break ;
@@ -2226,7 +2274,7 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
feature_set_id = zMapStyleCreateID((char *)g_quark_to_string(feature_set_name_id)) ;
- zMap_g_hashlist_insert(feature_sets->featureset_2_stylelist_out,
+ zMap_g_hashlist_insert(feature_sets->featureset_2_stylelist_out,
feature_set_id,
GUINT_TO_POINTER(feature_set_id)) ;
}
@@ -2251,7 +2299,7 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
- /* If the hashes aren't equal, we had to do a merge. Need to free the server
+ /* If the hashes aren't equal, we had to do a merge. Need to free the server
* created hash that will otherwise be left dangling... */
if (zmap_view->featureset_2_stylelist != feature_sets->featureset_2_stylelist_out)
{
@@ -2293,7 +2341,7 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
/* Store the curr styles for use in creating the context and drawing features. */
connect_data->curr_styles = get_styles->styles_out ;
-
+
break ;
}
case ZMAP_SERVERREQ_NEWCONTEXT:
@@ -2316,7 +2364,7 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
{
zMapLogWarning("Source %s, inferring Style modes from Features failed.",
view_con->url) ;
-
+
result = FALSE ;
}
@@ -2326,7 +2374,7 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
{
zMapLogWarning("Source %s, inferring Style modes from Features failed.",
view_con->url) ;
-
+
result = FALSE ;
}
@@ -2367,9 +2415,15 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
break ;
}
+ case ZMAP_SERVERREQ_GETSEQUENCE:
+ // never appears??
+ case ZMAP_SERVERREQ_TERMINATE:
+ {
+ break ;
+ }
default:
- {
+ {
zMapLogFatalLogicErr("switch(), unknown value: %d", req_any->type) ;
result = FALSE ;
@@ -2380,10 +2434,8 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
return result ;
}
-static void freeDataRequest(ZMapViewConnection view_con, ZMapServerReqAny req_any)
+static void freeDataRequest(ZMapServerReqAny req_any)
{
- g_free(view_con->request_data) ;
- view_con->request_data = NULL ;
zMapServerCreateRequestDestroy(req_any) ;
@@ -2392,7 +2444,7 @@ static void freeDataRequest(ZMapViewConnection view_con, ZMapServerReqAny req_an
-/*
+/*
* Callbacks for getting local sequences for passing to blixem.
*/
static gboolean processGetSeqRequests(ZMapViewConnection view_con, ZMapServerReqAny req_any)
@@ -2408,7 +2460,7 @@ static gboolean processGetSeqRequests(ZMapViewConnection view_con, ZMapServerReq
/* Got the sequences so launch blixem. */
if ((status = zmapViewCallBlixem(zmap_view,
- get_sequence->orig_feature,
+ get_sequence->orig_feature,
get_sequence->sequences,
get_sequence->flags,
&blixem_pid,
@@ -2419,7 +2471,7 @@ static gboolean processGetSeqRequests(ZMapViewConnection view_con, ZMapServerReq
result = TRUE ;
}
else
- {
+ {
zMapLogFatalLogicErr("wrong request type: %d", req_any->type) ;
result = FALSE ;
@@ -2491,121 +2543,141 @@ static void invoke_merge_in_names(gpointer list_data, gpointer user_data)
/* Allocate a connection and send over the request to get the sequence displayed. */
+/* NB: this is called from zmapViewConnect() and also zmapViewLoadFeatures() and commandCB (for DNA only) */
static ZMapViewConnection createConnection(ZMapView zmap_view,
- ZMapURL url, char *format,
+ ZMapViewConnection view_con,
+ ZMapFeatureContext context,
+ char *server_url, char *format,
int timeout, char *version,
char *styles, char *styles_file,
- char *featuresets_names, char *navigator_set_names,
- gboolean sequence_server, gboolean writeback_server,
- char *sequence, int start, int end)
+ GList *req_featuresets,
+ gboolean dna_requested, gboolean writeback_server,
+ gboolean terminate)
{
- ZMapViewConnection view_con = NULL ;
- GList *req_featuresets = NULL, *tmp_navigator_sets = NULL ;
+
ZMapThread thread ;
- gboolean status = TRUE ;
- gboolean dna_requested = FALSE ;
ConnectionData connect_data ;
+ gboolean existing = FALSE;
+ int url_parse_error ;
+ ZMapURL urlObj;
-
- /* User can specify feature set names that should be displayed in an ordered list. Order of
- * list determines order of columns. */
- if (featuresets_names)
+ if(view_con)
{
- /* If user only wants some featuresets displayed then build a list of their quark names. */
- req_featuresets = zMapFeatureString2QuarkList(featuresets_names) ;
-
-
- /* Check whether dna was requested, see comments below about setting up sequence req. */
- if ((zMap_g_list_find_quark(req_featuresets, zMapStyleCreateID(ZMAP_FIXED_STYLE_DNA_NAME))))
- dna_requested = TRUE ;
-
- g_list_foreach(zmap_view->window_list, invoke_merge_in_names, req_featuresets);
-
+ // use existing connection if not busy
+ if(view_con->step_list)
+ view_con = NULL;
+ else
+ existing = TRUE;
+if(existing) printf("using existing connection %s\n",view_con->url);
}
- /* Navigator styles are all predefined so no need to merge into main feature sets to get the styles. */
- if (navigator_set_names)
+ if(!view_con)
{
- tmp_navigator_sets = zmap_view->navigator_set_names = zMapFeatureString2QuarkList(navigator_set_names);
-
- /* We _must_ merge the set names into the navigator though. */
- /* The navigator knows nothing of view, so saving them there isn't really useful for getting them drawn.
- * N.B. This is zMapWindowNavigatorMergeInFeatureSetNames _not_ zMapWindowMergeInFeatureSetNames. */
- if(zmap_view->navigator_window)
- zMapWindowNavigatorMergeInFeatureSetNames(zmap_view->navigator_window, tmp_navigator_sets);
+ /* Parse the url and create connection. */
+ if (!(urlObj = url_parse(server_url, &url_parse_error)))
+ {
+ zMapLogWarning("GUI: url %s did not parse. Parse error < %s >\n",
+ server_url, url_error(url_parse_error)) ;
+ return(NULL);
+ }
+ /* Create the thread to service the connection requests, we give it a function that it will call
+ * to decode the requests we send it and a terminate function. */
+ if ((thread = zMapThreadCreate(zMapServerRequestHandler,
+ zMapServerTerminateHandler, zMapServerDestroyHandler)))
+ {
+ /* Create the connection struct. */
+ view_con = g_new0(ZMapViewConnectionStruct, 1) ;
+ view_con->parent_view = zmap_view ;
+ view_con->thread = thread ;
+ view_con->url = g_strdup(urlObj->url) ;
+printf("create thread for %s\n",view_con->url);
+ }
+ else
+ {
+ return(NULL);
+ }
}
- /* Create the thread to service the connection requests, we give it a function that it will call
- * to decode the requests we send it and a terminate function. */
- if (status && (thread = zMapThreadCreate(zMapServerRequestHandler,
- zMapServerTerminateHandler, zMapServerDestroyHandler)))
+ if(view_con)
{
- ZMapViewConnectionRequest request ;
- ZMapFeatureContext context ;
- ZMapServerReqAny req_any ;
-
-
- /* Create the connection struct. */
- view_con = g_new0(ZMapViewConnectionStruct, 1) ;
-
-
- /* THESE MUST GO ONCE STEP LIST SET UP PROPERLY..... */
- view_con->sequence_server = sequence_server ;
- view_con->writeback_server = writeback_server ;
-
-
- view_con->parent_view = zmap_view ;
+ ZMapServerReqAny req_any;
view_con->curr_request = ZMAPTHREAD_REQUEST_EXECUTE ;
- view_con->thread = thread ;
-
- view_con->url = g_strdup(url->url) ;
-
- /* Create data specific to this step list...and set it in the connection. */
- context = createContext(sequence, start, end, req_featuresets) ;
-
connect_data = g_new0(ConnectionDataStruct, 1) ;
connect_data->curr_context = context ;
-
+ if(terminate) // ie server->delayed
+ connect_data->dynamic_loading = TRUE ;
connect_data->featureset_2_stylelist = zMap_g_hashlist_create() ;
view_con->request_data = connect_data ;
-
+
+
+ view_con->step_list = zmapViewConnectionStepListCreate(dispatchContextRequests,
+ processDataRequests,
+ freeDataRequest);
/* CHECK WHAT THIS IS ABOUT.... */
/* Record info. for this session. */
- zmapViewSessionAddServer(zmap_view->session_data,
- url,
- format) ;
+ zmapViewSessionAddServer(zmap_view->session_data,urlObj,format) ;
+ connect_data->last_request = ZMAP_SERVERREQ_INVALID;
/* Set up this connection in the step list. */
- req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_CREATE, url, format, timeout, version) ;
- request = zmapViewStepListAddServerReq(zmap_view->step_list, view_con, ZMAP_SERVERREQ_CREATE, req_any) ;
- req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_OPEN) ;
- zmapViewStepListAddServerReq(zmap_view->step_list, view_con, ZMAP_SERVERREQ_OPEN, req_any) ;
- req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_GETSERVERINFO) ;
- zmapViewStepListAddServerReq(zmap_view->step_list, view_con, ZMAP_SERVERREQ_GETSERVERINFO, req_any) ;
- req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_FEATURESETS, req_featuresets, NULL) ;
- zmapViewStepListAddServerReq(zmap_view->step_list, view_con, ZMAP_SERVERREQ_FEATURESETS, req_any) ;
- req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_STYLES, styles, styles_file) ;
- zmapViewStepListAddServerReq(zmap_view->step_list, view_con, ZMAP_SERVERREQ_STYLES, req_any) ;
- req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_NEWCONTEXT, context) ;
- zmapViewStepListAddServerReq(zmap_view->step_list, view_con, ZMAP_SERVERREQ_NEWCONTEXT, req_any) ;
- req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_FEATURES) ;
- zmapViewStepListAddServerReq(zmap_view->step_list, view_con, ZMAP_SERVERREQ_FEATURES, req_any) ;
-
- connect_data->last_request = ZMAP_SERVERREQ_FEATURES ;
- if (sequence_server && dna_requested)
+ if(!existing)
+ {
+ req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_CREATE, urlObj, format, timeout, version) ;
+ zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_CREATE, req_any) ;
+ req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_OPEN) ;
+ zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_OPEN, req_any) ;
+ req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_GETSERVERINFO) ;
+ zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_GETSERVERINFO, req_any) ;
+ // how can this be? maybe we want to connect and req data later on. Right now not likely
+ connect_data->last_request = ZMAP_SERVERREQ_GETSERVERINFO ;
+ }
+
+ if(req_featuresets)
+ {
+ req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_FEATURESETS, req_featuresets, NULL) ;
+ zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_FEATURESETS, req_any) ;
+ req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_STYLES, styles, styles_file) ;
+ zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_STYLES, req_any) ;
+ req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_NEWCONTEXT, context) ;
+ zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_NEWCONTEXT, req_any) ;
+ req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_FEATURES) ;
+ zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_FEATURES, req_any) ;
+ connect_data->last_request = ZMAP_SERVERREQ_FEATURES ;
+ }
+
+ if (dna_requested)
{
req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_SEQUENCE) ;
- zmapViewStepListAddServerReq(zmap_view->step_list, view_con, ZMAP_SERVERREQ_SEQUENCE, req_any) ;
+ zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_SEQUENCE, req_any) ;
connect_data->last_request = ZMAP_SERVERREQ_SEQUENCE ;
}
- }
+ if(terminate)
+ {
+ req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_TERMINATE) ;
+ zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_TERMINATE, req_any) ;
+ connect_data->last_request = ZMAP_SERVERREQ_TERMINATE ;
+ }
+
+ if(!existing)
+ zmap_view->connection_list = g_list_append(zmap_view->connection_list, view_con) ;
+
+ /* Start the connection to the source. */
+ zmapViewStepListIter(view_con) ;
+ }
+ else
+ {
+ zMapLogWarning("GUI: url %s looks ok (host: %s\tport: %d)"
+ "but could not connect to server.",
+ urlObj->url,
+ urlObj->host,
+ urlObj->port) ;
+ }
return view_con ;
}
@@ -2620,6 +2692,9 @@ static void destroyConnection(ZMapViewConnection *view_conn_ptr)
g_free(view_conn->url) ;
+ if(view_conn->step_list)
+ zmapViewStepListDestroy(view_conn);
+
/* Need to destroy the types array here....... */
g_free(view_conn) ;
@@ -2654,7 +2729,7 @@ static void resetWindows(ZMapView zmap_view)
/* Signal all windows there is data to draw. */
static void displayDataWindows(ZMapView zmap_view,
- ZMapFeatureContext all_features,
+ ZMapFeatureContext all_features,
ZMapFeatureContext new_features, GData *new_styles,
gboolean undisplay)
{
@@ -2748,7 +2823,7 @@ static void killAllWindows(ZMapView zmap_view)
static ZMapViewWindow createWindow(ZMapView zmap_view, ZMapWindow window)
{
ZMapViewWindow view_window ;
-
+
view_window = g_new0(ZMapViewWindowStruct, 1) ;
view_window->parent_view = zmap_view ; /* back pointer. */
view_window->window = window ;
@@ -2792,13 +2867,13 @@ static void getFeatures(ZMapView zmap_view, ZMapServerReqGetFeatures feature_req
/* Error handling is rubbish here...stuff needs to be free whether there is an error or not.
- *
+ *
* new_features should be freed (but not the data...ahhhh actually the merge should
* free any replicated data...yes, that is what should happen. Then when it comes to
* the diff we should not free the data but should free all our structs...
- *
+ *
* We should free the context_inout context here....actually better
- * would to have a "free" flag............
+ * would to have a "free" flag............
* */
static gboolean mergeAndDrawContext(ZMapView view, ZMapFeatureContext context_in, GData *styles)
{
@@ -2828,7 +2903,7 @@ static gboolean justMergeContext(ZMapView view, ZMapFeatureContext *context_inou
if (view->revcomped_features)
{
zMapPrintTimer(NULL, "Merge Context has to rev comp first, starting") ;
-
+
zMapFeatureReverseComplement(new_features, view->orig_styles);
zMapPrintTimer(NULL, "Merge Context has to rev comp first, finished") ;
@@ -2859,28 +2934,28 @@ static void justDrawContext(ZMapView view, ZMapFeatureContext diff_context, GDat
{
/* Signal the ZMap that there is work to be done. */
displayDataWindows(view, view->features, diff_context, new_styles, FALSE) ;
-
+
/* Not sure about the timing of the next bit. */
-
+
/* We have to redraw the whole navigator here. This is a bit of
* a pain, but it's due to the scaling we do to make the rest of
- * the navigator work. If the length of the sequence changes the
- * all the previously drawn features need to move. It also
+ * the navigator work. If the length of the sequence changes the
+ * all the previously drawn features need to move. It also
* negates the need to keep state as to the length of the sequence,
* the number of times the scale bar has been drawn, etc... */
zMapWindowNavigatorReset(view->navigator_window); /* So reset */
zMapWindowNavigatorSetStrand(view->navigator_window, view->revcomped_features);
/* and draw with _all_ the view's features. */
zMapWindowNavigatorDrawFeatures(view->navigator_window, view->features, view->orig_styles);
-
+
/* signal our caller that we have data. */
(*(view_cbs_G->load_data))(view, view->app_data, NULL) ;
-
+
return ;
}
static void eraseAndUndrawContext(ZMapView view, ZMapFeatureContext context_inout)
-{
+{
ZMapFeatureContext diff_context = NULL;
if(!zMapFeatureContextErase(&(view->features), context_inout, &diff_context))
@@ -2888,7 +2963,7 @@ static void eraseAndUndrawContext(ZMapView view, ZMapFeatureContext context_inou
else
{
displayDataWindows(view, view->features, diff_context, NULL, TRUE);
-
+
zMapFeatureContextDestroy(diff_context, TRUE);
}
@@ -2924,19 +2999,13 @@ static void commandCB(ZMapWindow window, void *caller_data, void *window_data)
align_type = BLIXEM_MULTI_FEATURESET_MATCHES ;
else if (align_cmd->all_sets)
align_type = BLIXEM_ALL_FEATURESET_MATCHES ;
-
+
if ((status = zmapViewBlixemLocalSequences(view, align_cmd->feature, &local_sequences)))
{
if (!view->sequence_server)
{
zMapWarning("%s", "No sequence server was specified so cannot fetch raw sequences for blixem.") ;
}
- else if (view->step_list)
- {
- zMapLogCritical("GUI: %s", "View is already executing connection requests"
- " so cannot fetch local sequences for blixem.") ;
-
- }
else
{
ZMapViewConnection view_con ;
@@ -2945,26 +3014,31 @@ static void commandCB(ZMapWindow window, void *caller_data, void *window_data)
view_con = view->sequence_server ;
- if (!(view_con->sequence_server))
+ if (!view_con || !view_con->sequence_server)
{
zMapWarning("%s", "Sequence server incorrectly specified in config file"
" so cannot fetch local sequences for blixem.") ;
}
- else
+ else if(view_con->step_list)
+ {
+ zMapWarning("%s", "Sequence server is currently active"
+ " so cannot fetch local sequences for blixem.") ;
+ }
+ else
{
/* Create the step list that will be used to fetch the sequences. */
- view->step_list = zmapViewStepListCreate(NULL, processGetSeqRequests, NULL) ;
- zmapViewStepListAddStep(view->step_list, ZMAP_SERVERREQ_GETSEQUENCE,
+ view_con->step_list = zmapViewStepListCreate(NULL, processGetSeqRequests, NULL) ;
+ zmapViewStepListAddStep(view_con->step_list, ZMAP_SERVERREQ_GETSEQUENCE,
REQUEST_ONFAIL_CANCEL_STEPLIST) ;
/* Add the request to the step list. */
req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_GETSEQUENCE,
align_cmd->feature, local_sequences, align_type) ;
- request = zmapViewStepListAddServerReq(view->step_list,
+ request = zmapViewStepListAddServerReq(view_con->step_list,
view_con, ZMAP_SERVERREQ_GETSEQUENCE, req_any) ;
-
+
/* Start the step list. */
- zmapViewStepListIter(view->step_list) ;
+ zmapViewStepListIter(view_con) ;
}
}
}
@@ -2979,11 +3053,10 @@ static void commandCB(ZMapWindow window, void *caller_data, void *window_data)
break ;
}
-
case ZMAPWINDOW_CMD_GETFEATURES:
{
ZMapWindowCallbackGetFeatures get_data = (ZMapWindowCallbackGetFeatures)cmd_any ;
-
+
zmapViewLoadFeatures(view, get_data->block, get_data->feature_set_ids, get_data->start, get_data->end) ;
break ;
@@ -3166,7 +3239,7 @@ static void addAlignments(ZMapFeatureContext context)
/* Add the other alignment, note that we do this dumbly at the moment assuming
* that there is only one other alignment */
alignment = zMapFeatureAlignmentCreate(non_reference_seq, FALSE) ;
-
+
zMapFeatureContextAddAlignment(context, alignment, FALSE) ;
}
@@ -3286,9 +3359,9 @@ static gboolean getSequenceServers(ZMapView zmap_view, char *config_str)
zMapConfigDeleteStanzaSet(zmap_list) ; /* Not needed anymore. */
}
-
+
zMapConfigDestroyStanza(zmap_stanza) ;
-
+
zMapConfigIniDestroy(config) ;
result = TRUE ;
@@ -3336,7 +3409,7 @@ static gboolean checkSequenceToServerMatch(GList *seq_2_server, ZMapViewSequence
{
gboolean result = FALSE ;
GList *server_item ;
-
+
/* If the sequence is in the list then check the server names. */
if ((server_item = g_list_find_custom(seq_2_server, target_seq_server, findSequence)))
{
@@ -3361,7 +3434,7 @@ static gint findSequence(gconstpointer a, gconstpointer b)
gint result = -1 ;
ZMapViewSequence2Server seq_2_server = (ZMapViewSequence2Server)a ;
ZMapViewSequence2Server target_fetch = (ZMapViewSequence2Server)b ;
-
+
if ((g_ascii_strcasecmp(seq_2_server->sequence, target_fetch->sequence) == 0))
result = 0 ;
@@ -3396,6 +3469,7 @@ static gboolean checkContinue(ZMapView zmap_view)
switch (zmap_view->state)
{
case ZMAPVIEW_INIT:
+ case ZMAPVIEW_LOADED: // delayed servers get cleared up, we do not need connections to run
{
/* Nothing to do here I think.... */
connections = TRUE ;
@@ -3404,11 +3478,11 @@ static gboolean checkContinue(ZMapView zmap_view)
case ZMAPVIEW_CONNECTING:
case ZMAPVIEW_CONNECTED:
case ZMAPVIEW_LOADING:
- case ZMAPVIEW_LOADED:
+// case ZMAPVIEW_LOADED:
{
/* Kill the view as all connections have died. */
/* Threads have died because of their own errors....but the ZMap is not dying so
- * reset state to init and we should return an error here....(but how ?), we
+ * reset state to init and we should return an error here....(but how ?), we
* should not be outputting messages....I think..... */
/* need to reset here..... */
@@ -3573,7 +3647,7 @@ static void styleCB(GQuark key_id, gpointer data, gpointer user_data)
feature_set_id = zMapStyleCreateID((char *)g_quark_to_string(feature_set_name_id)) ;
- zMap_g_hashlist_insert(hash,
+ zMap_g_hashlist_insert(hash,
feature_set_id,
GUINT_TO_POINTER(feature_set_id)) ;
diff --git a/src/zmapView/zmapViewUtils.c b/src/zmapView/zmapViewUtils.c
index 1be8d8ce2..367b2b8f9 100755
--- a/src/zmapView/zmapViewUtils.c
+++ b/src/zmapView/zmapViewUtils.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.
@@ -23,13 +23,14 @@
* Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
*
* Description: Utility functions for a ZMapView.
- *
+ * StepLists changed to be the child of a connection by Malcolm Hinsley (mh17@sanger.ac.uk) 11 Mar 2010
+ *
* Exported functions: See ZMap/ZMapView.h for public functions and
* zmapView_P.h for private functions.
* HISTORY:
* Last edited: Mar 11 13:27 2010 (edgrif)
* Created: Mon Sep 20 10:29:15 2004 (edgrif)
- * CVS info: $Id: zmapViewUtils.c,v 1.18 2010-03-12 14:46:42 edgrif Exp $
+ * CVS info: $Id: zmapViewUtils.c,v 1.19 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -49,7 +50,7 @@ typedef struct
typedef struct
{
ZMapServerReqType request_type ;
- ZMapViewConnection connection ;
+// ZMapViewConnection connection ;
ZMapViewConnectionStep step ;
ZMapViewConnectionRequest request ;
} StepListFindStruct, *StepListFind ;
@@ -75,24 +76,24 @@ typedef struct
static void cwh_destroy_key(gpointer cwh_data) ;
static void cwh_destroy_value(gpointer cwh_data) ;
-static void stepDispatch(gpointer data, gpointer user_data) ;
-static void stepFinished(gpointer data, gpointer user_data) ;
+//static void stepDispatch(gpointer data, gpointer user_data) ;
+//static void stepFinished(gpointer data, gpointer user_data) ;
static ZMapViewConnectionStep stepListFindStep(ZMapViewConnectionStepList step_list, ZMapServerReqType request_type) ;
-static void stepFind(gpointer data, gpointer user_data) ;
-static void reqFind(gpointer data, gpointer user_data) ;
-static void connectionRemove(gpointer data, gpointer user_data) ;
+//static void stepFind(gpointer data, gpointer user_data) ;
+//static void reqFind(gpointer data, gpointer user_data) ;
+//static void connectionRemove(gpointer data, gpointer user_data) ;
static void stepDestroy(gpointer data, gpointer user_data) ;
-static void requestDestroy(gpointer data, gpointer user_data) ;
-static void isConnection(gpointer data, gpointer user_data) ;
-static void removeFailedConnections(ZMapViewConnectionStepList step_list, ZMapViewConnectionStep step) ;
-static GList *findFailedRequests(ZMapViewConnectionStep step) ;
-static void findFailed(gpointer data, gpointer user_data) ;
-static void removeFailed(gpointer data, gpointer user_data) ;
+//static void requestDestroy(gpointer data, gpointer user_data) ;
+//static void isConnection(gpointer data, gpointer user_data) ;
+//static void removeFailedConnections(ZMapViewConnectionStepList step_list, ZMapViewConnectionStep step) ;
+//static GList *findFailedRequests(ZMapViewConnectionStep step) ;
+//static void findFailed(gpointer data, gpointer user_data) ;
+//static void removeFailed(gpointer data, gpointer user_data) ;
static void getSetCB(void *data, void *user_data) ;
-/*
+/*
* ZMapView interface functions.
*/
@@ -152,12 +153,12 @@ ZMapViewSession zMapViewSessionGetData(ZMapViewWindow zmap_view_window)
-/*
+/*
* ZMapView internal package functions.
*/
-/* Not sure where this is used...check this out.... */
+/* Not sure where this is used...check this out.... in checkStateConnections() zmapView.c*/
gboolean zmapAnyConnBusy(GList *connection_list)
{
gboolean result = FALSE ;
@@ -171,7 +172,7 @@ gboolean zmapAnyConnBusy(GList *connection_list)
do
{
view_con = list_item->data ;
-
+
if (view_con->curr_request == ZMAPTHREAD_REQUEST_EXECUTE)
{
result = TRUE ;
@@ -187,10 +188,10 @@ gboolean zmapAnyConnBusy(GList *connection_list)
-/*
- *
+/*
+ *
* A series of functions for handling the stepping through of sending requests to slave threads.
- *
+ *
*/
@@ -223,7 +224,7 @@ void zmapViewStepListAddStep(ZMapViewConnectionStepList step_list, ZMapServerReq
first = TRUE ;
step = g_new0(ZMapViewConnectionStepStruct, 1) ;
- step->state = STEPLIST_PENDING ;
+ step->state = STEPLIST_INVALID ; // might not be requested
step->on_fail = on_fail ;
step->request = request_type ;
step_list->steps = g_list_append(step_list->steps, step) ;
@@ -236,7 +237,7 @@ void zmapViewStepListAddStep(ZMapViewConnectionStepList step_list, ZMapServerReq
/* Add a connection to the specified step in the step list. */
-ZMapViewConnectionRequest zmapViewStepListAddServerReq(ZMapViewConnectionStepList step_list,
+ZMapViewConnectionRequest zmapViewStepListAddServerReq(ZMapViewConnectionStepList step_list,
ZMapViewConnection view_con,
ZMapServerReqType request_type,
gpointer request_data)
@@ -247,12 +248,10 @@ ZMapViewConnectionRequest zmapViewStepListAddServerReq(ZMapViewConnectionStepLis
if ((step = stepListFindStep(step_list, request_type)))
{
request = g_new0(ZMapViewConnectionRequestStruct, 1) ;
- request->state = STEPLIST_PENDING ;
- request->step = step ;
- request->connection = view_con ;
+ step->state = request->state = STEPLIST_PENDING ; // some duplication here?
request->request_data = request_data ;
-
- step->connections = g_list_append(step->connections, request) ;
+ step->connection_req = request ;
+printf("add request %d to %s\n",request_type,view_con->url);
}
@@ -260,12 +259,42 @@ ZMapViewConnectionRequest zmapViewStepListAddServerReq(ZMapViewConnectionStepLis
}
+
+// create a complete step list. each step will be processed is a request is added
+// steps default to STEPLIST_INVALID
+ZMapViewConnectionStepList zmapViewConnectionStepListCreate(StepListDispatchCB dispatch_func,
+ StepListProcessDataCB process_func,
+ StepListFreeDataCB free_func)
+{
+ ZMapViewConnectionStepList step_list;
+
+ step_list = zmapViewStepListCreate(dispatch_func,
+ process_func,
+ free_func) ;
+ zmapViewStepListAddStep(step_list, ZMAP_SERVERREQ_CREATE, REQUEST_ONFAIL_CANCEL_THREAD) ;
+ zmapViewStepListAddStep(step_list, ZMAP_SERVERREQ_OPEN, REQUEST_ONFAIL_CANCEL_THREAD) ;
+ zmapViewStepListAddStep(step_list, ZMAP_SERVERREQ_GETSERVERINFO, REQUEST_ONFAIL_CANCEL_THREAD) ;
+ zmapViewStepListAddStep(step_list, ZMAP_SERVERREQ_FEATURESETS, REQUEST_ONFAIL_CANCEL_THREAD) ;
+ zmapViewStepListAddStep(step_list, ZMAP_SERVERREQ_STYLES, REQUEST_ONFAIL_CANCEL_THREAD) ;
+ zmapViewStepListAddStep(step_list, ZMAP_SERVERREQ_NEWCONTEXT,REQUEST_ONFAIL_CANCEL_THREAD) ;
+ zmapViewStepListAddStep(step_list, ZMAP_SERVERREQ_FEATURES, REQUEST_ONFAIL_CANCEL_THREAD) ;
+ zmapViewStepListAddStep(step_list, ZMAP_SERVERREQ_SEQUENCE, REQUEST_ONFAIL_CANCEL_THREAD) ;
+ zmapViewStepListAddStep(step_list, ZMAP_SERVERREQ_TERMINATE, REQUEST_ONFAIL_CANCEL_THREAD) ;
+
+ return(step_list);
+
+}
+
+
/* The meat of the step list stuff, check step list to see where we are and dispatch next
* step if we are ready for it.
- *
+ *
* */
-void zmapViewStepListIter(ZMapViewConnectionStepList step_list)
+void zmapViewStepListIter(ZMapViewConnection view_con)
{
+ ZMapViewConnectionStepList step_list = view_con->step_list;
+ gboolean result = FALSE;
+
if (step_list->current)
{
ZMapViewConnectionStep curr_step ;
@@ -276,29 +305,39 @@ void zmapViewStepListIter(ZMapViewConnectionStepList step_list)
{
case STEPLIST_PENDING:
{
- /* Dispatch all requests in this step. */
- g_list_foreach(curr_step->connections, stepDispatch, step_list) ;
+ /* All requests are in STEPLIST_PENDING state and after dispatching will go into STEPLIST_DISPATCHED. */
+
+ /* Call users dispatch func. */
+ if ((step_list->dispatch_func))
+ result = step_list->dispatch_func(view_con, curr_step->connection_req->request_data) ;
- curr_step->state = STEPLIST_DISPATCHED ;
+ if (result)
+ {
+ zMapThreadRequest(view_con->thread, curr_step->connection_req->request_data) ;
- /* Check to see if any connections failed and remove them from the steplist if they
- * did, this might result in there being no connections in the step list. */
- removeFailedConnections(step_list, curr_step) ;
-
+ curr_step->connection_req->state = STEPLIST_DISPATCHED ;
+ curr_step->state = STEPLIST_DISPATCHED ;
+ }
+ else
+ {
+ curr_step->connection_req->has_failed = TRUE ;
+
+
+ /* Check to see if any connections failed and remove them from the steplist if they
+ * did, this might result in there being no connections in the step list.
+ */
+// removeFailedConnections(step_list, curr_step) ;
+ }
break ;
}
case STEPLIST_DISPATCHED:
{
- gboolean finished = TRUE ;
-
- /* Check all requests, if all finished then change state to finished. */
- g_list_foreach(curr_step->connections, stepFinished, &finished) ;
-
- if (finished)
- curr_step->state = STEPLIST_FINISHED ;
+ if (curr_step->connection_req->state != STEPLIST_DISPATCHED)
+ curr_step->state = STEPLIST_FINISHED ;
break ;
}
+ case STEPLIST_INVALID: // if a step is not used then skip over it
case STEPLIST_FINISHED:
{
/* Move to next step, do not dispatch, that is our callers decision.
@@ -320,6 +359,21 @@ void zmapViewStepListIter(ZMapViewConnectionStepList step_list)
}
+
+static void stepFindReq(gpointer data, gpointer user_data)
+{
+ ZMapViewConnectionStep step = (ZMapViewConnectionStep)data ;
+ StepListFind step_find = (StepListFind)user_data ;
+
+ if (!(step_find->request_type) || step->request == step_find->request_type)
+ {
+ step_find->step = step ;
+ step_find->request = step->connection_req;
+ }
+
+ return ;
+}
+
/* Find a connections request in a given request step. */
ZMapViewConnectionRequest zmapViewStepListFindRequest(ZMapViewConnectionStepList step_list,
ZMapServerReqType request_type, ZMapViewConnection connection)
@@ -328,10 +382,10 @@ ZMapViewConnectionRequest zmapViewStepListFindRequest(ZMapViewConnectionStepList
StepListFindStruct step_find = {0} ;
step_find.request_type = request_type ;
- step_find.connection = connection ;
+// step_find.connection = connection ;
step_find.request = NULL ;
- g_list_foreach(step_list->steps, stepFind, &step_find) ;
+ g_list_foreach(step_list->steps, stepFindReq, &step_find) ;
request = step_find.request ;
@@ -342,59 +396,76 @@ ZMapViewConnectionRequest zmapViewStepListFindRequest(ZMapViewConnectionStepList
/* Process data from request, gets called from main connection loop of the View which itself is
* called whenever a connection thread returns data.
* */
-void zmapViewStepListStepProcessRequest(ZMapViewConnectionStepList step_list, ZMapViewConnectionRequest request)
+void zmapViewStepListStepProcessRequest(ZMapViewConnection view_con, ZMapViewConnectionRequest request)
{
gboolean result = TRUE ;
+ ZMapViewConnectionStepList step_list = view_con->step_list;
/* Call users request processing func, if this signals the connection has failed then
* remove it from the step list. */
if ((step_list->process_func))
- result = step_list->process_func(request->connection, request->request_data) ;
+ result = step_list->process_func(view_con, request->request_data) ;
if (result)
{
request->state = STEPLIST_FINISHED ;
}
- else
- {
- zmapViewStepListStepConnectionDeleteAll(step_list, request->connection) ;
- }
return ;
}
+/* Step list funcs. */
-/* A Connection failed so remove it from the step list. */
-void zmapViewStepListStepConnectionDeleteAll(ZMapViewConnectionStepList step_list, ZMapViewConnection connection)
+/* Free a step. */
+static void stepDestroy(gpointer data, gpointer user_data)
{
- StepListDeleteStruct delete_data = {NULL} ;
+ ZMapViewConnectionStep step = (ZMapViewConnectionStep)data ;
+ ZMapViewConnectionStepList step_list = (ZMapViewConnectionStepList)user_data ;
- delete_data.step_list = step_list ;
- delete_data.connection = connection ;
+ if(step->connection_req)
+ {
+ /* Call users free func. */
+ if ((step_list->free_func))
+ step_list->free_func(step->connection_req->request_data) ;
- g_list_foreach(step_list->steps, connectionRemove, &delete_data) ;
+ g_free(step->connection_req) ;
+ }
- return ;
-}
+ step->connection_req = NULL ;
+ g_free(step) ;
+ return ;
+}
+/* Free the list of steps. */
+void zmapViewStepListDestroy(ZMapViewConnection view_con)
+{
+ ZMapViewConnectionStepList step_list = view_con->step_list;
+ if(step_list)
+ {
+ g_list_foreach(step_list->steps, stepDestroy, step_list) ;
+ g_list_free(step_list->steps) ;
+ step_list->steps = NULL ;
-/* Test to see if there are any requests in the steps, use this after
- * doing a 'delete all' to check that there is still something to run. */
-gboolean zmapViewStepListAreConnections(ZMapViewConnectionStepList step_list)
-{
- gboolean connections = FALSE ;
+ g_free(step_list) ;
+ }
+ view_con->step_list = NULL;
- g_list_foreach(step_list->steps, isConnection, &connections) ;
+ if(view_con->request_data)
+ {
+ g_free(view_con->request_data) ;
+ view_con->request_data = NULL ;
+ }
- return connections ;
+ return ;
}
+
/* Test to see if there are any more steps to perform, does not look to see if there are requests. */
gboolean zmapViewStepListIsNext(ZMapViewConnectionStepList step_list)
{
@@ -408,35 +479,21 @@ gboolean zmapViewStepListIsNext(ZMapViewConnectionStepList step_list)
-/* Free the list of steps. */
-void zmapViewStepListDestroy(ZMapViewConnectionStepList step_list)
-{
- g_list_foreach(step_list->steps, stepDestroy, step_list) ;
- g_list_free(step_list->steps) ;
- step_list->steps = NULL ;
-
- g_free(step_list) ;
-
- return ;
-}
-
-
-
/*!
* Context Window Hash mini-package (CWH)
- *
+ *
* As the FooCanvas isn't an MVC canvas we need to draw a
* FeatureContext on multiple canvases. This happens in an
* asynchronous manner which means we can't just destroy the context
* immediately, if it needs to be freed at all. To overcome this the
* Window level calls back the View level after it's finished with the
* Context (finished drawing it). The View must then handle
- * destroying the Context, when it's not the view->features context,
+ * destroying the Context, when it's not the view->features context,
* when all the windows have returned. To acheive this we have this
* hash of lists of windows keyed on FeatureContext pointers.
- *
+ *
* zmapViewCWHHashCreate - Creates the hash
* zmapViewCWHSetList - Sets the list of windows (one time only, no appending!)
* zmapViewCWHIsLastWindow - tests if a window is the last one (for context)
@@ -483,7 +540,7 @@ void zmapViewCWHSetList(GHashTable *hash, ZMapFeatureContext context, GList *lis
/*!
* zmapViewCWHIsLastWindow checks whether the window is the last
* window in the list for the given feature context.
- *
+ *
* @param CWH HashTable *
* @param Feature Context
* @param ZMapWindow to look up
@@ -498,7 +555,7 @@ gboolean zmapViewCWHIsLastWindow(GHashTable *hash, ZMapFeatureContext context, Z
if((destroy_list = g_hash_table_lookup(hash, context)))
{
zMapAssert( destroy_list->window_list );
-
+
before = g_list_length(destroy_list->window_list);
/* The _only_ reason we need the struct! */
@@ -519,18 +576,18 @@ gboolean zmapViewCWHIsLastWindow(GHashTable *hash, ZMapFeatureContext context, Z
return last;
}
-/*!
+/*!
* zmapViewCWHRemoveContextWindowRemoves the window and if
* zmapViewCWHIsLastWindow returns true destroys the FeatureContext.
*
* @param CWH HashTeble *
* @param FeatureContext in/out as potentially destroyed
* @param ZMapWindow to remove from list
- * @param Boolean output set to notify if context is
- * the only one in the view i.e. == view->features
+ * @param Boolean output set to notify if context is
+ * the only one in the view i.e. == view->features
* @return Boolean to notify whether context was destroyed.
*/
-gboolean zmapViewCWHRemoveContextWindow(GHashTable *hash, ZMapFeatureContext *context,
+gboolean zmapViewCWHRemoveContextWindow(GHashTable *hash, ZMapFeatureContext *context,
ZMapWindow window, gboolean *is_only_context)
{
ContextDestroyList destroy_list = NULL;
@@ -607,7 +664,7 @@ void zmapViewSessionAddServer(ZMapViewSession session_data, ZMapURL url, char *f
server_data->scheme_data.pipe.query = g_strdup(url->query) ;
break ;
}
-
+
case SCHEME_FILE:
{
// mgh: file:// is now handled by pipe://, but as this is a view struct it is unchanged
@@ -707,6 +764,8 @@ void zmapViewSessionFreeServer(gpointer data, gpointer user_data_unused)
/* Set of noddy functions to do stuff to with the source_2_featureset mappings. */
/* Given the name of a source, return its featureset. */
+
+// mh17: this function is never called and has a bug: it ignores the source name
GQuark zmapViewSrc2FSetGetID(GHashTable *source_2_featureset, char *source_name)
{
GQuark set_id = 0 ;
@@ -744,137 +803,11 @@ GList *zmapViewSrc2FSetGetList(GHashTable *source_2_featureset, GList *source_li
-/*
+/*
* Internal routines.
*/
-
-/* Step list funcs. */
-
-/* Free a step. */
-static void stepDestroy(gpointer data, gpointer user_data)
-{
- ZMapViewConnectionStep step = (ZMapViewConnectionStep)data ;
- ZMapViewConnectionStepList step_list = (ZMapViewConnectionStepList)user_data ;
-
- g_list_foreach(step->connections, requestDestroy, step_list) ;
- g_list_free(step->connections) ;
- step->connections = NULL ;
-
- g_free(step) ;
-
- return ;
-}
-
-
-/* Trawls through whole */
-static void removeFailedConnections(ZMapViewConnectionStepList step_list, ZMapViewConnectionStep step)
-{
- GList *failed_requests ;
-
- if ((failed_requests = findFailedRequests(step)))
- {
- g_list_foreach(failed_requests, removeFailed, step_list) ;
- }
-
- return ;
-}
-
-
-static GList *findFailedRequests(ZMapViewConnectionStep step)
-{
- GList *failed_reqs = NULL ;
-
- g_list_foreach(step->connections, findFailed, &failed_reqs) ;
-
- return failed_reqs ;
-}
-
-
-static void findFailed(gpointer data, gpointer user_data)
-{
- ZMapViewConnectionRequest request = (ZMapViewConnectionRequest)data ;
- GList **failed_list = (GList **)user_data ;
-
- if (request->has_failed)
- *failed_list = g_list_append(*failed_list, request) ;
-
- return ;
-}
-
-
-static void removeFailed(gpointer data, gpointer user_data)
-{
- ZMapViewConnectionRequest request = (ZMapViewConnectionRequest)data ;
- ZMapViewConnectionStepList step_list = (ZMapViewConnectionStepList)user_data ;
-
- zmapViewStepListStepConnectionDeleteAll(step_list, request->connection) ;
-
- return ;
-}
-
-
-static void connectionRemove(gpointer data, gpointer user_data)
-{
- ZMapViewConnectionStep step = (ZMapViewConnectionStep)data ;
- StepListDelete delete_data = (StepListDelete)user_data ;
- StepListFindStruct step_find = {0} ;
-
- step_find.connection = delete_data->connection ;
-
- stepFind(data, &step_find) ;
-
- if (step_find.request)
- {
- step->connections = g_list_remove(step->connections, step_find.request) ;
- requestDestroy(step_find.request, delete_data->step_list) ;
- }
-
- return ;
-}
-
-
-
-/* All requests are in STEPLIST_PENDING state and after dispatching will go into STEPLIST_DISPATCHED. */
-static void stepDispatch(gpointer data, gpointer user_data)
-{
- ZMapViewConnectionRequest request = (ZMapViewConnectionRequest)data ;
- ZMapViewConnectionStepList step_list = (ZMapViewConnectionStepList)user_data ;
- gboolean result = TRUE ;
-
- /* Call users dispatch func. */
- if ((step_list->dispatch_func))
- result = step_list->dispatch_func(request->connection, request->request_data) ;
-
- if (result)
- {
- zMapThreadRequest(request->connection->thread, request->request_data) ;
-
- request->state = STEPLIST_DISPATCHED ;
- }
- else
- {
- request->has_failed = TRUE ;
- }
-
- return ;
-}
-
-
-/* Returns whether a request has finished. */
-static void stepFinished(gpointer data, gpointer user_data)
-{
- ZMapViewConnectionRequest request = (ZMapViewConnectionRequest)data ;
- gboolean *finished = (gboolean *)user_data ;
-
- if (request->state == STEPLIST_DISPATCHED)
- *finished = FALSE ;
-
- return ;
-}
-
-
/* Find a connections request in a given request step. */
static ZMapViewConnectionStep stepListFindStep(ZMapViewConnectionStepList step_list, ZMapServerReqType request_type)
{
@@ -884,71 +817,14 @@ static ZMapViewConnectionStep stepListFindStep(ZMapViewConnectionStepList step_l
step_find.request_type = request_type ;
step_find.step = NULL ;
- g_list_foreach(step_list->steps, stepFind, &step_find) ;
+ g_list_foreach(step_list->steps, stepFindReq, &step_find) ;
step = step_find.step ;
return step ;
}
-static void stepFind(gpointer data, gpointer user_data)
-{
- ZMapViewConnectionStep step = (ZMapViewConnectionStep)data ;
- StepListFind step_find = (StepListFind)user_data ;
- if (!(step_find->request_type) || step->request == step_find->request_type)
- {
- /* If there is a connection then go on and find it otherwise just return the step. */
- if (step_find->connection)
- g_list_foreach(step->connections, reqFind, user_data) ;
- else
- step_find->step = step ;
- }
-
- return ;
-}
-
-static void reqFind(gpointer data, gpointer user_data)
-{
- ZMapViewConnectionRequest request = (ZMapViewConnectionRequest)data ;
- StepListFind step_find = (StepListFind)user_data ;
-
- if (request->connection == step_find->connection)
- step_find->request = request ;
-
- return ;
-}
-
-
-static void isConnection(gpointer data, gpointer user_data)
-{
- ZMapViewConnectionStep step = (ZMapViewConnectionStep)data ;
- gboolean *connections = (gboolean *)user_data ;
-
- if (step->connections)
- *connections = TRUE ;
-
- return ;
-}
-
-
-
-/* Free a request within a step.
- * We do not free the view connections, they are taken care of elsewhere
- * in the view code. */
-static void requestDestroy(gpointer data, gpointer user_data)
-{
- ZMapViewConnectionRequest request = (ZMapViewConnectionRequest)data ;
- ZMapViewConnectionStepList step_list = (ZMapViewConnectionStepList)user_data ;
-
- /* Call users free func. */
- if ((step_list->free_func))
- step_list->free_func(request->connection, request->request_data) ;
-
- g_free(request) ;
-
- return ;
-}
@@ -986,7 +862,7 @@ static void getSetCB(void *data, void *user_data)
GetSetData set_data_cb = (GetSetData)user_data ;
GList *set_list = set_data_cb->set_list ;
ZMapGFFSet set_data ;
-
+
if ((set_data = g_hash_table_lookup(set_data_cb->source_2_featureset, GINT_TO_POINTER(source_id))))
{
diff --git a/src/zmapView/zmapView_P.h b/src/zmapView/zmapView_P.h
index f0a7f2a37..b45435d8b 100755
--- a/src/zmapView/zmapView_P.h
+++ b/src/zmapView/zmapView_P.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.
@@ -22,11 +22,11 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
* HISTORY:
* Last edited: Mar 11 13:27 2010 (edgrif)
* Created: Thu May 13 15:06:21 2004 (edgrif)
- * CVS info: $Id: zmapView_P.h,v 1.56 2010-03-12 14:46:42 edgrif Exp $
+ * CVS info: $Id: zmapView_P.h,v 1.57 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_VIEW_P_H
@@ -58,47 +58,21 @@ typedef enum
typedef struct _ZMapViewWindowStruct
{
ZMapView parent_view ;
-
+
ZMapWindow window ;
} ZMapViewWindowStruct ;
-/* Represents a single connection to a data source. */
-/* We need to maintain state for our connections otherwise we will try to issue requests that
- * they may not see. curr_request flip-flops between ZMAP_REQUEST_GETDATA and ZMAP_REQUEST_WAIT */
-typedef struct _ZMapViewConnectionStruct
-{
- /* I think we need some sort of status here.... */
- char *url ; /* For displaying in error messages etc. */
-
- /* THESE SHOULD GO, THEY NEED TO BE REPLACED BY THE NEW STEP STRUCT STUFF....... */
- /* Record whether this connection will serve up raw sequence or deal with feature edits. */
- gboolean sequence_server ;
- gboolean writeback_server ;
- /* */
-
- ZMapView parent_view ;
-
- ZMapThreadRequest curr_request ;
-
- ZMapThread thread ;
-
- gpointer request_data ; /* User data pointer, needed for step implementation. */
-
-} ZMapViewConnectionStruct, *ZMapViewConnection ;
-
-
-
-/*
+/*
* Control of data request to connections
- *
+ *
* Requests to servers are made as a series of steps specified using these structs.
* Each step is executed before and the result tested, each connection and the whole
* step list can be aborted.
- *
+ *
*/
@@ -116,12 +90,15 @@ typedef enum
} StepListActionOnFailureType ;
-/*
+
+/*
* Callbacks returning a boolean should return TRUE if the connection should continue,
* FALSE if it's failed, in this case the connection is immediately removed from the steplist.
*
*/
+typedef struct _ZMapViewConnectionStruct *ZMapViewConnection;
+
/* Callback for dispatching step requests. */
typedef gboolean (*StepListDispatchCB)(ZMapViewConnection connection, ZMapServerReqAny req_any) ;
@@ -129,7 +106,10 @@ typedef gboolean (*StepListDispatchCB)(ZMapViewConnection connection, ZMapServer
typedef gboolean (*StepListProcessDataCB)(ZMapViewConnection connection, ZMapServerReqAny req_any) ;
/* Callback for freeing step requests. */
-typedef void (*StepListFreeDataCB)(ZMapViewConnection connection, ZMapServerReqAny req_any) ;
+typedef void (*StepListFreeDataCB)(ZMapServerReqAny req_any) ;
+
+
+
/* Represents a request composed of a list of dispatchable steps
@@ -137,56 +117,81 @@ typedef void (*StepListFreeDataCB)(ZMapViewConnection connection, ZMapServerReqA
* before executing the next. */
typedef struct _ZMapViewConnectionStepListStruct
{
- GList *current ; /* Step being currently managed, set
- to first step on initialisation,
- NULL on termination. */
+ GList *current ; /* Step being currently managed, set
+ to first step on initialisation,
+ NULL on termination. */
- GList *steps ; /* List of ZMapViewConnectionStep to
- be dispatched. */
+ GList *steps ; /* List of ZMapViewConnectionStep to
+ be dispatched. */
- StepListDispatchCB dispatch_func ; /* Called prior to dispatching requests. */
- StepListProcessDataCB process_func ; /* Called when each request is processed. */
- StepListFreeDataCB free_func ; /* Called to free requests. */
+ StepListDispatchCB dispatch_func ; /* Called prior to dispatching requests. */
+ StepListProcessDataCB process_func ; /* Called when each request is processed. */
+ StepListFreeDataCB free_func ; /* Called to free requests. */
/* we may need a list of all connections here. */
} ZMapViewConnectionStepListStruct, *ZMapViewConnectionStepList ;
+/* Represents a sub-step to a connection that forms part of a step. */
+typedef struct _ZMapViewConnectionRequestStruct
+{
+ StepListStepState state ;
+
+ gboolean has_failed ; /* Set TRUE if callback returns FALSE. */
+
+ ZMapThreadReply reply ; /* Return code from request. */
+
+ gpointer request_data ; // pointer to parent connection's data
+
+} ZMapViewConnectionRequestStruct, *ZMapViewConnectionRequest ;
+
+
/* Represents a dispatchable step that is part of an overall request. */
typedef struct _ZMapViewConnectionStepStruct
{
StepListStepState state ;
- StepListActionOnFailureType on_fail ; /* What action to take if any part of
- this step fails. */
+ StepListActionOnFailureType on_fail ; /* What action to take if any part of
+ this step fails. */
- gdouble start_time ; /* start/end time of step. */
+ gdouble start_time ; /* start/end time of step. */
gdouble end_time ;
- ZMapServerReqType request ; /* Type of request. */
+ ZMapServerReqType request ; /* Type of request. */
+
+ ZMapViewConnectionRequest connection_req ;
- GList *connections ; /* List of ZMapViewConnectionRequest. */
} ZMapViewConnectionStepStruct, *ZMapViewConnectionStep ;
-/* Represents a sub-step to a connection that forms part of a step. */
-typedef struct _ZMapViewConnectionRequestStruct
+
+/* Represents a single connection to a data source. */
+/* We need to maintain state for our connections otherwise we will try to issue requests that
+ * they may not see. curr_request flip-flops between ZMAP_REQUEST_GETDATA and ZMAP_REQUEST_WAIT */
+typedef struct _ZMapViewConnectionStruct
{
- StepListStepState state ;
+ /* I think we need some sort of status here.... */
+
+ char *url ; /* For displaying in error messages etc. */
- gboolean has_failed ; /* Set TRUE if callback returns FALSE. */
+ /* THESE SHOULD GO, THEY NEED TO BE REPLACED BY THE NEW STEP STRUCT STUFF....... */
+ /* Record whether this connection will serve up raw sequence or deal with feature edits. */
+ gboolean sequence_server ;
+ gboolean writeback_server ;
+ /* */
- ZMapThreadReply reply ; /* Return code from request. */
+ ZMapView parent_view ;
- ZMapViewConnectionStep step ; /* Parent step. */
+ ZMapThreadRequest curr_request ;
- ZMapViewConnection connection ;
+ ZMapThread thread ;
- gpointer request_data ;
+ gpointer request_data ; /* User data pointer, needed for step implementation. */
-} ZMapViewConnectionRequestStruct, *ZMapViewConnectionRequest ;
+ ZMapViewConnectionStepList step_list ; /* List of steps required to get data from server. */
+} ZMapViewConnectionStruct;
@@ -250,7 +255,7 @@ typedef struct _ZMapViewStruct
sequence from. */
ZMapViewConnection writeback_server ; /* Which connection to send edits to. */
- ZMapViewConnectionStepList step_list ; /* List of steps required to get data from server. */
+// ZMapViewConnectionStepList step_list ; /* List of steps required to get data from server. */
/* The features....needs thought as to how this updated/constructed..... */
ZMapFeatureContext features ;
@@ -280,7 +285,7 @@ typedef struct _ZMapViewStruct
ZMapXRemoteObj xremote_client;
GList *navigator_set_names;
-
+
/* view spawns blixem processes when requested, kill_blixems flag controls whether they are
* killed when view dies (default is TRUE). */
gboolean kill_blixems ;
@@ -332,19 +337,22 @@ ZMapViewConnectionStepList zmapViewStepListCreate(StepListDispatchCB dispatch_fu
StepListFreeDataCB free_func) ;
void zmapViewStepListAddStep(ZMapViewConnectionStepList step_list, ZMapServerReqType request_type,
StepListActionOnFailureType on_fail) ;
-ZMapViewConnectionRequest zmapViewStepListAddServerReq(ZMapViewConnectionStepList step_list,
+ZMapViewConnectionRequest zmapViewStepListAddServerReq(ZMapViewConnectionStepList step_list,
ZMapViewConnection view_con,
ZMapServerReqType request_type,
gpointer request_data) ;
-void zmapViewStepListIter(ZMapViewConnectionStepList step_list) ;
-void zmapViewStepListStepProcessRequest(ZMapViewConnectionStepList step_list, ZMapViewConnectionRequest request) ;
+ZMapViewConnectionStepList zmapViewConnectionStepListCreate(StepListDispatchCB dispatch_func,
+ StepListProcessDataCB process_func,
+ StepListFreeDataCB free_func);
+void zmapViewStepListIter(ZMapViewConnection view_con) ;
+void zmapViewStepListStepProcessRequest(ZMapViewConnection view_con, ZMapViewConnectionRequest request) ;
ZMapViewConnectionRequest zmapViewStepListFindRequest(ZMapViewConnectionStepList step_list,
ZMapServerReqType request_type, ZMapViewConnection connection) ;
-void zmapViewStepListStepConnectionDeleteAll(ZMapViewConnectionStepList step_list, ZMapViewConnection connection) ;
+void zmapViewStepListStepConnectionDeleteAll(ZMapViewConnection connection) ;
gboolean zmapViewStepListAreConnections(ZMapViewConnectionStepList step_list) ;
gboolean zmapViewStepListIsNext(ZMapViewConnectionStepList step_list) ;
void zmapViewStepDestroy(gpointer data, gpointer user_data) ;
-void zmapViewStepListDestroy(ZMapViewConnectionStepList step_list) ;
+void zmapViewStepListDestroy(ZMapViewConnection view_conn) ;
void zmapViewLoadFeatures(ZMapView view, ZMapFeatureBlock block_orig, GList *req_featuresets,
int features_start, int features_end) ;
diff --git a/src/zmapWindow/zmapWindowDNAList.c b/src/zmapWindow/zmapWindowDNAList.c
index 4afd16fe8..d947e8bc0 100755
--- a/src/zmapWindow/zmapWindowDNAList.c
+++ b/src/zmapWindow/zmapWindowDNAList.c
@@ -29,11 +29,12 @@
* HISTORY:
* Last edited: Jun 16 15:19 2008 (rds)
* Created: Mon Oct 9 15:21:36 2006 (edgrif)
- * CVS info: $Id: zmapWindowDNAList.c,v 1.13 2010-03-04 15:12:47 mh17 Exp $
+ * CVS info: $Id: zmapWindowDNAList.c,v 1.14 2010-03-15 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
#include <glib.h>
+#include <ZMap/zmapBase.h>
#include <ZMap/zmapUtils.h>
#include <ZMap/zmapSequence.h>
#include <ZMap/zmapDNA.h>
--
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