From e8a9ddc8b7cf84ad1b70e60c9179fc6e7351b10e Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Wed, 2 Feb 2005 15:08:36 +0000
Subject: [PATCH] rework feature code display.
---
src/zmapFeature/zmapFeatureTypes.c | 314 +++++++++++++++++++++++++++++
1 file changed, 314 insertions(+)
create mode 100755 src/zmapFeature/zmapFeatureTypes.c
diff --git a/src/zmapFeature/zmapFeatureTypes.c b/src/zmapFeature/zmapFeatureTypes.c
new file mode 100755
index 000000000..99362818b
--- /dev/null
+++ b/src/zmapFeature/zmapFeatureTypes.c
@@ -0,0 +1,314 @@
+/* File: zmapFeatureTypes.c
+ * Author: Ed Griffiths (edgrif@sanger.ac.uk)
+ * Copyright (c) Sanger Institute, 2004
+ *-------------------------------------------------------------------
+ * ZMap is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
+ *-------------------------------------------------------------------
+ * This file is part of the ZMap genome database package
+ * originated by
+ * Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
+ * Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
+ *
+ * Description: Functions for manipulating Type structs and sets of
+ * type structs.c
+ *
+ * Exported functions: See ZMap/zmapFeature.h
+ * HISTORY:
+ * Last edited: Feb 1 09:30 2005 (edgrif)
+ * Created: Tue Dec 14 13:15:11 2004 (edgrif)
+ * CVS info: $Id: zmapFeatureTypes.c,v 1.1 2005-02-02 15:08:36 edgrif Exp $
+ *-------------------------------------------------------------------
+ */
+
+#include <ZMap/zmapUtils.h>
+#include <ZMap/zmapConfig.h>
+#include <zmapFeature_P.h>
+
+
+/* Think about defaults, how should they be set, should we force user to set them ? */
+#define ZMAPFEATURE_DEFAULT_WIDTH 10.0 /* of features being displayed */
+
+
+static void doTypeSets(GQuark key_id, gpointer data, gpointer user_data) ;
+static void typePrintFunc(GQuark key_id, gpointer data, gpointer user_data) ;
+
+
+
+/* Create a new type for displaying features. */
+ZMapFeatureTypeStyle zMapFeatureTypeCreate(char *name,
+ char *outline, char *foreground, char *background,
+ float width, gboolean show_up_strand, int min_mag)
+{
+ ZMapFeatureTypeStyle new_type = NULL ;
+ GString *name_canonical ;
+
+ /* I am unsure if this is a good thing to do here, I'm attempting to make sure the type is
+ * "sane" but no more than that. */
+ zMapAssert(name && *name
+ && outline && *outline && foreground && *foreground && background && *background
+ && width > 0.0 && min_mag >= 0) ;
+
+
+ new_type = g_new0(ZMapFeatureTypeStyleStruct, 1) ;
+
+ /* lowercase the name to make it canonical. */
+ name_canonical = g_string_new(name) ;
+ name_canonical = g_string_ascii_down(name_canonical) ;
+ new_type->name = g_strdup(name_canonical->str) ;
+ g_string_free(name_canonical, TRUE) ;
+
+ gdk_color_parse(outline, &new_type->outline) ;
+ gdk_color_parse(foreground, &new_type->foreground) ;
+ gdk_color_parse(background, &new_type->background) ;
+
+ new_type->width = width ;
+ new_type->showUpStrand = show_up_strand ;
+ new_type->min_mag = min_mag ;
+
+ return new_type ;
+}
+
+
+/* Copy an existing type. */
+ZMapFeatureTypeStyle zMapFeatureTypeCopy(ZMapFeatureTypeStyle type)
+{
+ ZMapFeatureTypeStyle new_type = NULL ;
+
+ zMapAssert(type) ;
+
+ new_type = g_new0(ZMapFeatureTypeStyleStruct, 1) ;
+ *new_type = *type ; /* n.b. struct copy. */
+ new_type->name = g_strdup(type->name) ;
+
+ return new_type ;
+}
+
+
+/* Destroy the type, freeing all resources. */
+void zMapFeatureTypeDestroy(ZMapFeatureTypeStyle type)
+{
+ zMapAssert(type && type->name) ;
+
+ g_free(type->name) ;
+
+ g_free(type) ;
+
+ return ;
+}
+
+
+
+
+
+
+
+gboolean zMapFeatureTypeSetAugment(GData **current, GData **new)
+{
+ gboolean result = FALSE ;
+
+ zMapAssert(new && *new) ;
+
+ if (!current || !*current)
+ g_datalist_init(current) ;
+
+ g_datalist_foreach(new, doTypeSets, (void *)current) ;
+
+ result = TRUE ; /* currently shouldn't fail.... */
+
+ return result ;
+}
+
+
+
+/* Read the type/method/source (call it what you will) information from the given file
+ * which currently must reside in the users $HOME/.ZMap directory. */
+GData *zMapFeatureTypeGetFromFile(char *types_file_name)
+{
+ GData *types = NULL ;
+ gboolean result = FALSE ;
+ ZMapConfigStanzaSet types_list = NULL ;
+ ZMapConfig config ;
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ char *types_file_name = "ZMapTypes" ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
+
+ if ((config = zMapConfigCreateFromFile(NULL, types_file_name)))
+ {
+ ZMapConfigStanza types_stanza ;
+
+ /* Set up default values for variables in the stanza. Elements here must match
+ * those being loaded below or you might segfault.
+ * IF YOU ADD ANY ELEMENTS TO THIS ARRAY THEN MAKE SURE YOU UPDATE THE INIT STATEMENTS
+ * FOLLOWING THIS ARRAY SO THEY POINT AT THE RIGHT ELEMENTS....!!!!!!!! */
+ ZMapConfigStanzaElementStruct types_elements[] = {{"name" , ZMAPCONFIG_STRING, {NULL}},
+ {"outline" , ZMAPCONFIG_STRING, {"black"}},
+ {"foreground" , ZMAPCONFIG_STRING, {"white"}},
+ {"background" , ZMAPCONFIG_STRING, {"black"}},
+ {"width" , ZMAPCONFIG_FLOAT , {NULL}},
+ {"showUpStrand", ZMAPCONFIG_BOOL , {NULL}},
+ {"minmag" , ZMAPCONFIG_INT , {NULL}},
+ {NULL, -1, {NULL}}} ;
+
+ /* minmag should be a float !!! */
+
+
+ /* Must init separately as compiler cannot statically init different union types....sigh.... */
+ types_elements[4].data.f = ZMAPFEATURE_DEFAULT_WIDTH ;
+
+
+ types_stanza = zMapConfigMakeStanza("Type", types_elements) ;
+
+ if (!zMapConfigFindStanzas(config, types_stanza, &types_list))
+ result = FALSE ;
+ else
+ result = TRUE ;
+ }
+
+ /* Set up connections to the named types. */
+ if (result)
+ {
+ int num_types = 0 ;
+ ZMapConfigStanza next_types ;
+
+ g_datalist_init(&types) ;
+
+ /* 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. */
+ next_types = NULL ;
+ while (result
+ && ((next_types = zMapConfigGetNextStanza(types_list, next_types)) != NULL))
+ {
+ char *name ;
+
+ /* Name must be set so if its not found then don't make a struct.... */
+ if ((name = zMapConfigGetElementString(next_types, "name")))
+ {
+ ZMapFeatureTypeStyle new_type ;
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ ZMapFeatureTypeStyle new_type = g_new0(ZMapFeatureTypeStyleStruct, 1) ;
+
+ /* NB Elements here must match those pre-initialised above or you might segfault. */
+
+ gdk_color_parse(zMapConfigGetElementString(next_types, "outline" ), &new_type->outline ) ;
+ gdk_color_parse(zMapConfigGetElementString(next_types, "foreground"), &new_type->foreground) ;
+ gdk_color_parse(zMapConfigGetElementString(next_types, "background"), &new_type->background) ;
+ new_type->width = zMapConfigGetElementFloat(next_types, "width") ;
+ new_type->showUpStrand = zMapConfigGetElementBool(next_types, "showUpStrand") ;
+ new_type->min_mag = zMapConfigGetElementInt(next_types, "minmag") ;
+
+ /* lowercase the name (aka type).....and FREE the memory....sigh...... */
+ name_canonical = g_string_new(name) ;
+ name_canonical = g_string_ascii_down(name_canonical) ;
+ new_type->name = g_strdup(name_canonical->str) ;
+ g_string_free(name_canonical, TRUE) ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
+ new_type = zMapFeatureTypeCreate(name,
+ zMapConfigGetElementString(next_types, "outline"),
+ zMapConfigGetElementString(next_types, "foreground"),
+ zMapConfigGetElementString(next_types, "background"),
+ zMapConfigGetElementFloat(next_types, "width"),
+ zMapConfigGetElementBool(next_types, "showUpStrand"),
+ zMapConfigGetElementInt(next_types, "minmag")) ;
+
+ g_datalist_set_data(&types, new_type->name, new_type) ;
+ num_types++ ;
+ }
+ else
+ {
+ zMapLogWarning("config file \"%s\" has a \"Type\" stanza which has no \"name\" element, "
+ "the stanza has been ignored.", types_file_name) ;
+ }
+ }
+
+ /* Found no valid types.... */
+ if (!num_types)
+ result = FALSE ;
+ }
+
+ /* clean up. */
+ if (types_list)
+ zMapConfigDeleteStanzaSet(types_list) ;
+
+
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ /* debug.... */
+ printAllTypes(types, "getTypesFromFile()") ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
+
+
+ return types ;
+}
+
+
+void zMapFeatureTypePrintAll(GData *type_set, char *user_string)
+{
+ printf("\nTypes at %s\n", user_string) ;
+
+ g_datalist_foreach(&type_set, typePrintFunc, NULL) ;
+
+ return ;
+}
+
+
+
+
+
+/*
+ * Internal routines
+ */
+
+
+
+static void doTypeSets(GQuark key_id, gpointer data, gpointer user_data)
+{
+ ZMapFeatureTypeStyle new_type = (ZMapFeatureTypeStyle)data ;
+ GData **current_out = (GData **)user_data ;
+ GData *current = *current_out ;
+
+ if (!g_datalist_id_get_data(¤t, key_id))
+ {
+ /* copy the struct and then add it to the current set. */
+ ZMapFeatureTypeStyle type ;
+
+ type = zMapFeatureTypeCopy(new_type) ;
+
+ g_datalist_id_set_data(¤t, key_id, type) ;
+ }
+
+ *current_out = current ;
+
+ return ;
+}
+
+
+static void typePrintFunc(GQuark key_id, gpointer data, gpointer user_data)
+{
+ ZMapFeatureTypeStyle style = (ZMapFeatureTypeStyle)data ;
+ char *style_name = (char *)g_quark_to_string(key_id) ;
+
+ printf("\t%s: \t%f \t%d\n", style_name, style->width, style->showUpStrand) ;
+
+ return ;
+}
+
+
--
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