From 165716d0ce0d98229b46b57346c3d1a7c763b826 Mon Sep 17 00:00:00 2001
From: rds <rds>
Date: Sun, 7 Jun 2009 08:18:56 +0000
Subject: [PATCH] remove old objects now containers used
---
src/zmapWindow/zmapWindowItemFeatureBlock.c | 404 -------
src/zmapWindow/zmapWindowItemFeatureBlock.h | 87 --
src/zmapWindow/zmapWindowItemFeatureBlock_I.h | 69 --
src/zmapWindow/zmapWindowItemFeatureSet.c | 1035 -----------------
src/zmapWindow/zmapWindowItemFeatureSet.h | 119 --
src/zmapWindow/zmapWindowItemFeatureSet_I.h | 108 --
6 files changed, 1822 deletions(-)
delete mode 100755 src/zmapWindow/zmapWindowItemFeatureBlock.c
delete mode 100755 src/zmapWindow/zmapWindowItemFeatureBlock.h
delete mode 100755 src/zmapWindow/zmapWindowItemFeatureBlock_I.h
delete mode 100755 src/zmapWindow/zmapWindowItemFeatureSet.c
delete mode 100755 src/zmapWindow/zmapWindowItemFeatureSet.h
delete mode 100755 src/zmapWindow/zmapWindowItemFeatureSet_I.h
diff --git a/src/zmapWindow/zmapWindowItemFeatureBlock.c b/src/zmapWindow/zmapWindowItemFeatureBlock.c
deleted file mode 100755
index a5b421361..000000000
--- a/src/zmapWindow/zmapWindowItemFeatureBlock.c
+++ /dev/null
@@ -1,404 +0,0 @@
-/* File: zmapWindowItemFeatureBlock.c
- * Author: Roy Storey (rds@sanger.ac.uk)
- * Copyright (c) 2007: Genome Research Ltd.
- *-------------------------------------------------------------------
- * ZMap is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
- *-------------------------------------------------------------------
- * This file is part of the ZMap genome database package
- * originally written by:
- *
- * Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
- * Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
- *
- * Description:
- *
- * Exported functions: See XXXXXXXXXXXXX.h
- * HISTORY:
- * Last edited: Apr 20 11:20 2009 (rds)
- * Created: Mon Jul 30 13:09:33 2007 (rds)
- * CVS info: $Id: zmapWindowItemFeatureBlock.c,v 1.3 2009-04-20 11:05:28 rds Exp $
- *-------------------------------------------------------------------
- */
-
-#include <ZMap/zmapSeqBitmap.h>
-#include <zmapWindowItemFeatureBlock_I.h>
-#include <zmapWindowItemFeatureSet.h>
-#include <zmapWindow_P.h> /* ITEM_FEATURE_SET_DATA */
-
-enum
- {
- ITEM_FEATURE_BLOCK_0, /* zero == invalid prop value */
- };
-
-static ZMapSeqBitmap get_bitmap_for_style(ZMapWindowItemFeatureBlockData block_data,
- ZMapFeatureBlock block,
- ZMapFeatureTypeStyle style);
-static ZMapSeqBitmap get_bitmap_for_key(ZMapWindowItemFeatureBlockData block_data,
- ZMapFeatureBlock block,
- GQuark key);
-
-
-static void zmap_window_item_feature_block_class_init (ZMapWindowItemFeatureBlockDataClass block_data_class);
-static void zmap_window_item_feature_block_init (ZMapWindowItemFeatureBlockData block_data);
-static void zmap_window_item_feature_block_set_property(GObject *gobject,
- guint param_id,
- const GValue *value,
- GParamSpec *pspec);
-static void zmap_window_item_feature_block_get_property(GObject *gobject,
- guint param_id,
- GValue *value,
- GParamSpec *pspec);
-static void zmap_window_item_feature_block_dispose (GObject *object);
-static void zmap_window_item_feature_block_finalize (GObject *object);
-
-
-static GObjectClass *parent_class_G = NULL;
-
-
-GType zmapWindowItemFeatureBlockGetType(void)
-{
- static GType group_type = 0;
-
- if (!group_type)
- {
- static const GTypeInfo group_info =
- {
- sizeof (zmapWindowItemFeatureBlockDataClass),
- (GBaseInitFunc) NULL,
- (GBaseFinalizeFunc) NULL,
- (GClassInitFunc) zmap_window_item_feature_block_class_init,
- NULL, /* class_finalize */
- NULL, /* class_data */
- sizeof (zmapWindowItemFeatureBlockData),
- 0, /* n_preallocs */
- (GInstanceInitFunc) zmap_window_item_feature_block_init
- };
-
- group_type = g_type_register_static (G_TYPE_OBJECT,
- "zmapWindowItemFeatureBlockData",
- &group_info,
- 0);
- }
-
- return group_type;
-}
-
-
-ZMapWindowItemFeatureBlockData zmapWindowItemFeatureBlockCreate(ZMapWindow window)
-{
- ZMapWindowItemFeatureBlockData block_data;
-
- if((block_data = g_object_new(zmapWindowItemFeatureBlockGetType(), NULL)))
- {
- block_data->window = window;
- }
-
- return block_data;
-}
-
-void zmapWindowItemFeatureBlockAddCompressedColumn(ZMapWindowItemFeatureBlockData block_data,
- FooCanvasGroup *container)
-{
-
- block_data->compressed_cols = g_list_append(block_data->compressed_cols, container) ;
-
- return ;
-}
-
-GList *zmapWindowItemFeatureBlockRemoveCompressedColumns(ZMapWindowItemFeatureBlockData block_data)
-{
- GList *list = NULL;
-
- list = block_data->compressed_cols;
- block_data->compressed_cols = NULL;
-
- return list;
-}
-
-void zmapWindowItemFeatureBlockAddBumpedColumn(ZMapWindowItemFeatureBlockData block_data,
- FooCanvasGroup *container)
-{
-
- block_data->bumped_cols = g_list_append(block_data->bumped_cols, container) ;
-
- return ;
-}
-
-GList *zmapWindowItemFeatureBlockRemoveBumpedColumns(ZMapWindowItemFeatureBlockData block_data)
-{
- GList *list = NULL;
-
- list = block_data->bumped_cols;
- block_data->bumped_cols = NULL;
-
- return list;
-}
-
-ZMapWindow zmapWindowItemFeatureBlockGetWindow(ZMapWindowItemFeatureBlockData block_data)
-{
- ZMapWindow window = NULL;
-
- g_return_val_if_fail(ZMAP_IS_WINDOW_ITEM_FEATURE_BLOCK(block_data), window);
-
- window = block_data->window;
-
- return window;
-}
-
-void zmapWindowItemFeatureBlockMarkRegion(ZMapWindowItemFeatureBlockData block_data,
- ZMapFeatureBlock block)
-{
- ZMapSeqBitmap bitmap;
-
- if((bitmap = get_bitmap_for_key(block_data, block, block->unique_id)))
- {
- if(block->features_start == 0)
- block->features_start = block->block_to_sequence.q1;
-
- if(block->features_end == 0)
- block->features_end = block->block_to_sequence.q2;
-
- zmapSeqBitmapMarkRegion(bitmap, block->features_start, block->features_end);
- }
-
- return ;
-}
-
-void zmapWindowItemFeatureBlockMarkRegionForColumn(ZMapWindowItemFeatureBlockData block_data,
- ZMapFeatureBlock block,
- ZMapWindowItemFeatureSetData set_data)
-{
- ZMapSeqBitmap bitmap;
-
- if((bitmap = get_bitmap_for_key(block_data, block, set_data->unique_id)))
- {
- if(block->features_start == 0)
- block->features_start = block->block_to_sequence.q1;
-
- if(block->features_end == 0)
- block->features_end = block->block_to_sequence.q2;
-
- zmapSeqBitmapMarkRegion(bitmap, block->features_start, block->features_end);
- }
-
- return ;
-}
-
-GList *zmapWindowItemFeatureBlockFilterMarkedColumns(ZMapWindowItemFeatureBlockData block_data,
- GList *list, int world1, int world2)
-{
- GList *key_list;
-
- key_list = list;
-
- while(key_list)
- {
- ZMapSeqBitmap bitmap;
- GQuark key;
- GList *tmp_list;
-
- tmp_list = key_list->next;
-
- key = GPOINTER_TO_UINT(key_list->data);
-
- /* we don't want to create anything... */
- if((bitmap = get_bitmap_for_key(block_data, NULL, key)))
- {
- if(zmapSeqBitmapIsRegionFullyMarked(bitmap, world1, world2))
- list = g_list_delete_link(list, key_list);
- }
-
- key_list = tmp_list;
- }
-
- return list;
-}
-
-gboolean zmapWindowItemFeatureBlockIsColumnLoaded(ZMapWindowItemFeatureBlockData block_data,
- FooCanvasGroup *column_group, int world1, int world2)
-{
- ZMapWindowItemFeatureSetData set_data;
- ZMapSeqBitmap bitmap;
- gboolean fully_marked = FALSE;
-
- if((set_data = g_object_get_data(G_OBJECT(column_group), ITEM_FEATURE_SET_DATA)))
- {
- if((bitmap = get_bitmap_for_key(block_data, NULL, set_data->unique_id)))
- {
- fully_marked = zmapSeqBitmapIsRegionFullyMarked(bitmap, world1, world2);
- }
- }
-
- return fully_marked;
-}
-
-ZMapWindowItemFeatureBlockData zmapWindowItemFeatureBlockDestroy(ZMapWindowItemFeatureBlockData item_feature_block)
-{
- g_object_unref(G_OBJECT(item_feature_block));
-
- item_feature_block = NULL;
-
- return item_feature_block;
-}
-
-
-/* INTERNAL */
-
-static ZMapSeqBitmap get_bitmap_for_style(ZMapWindowItemFeatureBlockData block_data,
- ZMapFeatureBlock block,
- ZMapFeatureTypeStyle style)
-{
- ZMapSeqBitmap bitmap;
- GQuark key;
-
- key = zMapStyleGetUniqueID(style);
-
- bitmap = get_bitmap_for_key(block_data, block, key);
-
- return bitmap;
-}
-
-static ZMapSeqBitmap get_bitmap_for_key(ZMapWindowItemFeatureBlockData block_data,
- ZMapFeatureBlock block,
- GQuark key)
-{
- ZMapSeqBitmap bitmap = NULL;
-
- if(!(bitmap = g_hash_table_lookup(block_data->loaded_region_hash, GUINT_TO_POINTER(key))))
- {
- if(block)
- {
- int length;
-
- length = block->block_to_sequence.q2 - block->block_to_sequence.q1 + 1;
-
- bitmap = zmapSeqBitmapCreate(block->block_to_sequence.q1, length, 9000);
-
- g_hash_table_insert(block_data->loaded_region_hash, GUINT_TO_POINTER(key), bitmap);
- }
- }
-
- return bitmap;
-}
-
-
-
-/* Object code */
-static void zmap_window_item_feature_block_class_init(ZMapWindowItemFeatureBlockDataClass block_data_class)
-{
- GObjectClass *gobject_class;
-
- gobject_class = (GObjectClass *)block_data_class;
-
- gobject_class->set_property = zmap_window_item_feature_block_set_property;
- gobject_class->get_property = zmap_window_item_feature_block_get_property;
-
- parent_class_G = g_type_class_peek_parent(block_data_class);
-
-#ifdef RDS_DONT_INCLUDE
- /* width */
- g_object_class_install_property(gobject_class,
- ITEM_FEATURE_BLOCK_WIDTH,
- g_param_spec_double(ZMAPSTYLE_PROPERTY_WIDTH,
- ZMAPSTYLE_PROPERTY_WIDTH,
- "The minimum width the column should be displayed at.",
- 0.0, 32000.00, 16.0,
- ZMAP_PARAM_STATIC_RO));
-#endif
-
- gobject_class->dispose = zmap_window_item_feature_block_dispose;
- gobject_class->finalize = zmap_window_item_feature_block_finalize;
-
- return ;
-}
-
-static void zmap_window_item_feature_block_init(ZMapWindowItemFeatureBlockData block_data)
-{
- block_data->loaded_region_hash = g_hash_table_new_full(NULL, NULL, NULL, (GDestroyNotify)zmapSeqBitmapDestroy);
- block_data->compressed_cols = NULL;
- return ;
-}
-
-static void zmap_window_item_feature_block_set_property(GObject *gobject,
- guint param_id,
- const GValue *value,
- GParamSpec *pspec)
-{
-
- switch(param_id)
- {
- default:
- G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
- break;
- }
-
- return ;
-}
-
-static void zmap_window_item_feature_block_get_property(GObject *gobject,
- guint param_id,
- GValue *value,
- GParamSpec *pspec)
-{
- ZMapWindowItemFeatureBlockData block_data;
-
- block_data = ZMAP_WINDOW_ITEM_FEATURE_BLOCK(gobject);
-
- switch(param_id)
- {
- default:
- G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
- break;
- }
-
- return ;
-}
-
-static void zmap_window_item_feature_block_dispose(GObject *object)
-{
- ZMapWindowItemFeatureBlockData block_data;
- GObjectClass *gobject_class = G_OBJECT_CLASS(parent_class_G);
-
- block_data = ZMAP_WINDOW_ITEM_FEATURE_BLOCK(object);
-
- block_data->window = NULL; /* not ours */
-
- /* compressed and bumped columns are not ours. canvas owns them, just free the lists */
- if(block_data->compressed_cols)
- g_list_free(block_data->compressed_cols) ;
-
- if(block_data->bumped_cols)
- g_list_free(block_data->bumped_cols);
-
- if(block_data->loaded_region_hash)
- g_hash_table_destroy(block_data->loaded_region_hash);
-
- if(gobject_class->dispose)
- (*gobject_class->dispose)(object);
-
- return ;
-}
-
-static void zmap_window_item_feature_block_finalize(GObject *object)
-{
- GObjectClass *gobject_class = G_OBJECT_CLASS(parent_class_G);
-
- if(gobject_class->finalize)
- (*gobject_class->finalize)(object);
-
- return ;
-}
-
diff --git a/src/zmapWindow/zmapWindowItemFeatureBlock.h b/src/zmapWindow/zmapWindowItemFeatureBlock.h
deleted file mode 100755
index d3d07a28d..000000000
--- a/src/zmapWindow/zmapWindowItemFeatureBlock.h
+++ /dev/null
@@ -1,87 +0,0 @@
-/* File: zmapWindowItemFeatureBlock.h
- * Author: Roy Storey (rds@sanger.ac.uk)
- * Copyright (c) 2009: Genome Research Ltd.
- *-------------------------------------------------------------------
- * ZMap is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
- *-------------------------------------------------------------------
- * This file is part of the ZMap genome database package
- * originally written by:
- *
- * Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
- * Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
- *
- * Description:
- *
- * Exported functions: See XXXXXXXXXXXXX.h
- * HISTORY:
- * Last edited: Apr 16 15:11 2009 (rds)
- * Created: Fri Feb 6 15:32:46 2009 (rds)
- * CVS info: $Id: zmapWindowItemFeatureBlock.h,v 1.2 2009-04-16 14:37:24 rds Exp $
- *-------------------------------------------------------------------
- */
-
-#ifndef __ZMAP_WINDOW_ITEM_FEATURE_BLOCK_H__
-#define __ZMAP_WINDOW_ITEM_FEATURE_BLOCK_H__
-
-#include <glib.h>
-#include <glib-object.h>
-#include <ZMap/zmapWindow.h>
-
-#define ZMAP_TYPE_WINDOW_ITEM_FEATURE_BLOCK (zmapWindowItemFeatureBlockGetType())
-#define ZMAP_WINDOW_ITEM_FEATURE_BLOCK(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_ITEM_FEATURE_BLOCK, zmapWindowItemFeatureBlockData))
-#define ZMAP_WINDOW_ITEM_FEATURE_BLOCK_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_ITEM_FEATURE_BLOCK, zmapWindowItemFeatureBlockData const))
-#define ZMAP_WINDOW_ITEM_FEATURE_BLOCK_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_WINDOW_ITEM_FEATURE_BLOCK, zmapWindowItemFeatureBlockDataClass))
-#define ZMAP_IS_WINDOW_ITEM_FEATURE_BLOCK(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_WINDOW_ITEM_FEATURE_BLOCK))
-#define ZMAP_WINDOW_ITEM_FEATURE_BLOCK_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_WINDOW_ITEM_FEATURE_BLOCK, zmapWindowItemFeatureBlockDataClass))
-
-
-/* Instance */
-typedef struct _zmapWindowItemFeatureBlockDataStruct zmapWindowItemFeatureBlockData, *ZMapWindowItemFeatureBlockData;
-
-/* Class */
-typedef struct _zmapWindowItemFeatureBlockDataClassStruct zmapWindowItemFeatureBlockDataClass, *ZMapWindowItemFeatureBlockDataClass ;
-
-
-
-/* Public funcs */
-GType zmapWindowItemFeatureBlockGetType(void);
-
-ZMapWindowItemFeatureBlockData zmapWindowItemFeatureBlockCreate(ZMapWindow window);
-
-
-void zmapWindowItemFeatureBlockAddCompressedColumn(ZMapWindowItemFeatureBlockData block_data,
- FooCanvasGroup *container);
-GList *zmapWindowItemFeatureBlockRemoveCompressedColumns(ZMapWindowItemFeatureBlockData block_data);
-void zmapWindowItemFeatureBlockAddBumpedColumn(ZMapWindowItemFeatureBlockData block_data,
- FooCanvasGroup *container);
-GList *zmapWindowItemFeatureBlockRemoveBumpedColumns(ZMapWindowItemFeatureBlockData block_data);
-ZMapWindow zmapWindowItemFeatureBlockGetWindow(ZMapWindowItemFeatureBlockData block_data);
-void zmapWindowItemFeatureBlockMarkRegion(ZMapWindowItemFeatureBlockData block_data,
- ZMapFeatureBlock block);
-void zmapWindowItemFeatureBlockMarkRegionForStyle(ZMapWindowItemFeatureBlockData block_data,
- ZMapFeatureBlock block,
- ZMapFeatureTypeStyle style);
-GList *zmapWindowItemFeatureBlockFilterMarkedColumns(ZMapWindowItemFeatureBlockData block_data,
- GList *list, int world1, int world2);
-gboolean zmapWindowItemFeatureBlockIsColumnLoaded(ZMapWindowItemFeatureBlockData block_data,
- FooCanvasGroup *column_group, int world1, int world2);
-
-
-ZMapWindowItemFeatureBlockData zmapWindowItemFeatureBlockDestroy(ZMapWindowItemFeatureBlockData block_data);
-
-
-
-#endif /* __ZMAP_WINDOW_ITEM_FEATURE_BLOCK_H__ */
diff --git a/src/zmapWindow/zmapWindowItemFeatureBlock_I.h b/src/zmapWindow/zmapWindowItemFeatureBlock_I.h
deleted file mode 100755
index 2b8c7165e..000000000
--- a/src/zmapWindow/zmapWindowItemFeatureBlock_I.h
+++ /dev/null
@@ -1,69 +0,0 @@
-/* File: zmapWindowItemFeatureBlock_I.h
- * Author: Roy Storey (rds@sanger.ac.uk)
- * Copyright (c) 2009: Genome Research Ltd.
- *-------------------------------------------------------------------
- * ZMap is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
- *-------------------------------------------------------------------
- * This file is part of the ZMap genome database package
- * originally written by:
- *
- * Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
- * Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
- *
- * Description:
- *
- * Exported functions: See XXXXXXXXXXXXX.h
- * HISTORY:
- * Last edited: Apr 16 14:59 2009 (rds)
- * Created: Fri Feb 6 11:49:03 2009 (rds)
- * CVS info: $Id: zmapWindowItemFeatureBlock_I.h,v 1.2 2009-04-16 14:37:29 rds Exp $
- *-------------------------------------------------------------------
- */
-
-#ifndef __ZMAP_WINDOW_ITEM_FEATURE_BLOCK_I_H__
-#define __ZMAP_WINDOW_ITEM_FEATURE_BLOCK_I_H__
-
-#include <zmapWindowItemFeatureBlock.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 ZMAP_BIN_MAX_VALUE(BITMAP) ((1 << BITMAP->bin_depth) - 1)
-
-typedef struct _zmapWindowItemFeatureBlockDataStruct
-{
- GObject __parent__;
-
- ZMapWindow window;
-
- GList *compressed_cols, *bumped_cols ;
-
- GHashTable *loaded_region_hash;
-
-} zmapWindowItemFeatureBlockDataStruct;
-
-
-typedef struct _zmapWindowItemFeatureBlockDataClassStruct
-{
- GObjectClass __parent__;
-
-} zmapWindowItemFeatureBlockDataClassStruct;
-
-
-
-#endif /* __ZMAP_WINDOW_ITEM_FEATURE_BLOCK_I_H__ */
diff --git a/src/zmapWindow/zmapWindowItemFeatureSet.c b/src/zmapWindow/zmapWindowItemFeatureSet.c
deleted file mode 100755
index e52e0bf2b..000000000
--- a/src/zmapWindow/zmapWindowItemFeatureSet.c
+++ /dev/null
@@ -1,1035 +0,0 @@
-/* File: zmapWindowItemFeatureSet.c
- * Author: Roy Storey (rds@sanger.ac.uk)
- * Copyright (c) 2007: Genome Research Ltd.
- *-------------------------------------------------------------------
- * ZMap is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
- *-------------------------------------------------------------------
- * This file is part of the ZMap genome database package
- * originally written by:
- *
- * Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
- * Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
- *
- * Description:
- *
- * Exported functions: See XXXXXXXXXXXXX.h
- * HISTORY:
- * Last edited: May 7 16:01 2009 (rds)
- * Created: Mon Jul 30 13:09:33 2007 (rds)
- * CVS info: $Id: zmapWindowItemFeatureSet.c,v 1.17 2009-05-07 21:35:14 rds Exp $
- *-------------------------------------------------------------------
- */
-#include <string.h> /* memset */
-
-#include <ZMap/zmapUtils.h>
-#include <zmapWindowItemFeatureSet_I.h>
-#include <zmapWindowContainer.h>
-
-enum
- {
- ITEM_FEATURE_SET_0, /* zero == invalid prop value */
- ITEM_FEATURE_SET_WIDTH,
- ITEM_FEATURE_SET_VISIBLE,
- ITEM_FEATURE_SET_BUMP_MODE,
- ITEM_FEATURE_SET_DEFAULT_BUMP_MODE,
- ITEM_FEATURE_SET_FRAME_MODE,
- ITEM_FEATURE_SET_SHOW_WHEN_EMPTY,
- ITEM_FEATURE_SET_DEFERRED,
- ITEM_FEATURE_SET_STRAND_SPECIFIC,
- ITEM_FEATURE_SET_BUMP_SPACING,
- ITEM_FEATURE_SET_JOIN_ALIGNS,
- };
-
-typedef struct
-{
- GValue *gvalue;
- const char *spec_name;
- guint param_id;
-} ItemFeatureValueDataStruct, *ItemFeatureValueData;
-
-typedef struct
-{
- GList *list;
- ZMapFeature feature;
-}ListFeatureStruct, *ListFeature;
-
-typedef struct
-{
- GQueue *queue;
- ZMapFeature feature;
-}QueueFeatureStruct, *QueueFeature;
-
-static void zmap_window_item_feature_set_class_init (ZMapWindowItemFeatureSetDataClass set_data_class);
-static void zmap_window_item_feature_set_init (ZMapWindowItemFeatureSetData set_data);
-static void zmap_window_item_feature_set_set_property(GObject *gobject,
- guint param_id,
- const GValue *value,
- GParamSpec *pspec);
-static void zmap_window_item_feature_set_get_property(GObject *gobject,
- guint param_id,
- GValue *value,
- GParamSpec *pspec);
-static void zmap_window_item_feature_set_dispose (GObject *object);
-static void zmap_window_item_feature_set_finalize (GObject *object);
-
-
-static void extract_value_from_style_table(gpointer key, gpointer value, gpointer user_data);
-static void reset_bump_mode_cb(gpointer key, gpointer value, gpointer user_data);
-static void queueRemoveFromList(gpointer queue_data, gpointer user_data);
-static void listRemoveFromList(gpointer list_data, gpointer user_data);
-static void removeList(gpointer data, gpointer user_data_unused) ;
-static void zmap_g_queue_replace(GQueue *queue, gpointer old, gpointer new);
-
-
-static GObjectClass *parent_class_G = NULL;
-
-gboolean zmap_g_return_moan(char *file, int line)
-{
- g_warning("Failed @ %s:%d", file, line);
-
- return FALSE;
-}
-
-GType zmapWindowItemFeatureSetGetType(void)
-{
- static GType group_type = 0;
-
- if (!group_type)
- {
- static const GTypeInfo group_info =
- {
- sizeof (zmapWindowItemFeatureSetDataClass),
- (GBaseInitFunc) NULL,
- (GBaseFinalizeFunc) NULL,
- (GClassInitFunc) zmap_window_item_feature_set_class_init,
- NULL, /* class_finalize */
- NULL, /* class_data */
- sizeof (zmapWindowItemFeatureSetData),
- 0, /* n_preallocs */
- (GInstanceInitFunc) zmap_window_item_feature_set_init
- };
-
- group_type = g_type_register_static (G_TYPE_OBJECT,
- "zmapWindowItemFeatureSetData",
- &group_info,
- 0);
- }
-
- return group_type;
-}
-
-
-ZMapWindowItemFeatureSetData zmapWindowItemFeatureSetCreate(ZMapWindow window,
- FooCanvasGroup *column_container,
- GQuark feature_set_unique_id,
- GQuark feature_set_original_id, /* unused! */
- GList *style_list,
- ZMapStrand strand,
- ZMapFrame frame)
-{
- ZMapWindowItemFeatureSetData set_data = NULL;
-
- g_return_val_if_fail(window != NULL, set_data);
- g_return_val_if_fail(column_container != NULL, set_data);
- g_return_val_if_fail(feature_set_unique_id != 0, set_data);
-
- if((set_data = g_object_new(zmapWindowItemFeatureSetGetType(), NULL)))
- {
- GList *list;
-
- set_data->window = window;
- set_data->strand = strand;
- set_data->frame = frame;
- /* set_data->style_id = 0;*/ /* feature_set_original_id */
- set_data->unique_id = feature_set_unique_id;
-
- if((list = g_list_first(style_list)))
- {
- do
- {
- ZMapFeatureTypeStyle style;
-
- style = (ZMapFeatureTypeStyle)(list->data);
-
- zmapWindowItemFeatureSetStyleFromStyle(set_data, style);
- }
- while((list = g_list_next(list)));
- }
-
- set_data->column_container = column_container;
-
- zmapWindowContainerSetVisibility(column_container, FALSE);
-
- zmapWindowContainerSetData(column_container, ITEM_FEATURE_SET_DATA, set_data);
- }
-
- return set_data;
-}
-
-void zmapWindowItemFeatureSetAttachFeatureSet(ZMapWindowItemFeatureSetData set_data,
- ZMapFeatureSet feature_set_to_attach)
-{
-
- if(feature_set_to_attach && !set_data->settings.has_feature_set)
- {
- ZMapWindowStats stats = NULL;
-
- zmapWindowContainerSetData(set_data->column_container, ITEM_FEATURE_DATA, feature_set_to_attach) ;
- set_data->settings.has_feature_set = TRUE;
-
- if((stats = zmapWindowStatsCreate((ZMapFeatureAny)feature_set_to_attach)))
- {
- zmapWindowContainerSetData(set_data->column_container, ITEM_FEATURE_STATS, stats);
- set_data->settings.has_stats = TRUE;
- }
- }
- else
- {
- /* We don't attach a feature set if there's already one
- * attached. This works for the good as the merge will
- * create featuresets which get destroyed after drawing
- * in the case of a pre-exisiting featureset. We don't
- * want these attached, as the original will also get
- * destroyed and the one attached will point to a set
- * which has been freed! */
- }
-
- return ;
-}
-
-ZMapFeatureSet zmapWindowItemFeatureSetRecoverFeatureSet(ZMapWindowItemFeatureSetData set_data)
-{
- ZMapFeatureSet feature_set = NULL;
-
- if(set_data->settings.has_feature_set)
- {
- feature_set = g_object_get_data(G_OBJECT(set_data->column_container), ITEM_FEATURE_DATA);
-
- if(!feature_set)
- {
- g_warning("%s", "No Feature Set!");
- set_data->settings.has_feature_set = FALSE;
- }
- }
-
- return feature_set;
-}
-
-ZMapWindowStats zmapWindowItemFeatureSetRecoverStats(ZMapWindowItemFeatureSetData set_data)
-{
- ZMapWindowStats stats = NULL;
-
- if(set_data->settings.has_stats)
- {
- stats = g_object_get_data(G_OBJECT(set_data->column_container), ITEM_FEATURE_STATS);
-
- if(!stats)
- {
- g_warning("%s", "No Stats!");
- set_data->settings.has_stats = FALSE;
- }
- }
-
- return stats;
-}
-
-/*!
- * \brief Gets the style we must use to draw with, given a style
- */
-ZMapFeatureTypeStyle zmapWindowItemFeatureSetStyleFromStyle(ZMapWindowItemFeatureSetData set_data,
- ZMapFeatureTypeStyle style2copy)
-{
- ZMapFeatureTypeStyle duplicated = NULL;
-
- g_return_val_if_fail(ZMAP_IS_WINDOW_ITEM_FEATURE_SET(set_data), duplicated);
- g_return_val_if_fail(ZMAP_IS_FEATURE_STYLE(style2copy), duplicated);
-
- if(!(duplicated = zmapWindowStyleTableFind(set_data->style_table, zMapStyleGetUniqueID(style2copy))))
- {
- int s = sizeof(set_data->lazy_loaded);
-
- duplicated = zmapWindowStyleTableAddCopy(set_data->style_table, style2copy);
-
- memset(&set_data->lazy_loaded, 0, s);
- }
-
- return duplicated;
-}
-
-ZMapFeatureTypeStyle zmapWindowItemFeatureSetStyleFromID(ZMapWindowItemFeatureSetData set_data,
- GQuark style_unique_id)
-{
- ZMapFeatureTypeStyle duplicated = NULL;
-
- g_return_val_if_fail(ZMAP_IS_WINDOW_ITEM_FEATURE_SET(set_data), duplicated);
-
- if(!(duplicated = zmapWindowStyleTableFind(set_data->style_table, style_unique_id)))
- {
- zMapAssertNotReached();
- }
-
- return duplicated;
-}
-
-/* Warning! This is dynamic and will pick the original id over unique id */
-GQuark zmapWindowItemFeatureSetColumnDisplayName(ZMapWindowItemFeatureSetData set_data)
-{
- ZMapFeatureSet feature_set;
- GQuark display_id = 0;
-
- if((feature_set = zmapWindowItemFeatureSetRecoverFeatureSet(set_data)))
- display_id = feature_set->original_id;
- else
- display_id = set_data->unique_id;
-
- return display_id;
-}
-
-ZMapWindow zmapWindowItemFeatureSetGetWindow(ZMapWindowItemFeatureSetData set_data)
-{
- ZMapWindow window = NULL;
-
- g_return_val_if_fail(ZMAP_IS_WINDOW_ITEM_FEATURE_SET(set_data), window);
-
- window = set_data->window;
-
- return window;
-}
-
-ZMapStrand zmapWindowItemFeatureSetGetStrand(ZMapWindowItemFeatureSetData set_data)
-{
- ZMapStrand strand = ZMAPSTRAND_NONE;
-
- g_return_val_if_fail(ZMAP_IS_WINDOW_ITEM_FEATURE_SET(set_data), strand);
-
- strand = set_data->strand;
-
- return strand;
-}
-
-ZMapFrame zmapWindowItemFeatureSetGetFrame (ZMapWindowItemFeatureSetData set_data)
-{
- ZMapFrame frame = ZMAPFRAME_NONE;
-
- g_return_val_if_fail(ZMAP_IS_WINDOW_ITEM_FEATURE_SET(set_data), frame);
-
- frame = set_data->frame;
-
- return frame;
-}
-
-
-ZMapFeatureTypeStyle zmapWindowItemFeatureSetGetStyle(ZMapWindowItemFeatureSetData set_data,
- ZMapFeature feature)
-{
- ZMapFeatureTypeStyle style = NULL;
-
- style = zmapWindowStyleTableFind(set_data->style_table, set_data->unique_id);
-
- return style;
-}
-
-double zmapWindowItemFeatureSetGetWidth(ZMapWindowItemFeatureSetData set_data)
-{
- double width = 0.0;
-
- g_object_get(G_OBJECT(set_data),
- ZMAPSTYLE_PROPERTY_WIDTH, &width,
- NULL);
-
- return width;
-}
-
-double zmapWindowItemFeatureGetBumpSpacing(ZMapWindowItemFeatureSetData set_data)
-{
- double spacing;
-
- g_object_get(G_OBJECT(set_data),
- ZMAPSTYLE_PROPERTY_BUMP_SPACING, &spacing,
- NULL);
-
- return spacing;
-}
-
-gboolean zmapWindowItemFeatureSetGetMagValues(ZMapWindowItemFeatureSetData set_data,
- double *min_mag_out, double *max_mag_out)
-{
- ZMapFeatureTypeStyle style = NULL;
- gboolean mag_sens = FALSE;
-
- if((style = zmapWindowStyleTableFind(set_data->style_table, set_data->unique_id)))
- {
- double min_mag;
- double max_mag;
-
- min_mag = zMapStyleGetMinMag(style) ;
- max_mag = zMapStyleGetMaxMag(style) ;
-
- if (min_mag != 0.0 || max_mag != 0.0)
- mag_sens = TRUE;
-
- if(min_mag_out)
- *min_mag_out = min_mag;
- if(max_mag_out)
- *max_mag_out = max_mag;
- }
-
- return mag_sens;
-}
-
-ZMapStyleColumnDisplayState zmapWindowItemFeatureSetGetDisplay(ZMapWindowItemFeatureSetData set_data)
-{
- ZMapStyleColumnDisplayState display = ZMAPSTYLE_COLDISPLAY_SHOW;
-
- if(!set_data->lazy_loaded.display_state)
- {
- g_object_get(G_OBJECT(set_data),
- ZMAPSTYLE_PROPERTY_DISPLAY_MODE, &(set_data->settings.display_state),
- NULL);
- }
-
- display = set_data->settings.display_state;
-
- return display;
-}
-
-void zmapWindowItemFeatureSetDisplay(ZMapWindowItemFeatureSetData set_data, ZMapStyleColumnDisplayState state)
-{
- ZMapFeatureTypeStyle style;
-
- if((style = zmapWindowStyleTableFind(set_data->style_table, set_data->unique_id)))
- {
- g_object_set(G_OBJECT(style),
- ZMAPSTYLE_PROPERTY_DISPLAY_MODE, state,
- NULL);
- }
-
- return ;
-}
-
-gboolean zmapWindowItemFeatureSetShowWhenEmpty(ZMapWindowItemFeatureSetData set_data)
-{
- gboolean show = FALSE;
-
- if(!set_data->lazy_loaded.show_when_empty)
- {
- g_object_get(G_OBJECT(set_data),
- ZMAPSTYLE_PROPERTY_SHOW_WHEN_EMPTY, &(set_data->settings.show_when_empty),
- NULL);
- set_data->lazy_loaded.show_when_empty = 1;
- }
-
- show = set_data->settings.show_when_empty;
-
- return show;
-}
-
-ZMapStyle3FrameMode zmapWindowItemFeatureSetGetFrameMode(ZMapWindowItemFeatureSetData set_data)
-{
- ZMapStyle3FrameMode frame_mode = ZMAPSTYLE_3_FRAME_INVALID;
-
- g_return_val_if_fail(ZMAP_IS_WINDOW_ITEM_FEATURE_SET(set_data), frame_mode);
-
- if(!set_data->lazy_loaded.frame_mode)
- {
- g_object_get(G_OBJECT(set_data),
- ZMAPSTYLE_PROPERTY_FRAME_MODE, &(set_data->settings.frame_mode),
- NULL);
- //set_data->lazy_loaded.frame_mode = 1;
- }
-
- frame_mode = set_data->settings.frame_mode;
-
- return frame_mode;
-}
-
-gboolean zmapWindowItemFeatureSetIsFrameSpecific(ZMapWindowItemFeatureSetData set_data,
- ZMapStyle3FrameMode *frame_mode_out)
-{
- ZMapStyle3FrameMode frame_mode = ZMAPSTYLE_3_FRAME_INVALID;
- gboolean frame_specific = FALSE;
-
- g_return_val_if_fail(ZMAP_IS_WINDOW_ITEM_FEATURE_SET(set_data), FALSE);
-
- if(!set_data->lazy_loaded.frame_specific)
- {
- frame_mode = zmapWindowItemFeatureSetGetFrameMode(set_data) ;
-
- //set_data->lazy_loaded.frame_specific = 1;
-
- if(frame_mode != ZMAPSTYLE_3_FRAME_NEVER)
- set_data->settings.frame_specific = TRUE;
-
- if(frame_mode == ZMAPSTYLE_3_FRAME_INVALID)
- {
- zMapLogWarning("Frame mode for column %s is invalid.", g_quark_to_string(set_data->unique_id));
- set_data->settings.frame_specific = FALSE;
- }
- }
-
- frame_specific = set_data->settings.frame_specific;
-
- if(frame_mode_out)
- *frame_mode_out = frame_mode;
-
- return frame_specific;
-}
-
-gboolean zmapWindowItemFeatureSetIsStrandSpecific(ZMapWindowItemFeatureSetData set_data)
-{
- gboolean strand_specific = FALSE;
-
- g_object_get(G_OBJECT(set_data),
- ZMAPSTYLE_PROPERTY_STRAND_SPECIFIC, &(set_data->settings.strand_specific),
- NULL);
-
- strand_specific = set_data->settings.strand_specific;
-
- return strand_specific;
-}
-
-ZMapStyleBumpMode zmapWindowItemFeatureSetGetBumpMode(ZMapWindowItemFeatureSetData set_data)
-{
- ZMapStyleBumpMode mode = ZMAPBUMP_UNBUMP;
-
- g_object_get(G_OBJECT(set_data),
- ZMAPSTYLE_PROPERTY_BUMP_MODE, &(set_data->settings.bump_mode),
- NULL);
-
- mode = set_data->settings.bump_mode;
-
- return mode;
-}
-
-ZMapStyleBumpMode zmapWindowItemFeatureSetGetDefaultBumpMode(ZMapWindowItemFeatureSetData set_data)
-{
- ZMapStyleBumpMode mode = ZMAPBUMP_UNBUMP;
-
- g_object_get(G_OBJECT(set_data),
- ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE, &(set_data->settings.default_bump_mode),
- NULL);
-
- mode = set_data->settings.default_bump_mode;
-
- return mode;
-}
-
-ZMapStyleBumpMode zmapWindowItemFeatureSetResetBumpModes(ZMapWindowItemFeatureSetData set_data)
-{
- ZMapStyleBumpMode mode = ZMAPBUMP_UNBUMP;
- ItemFeatureValueDataStruct value_data = {NULL};
- GValue value = {0};
-
- g_value_init(&value, G_TYPE_UINT);
-
- value_data.spec_name = ZMAPSTYLE_PROPERTY_BUMP_MODE;
- value_data.gvalue = &value;
- value_data.param_id = ITEM_FEATURE_SET_BUMP_MODE;
-
- g_hash_table_foreach(set_data->style_table, reset_bump_mode_cb, &value_data);
-
- mode = g_value_get_uint(&value);
-
- return mode;
-}
-
-gboolean zmapWindowItemFeatureSetJoinAligns(ZMapWindowItemFeatureSetData set_data, unsigned int *threshold)
-{
- gboolean result = FALSE;
- unsigned int tmp = 0;
-
- if(threshold)
- {
- g_object_get(G_OBJECT(set_data),
- ZMAPSTYLE_PROPERTY_ALIGNMENT_BETWEEN_ERROR, &tmp,
- NULL);
-
- if(tmp != 0)
- {
- *threshold = tmp;
- result = TRUE;
- }
- }
-
- return result;
-}
-
-gboolean zmapWindowItemFeatureSetGetDeferred(ZMapWindowItemFeatureSetData set_data)
-{
- gboolean is_deferred = FALSE;
-
- /* Not cached! */
- g_object_get(G_OBJECT(set_data),
- ZMAPSTYLE_PROPERTY_DEFERRED, &is_deferred,
- NULL);
-
- return is_deferred;
-}
-
-/* As we keep a list of the item we need to delete them at times. This is actually _not_
- * used ATM (Apr 2008) as the reason it was written turned out to have a better solution
- * RT# 63281. Anyway the code is here if needed.
- */
-void zmapWindowItemFeatureSetFeatureRemove(ZMapWindowItemFeatureSetData item_feature_set,
- ZMapFeature feature)
-{
- QueueFeatureStruct queue_feature;
-
- queue_feature.queue = item_feature_set->user_hidden_stack;
- queue_feature.feature = feature;
- /* user_hidden_stack is a copy of the list in focus. We need to
- * remove items when they get destroyed */
- g_queue_foreach(queue_feature.queue, queueRemoveFromList, &queue_feature);
-
- return ;
-}
-
-
-ZMapWindowItemFeatureSetData zmapWindowItemFeatureSetDestroy(ZMapWindowItemFeatureSetData item_feature_set)
-{
- g_object_unref(G_OBJECT(item_feature_set));
-
- item_feature_set = NULL;
-
- return item_feature_set;
-}
-
-/* This function is written the wrong way round. It should be
- * re-written, along with extract_value_from_style_table so that
- * this function is part of utils and extract_value_from_style_table
- * calls it. It wouldn't need to be here then! */
-gboolean zmapWindowStyleListGetSetting(GList *list_of_styles,
- char *setting_name,
- GValue *value_in_out)
-{
- GList *list;
- gboolean result = FALSE;
-
- if(value_in_out && (list = g_list_first(list_of_styles)))
- {
- ItemFeatureValueDataStruct value_data = {};
- GObjectClass *object_class;
- GParamSpec *param_spec;
-
- object_class = g_type_class_peek(ZMAP_TYPE_WINDOW_ITEM_FEATURE_SET);
-
- if((param_spec = g_object_class_find_property(object_class, setting_name)))
- {
- value_data.param_id = param_spec->param_id;
- value_data.spec_name = setting_name;
- value_data.gvalue = value_in_out;
-
- result = TRUE;
-
- do
- {
- ZMapFeatureTypeStyle style;
- GQuark unique_id;
-
- style = ZMAP_FEATURE_STYLE(list->data);
- unique_id = zMapStyleGetUniqueID(style);
- extract_value_from_style_table(GINT_TO_POINTER(unique_id), style, &value_data);
- }
- while((list = g_list_next(list)));
- }
- }
-
- return result;
-}
-
-
-/* Object code */
-static void zmap_window_item_feature_set_class_init(ZMapWindowItemFeatureSetDataClass set_data_class)
-{
- GObjectClass *gobject_class;
-
- gobject_class = (GObjectClass *)set_data_class;
-
- gobject_class->set_property = zmap_window_item_feature_set_set_property;
- gobject_class->get_property = zmap_window_item_feature_set_get_property;
-
- parent_class_G = g_type_class_peek_parent(set_data_class);
-
- /* width */
- g_object_class_install_property(gobject_class,
- ITEM_FEATURE_SET_WIDTH,
- g_param_spec_double(ZMAPSTYLE_PROPERTY_WIDTH,
- ZMAPSTYLE_PROPERTY_WIDTH,
- "The minimum width the column should be displayed at.",
- 0.0, 32000.00, 16.0,
- ZMAP_PARAM_STATIC_RO));
- /* Bump spacing */
- g_object_class_install_property(gobject_class,
- ITEM_FEATURE_SET_BUMP_SPACING,
- g_param_spec_double(ZMAPSTYLE_PROPERTY_BUMP_SPACING,
- ZMAPSTYLE_PROPERTY_BUMP_SPACING,
- "The x coord spacing between features when bumping.",
- 0.0, 32000.00, 1.0,
- ZMAP_PARAM_STATIC_RO));
- /* display mode */
- g_object_class_install_property(gobject_class,
- ITEM_FEATURE_SET_VISIBLE,
- g_param_spec_uint(ZMAPSTYLE_PROPERTY_DISPLAY_MODE,
- ZMAPSTYLE_PROPERTY_DISPLAY_MODE,
- "[ hide | show_hide | show ]",
- ZMAPSTYLE_COLDISPLAY_INVALID,
- ZMAPSTYLE_COLDISPLAY_SHOW,
- ZMAPSTYLE_COLDISPLAY_INVALID,
- ZMAP_PARAM_STATIC_RO));
-
- /* bump mode */
- g_object_class_install_property(gobject_class,
- ITEM_FEATURE_SET_BUMP_MODE,
- g_param_spec_uint(ZMAPSTYLE_PROPERTY_BUMP_MODE,
- ZMAPSTYLE_PROPERTY_BUMP_MODE,
- "The Bump Mode",
- ZMAPBUMP_INVALID,
- ZMAPBUMP_END,
- ZMAPBUMP_INVALID,
- ZMAP_PARAM_STATIC_RO));
- /* bump default */
- g_object_class_install_property(gobject_class,
- ITEM_FEATURE_SET_DEFAULT_BUMP_MODE,
- g_param_spec_uint(ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE,
- ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE,
- "The Default Bump Mode",
- ZMAPBUMP_INVALID,
- ZMAPBUMP_END,
- ZMAPBUMP_INVALID,
- ZMAP_PARAM_STATIC_RO));
- /* bump default */
- g_object_class_install_property(gobject_class,
- ITEM_FEATURE_SET_JOIN_ALIGNS,
- g_param_spec_uint(ZMAPSTYLE_PROPERTY_ALIGNMENT_BETWEEN_ERROR,
- ZMAPSTYLE_PROPERTY_ALIGNMENT_BETWEEN_ERROR,
- "match threshold",
- 0, 1000, 0,
- ZMAP_PARAM_STATIC_RO));
- /* Frame mode */
- g_object_class_install_property(gobject_class,
- ITEM_FEATURE_SET_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,
- ZMAP_PARAM_STATIC_RO));
-
- /* Strand specific */
- g_object_class_install_property(gobject_class,
- ITEM_FEATURE_SET_STRAND_SPECIFIC,
- g_param_spec_boolean(ZMAPSTYLE_PROPERTY_STRAND_SPECIFIC,
- "Strand specific",
- "Defines strand sensitive display.",
- TRUE, ZMAP_PARAM_STATIC_RO));
-
- /* Show when empty */
- g_object_class_install_property(gobject_class,
- ITEM_FEATURE_SET_SHOW_WHEN_EMPTY,
- g_param_spec_boolean(ZMAPSTYLE_PROPERTY_SHOW_WHEN_EMPTY,
- ZMAPSTYLE_PROPERTY_SHOW_WHEN_EMPTY,
- "Does the Style get shown when empty",
- TRUE, ZMAP_PARAM_STATIC_RO));
-
- /* Deferred */
- g_object_class_install_property(gobject_class,
- ITEM_FEATURE_SET_DEFERRED,
- g_param_spec_boolean(ZMAPSTYLE_PROPERTY_DEFERRED,
- ZMAPSTYLE_PROPERTY_DEFERRED,
- "Is this deferred",
- FALSE, ZMAP_PARAM_STATIC_RO));
-
-
- gobject_class->dispose = zmap_window_item_feature_set_dispose;
- gobject_class->finalize = zmap_window_item_feature_set_finalize;
-
- return ;
-}
-
-static void zmap_window_item_feature_set_init(ZMapWindowItemFeatureSetData set_data)
-{
-
- set_data->style_table = zmapWindowStyleTableCreate();
- set_data->user_hidden_stack = g_queue_new();
-
- return ;
-}
-
-static void zmap_window_item_feature_set_set_property(GObject *gobject,
- guint param_id,
- const GValue *value,
- GParamSpec *pspec)
-{
-
- switch(param_id)
- {
- default:
- G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
- break;
- }
-
- return ;
-}
-
-static void zmap_window_item_feature_set_get_property(GObject *gobject,
- guint param_id,
- GValue *value,
- GParamSpec *pspec)
-{
- ZMapWindowItemFeatureSetData set_data;
-
- set_data = ZMAP_WINDOW_ITEM_FEATURE_SET(gobject);
-
- switch(param_id)
- {
- case ITEM_FEATURE_SET_BUMP_SPACING:
- case ITEM_FEATURE_SET_WIDTH:
- case ITEM_FEATURE_SET_VISIBLE:
- case ITEM_FEATURE_SET_BUMP_MODE:
- case ITEM_FEATURE_SET_DEFAULT_BUMP_MODE:
- case ITEM_FEATURE_SET_FRAME_MODE:
- case ITEM_FEATURE_SET_SHOW_WHEN_EMPTY:
- case ITEM_FEATURE_SET_DEFERRED:
- case ITEM_FEATURE_SET_STRAND_SPECIFIC:
- case ITEM_FEATURE_SET_JOIN_ALIGNS:
- {
- ItemFeatureValueDataStruct value_data = {NULL};
-
- value_data.spec_name = g_param_spec_get_name(pspec);
- value_data.gvalue = value;
- value_data.param_id = param_id;
-
- g_hash_table_foreach(set_data->style_table, extract_value_from_style_table, &value_data);
- }
- break;
- default:
- G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
- break;
- }
-
- return ;
-}
-
-static void zmap_window_item_feature_set_dispose(GObject *object)
-{
- ZMapWindowItemFeatureSetData set_data;
- GObjectClass *gobject_class = G_OBJECT_CLASS(parent_class_G);
-
- set_data = ZMAP_WINDOW_ITEM_FEATURE_SET(object);
-
- set_data->window = NULL; /* not ours */
-
- if(set_data->style_table)
- {
- zmapWindowStyleTableDestroy(set_data->style_table);
- set_data->style_table = NULL;
- }
-
- if(set_data->user_hidden_stack)
- {
- if(!g_queue_is_empty(set_data->user_hidden_stack))
- g_queue_foreach(set_data->user_hidden_stack, removeList, NULL) ;
-
- g_queue_free(set_data->user_hidden_stack);
-
- set_data->user_hidden_stack = NULL;
- }
-
- if(gobject_class->dispose)
- (*gobject_class->dispose)(object);
-
- return ;
-}
-
-static void zmap_window_item_feature_set_finalize(GObject *object)
-{
- GObjectClass *gobject_class = G_OBJECT_CLASS(parent_class_G);
-
- if(gobject_class->finalize)
- (*gobject_class->finalize)(object);
-
- return ;
-}
-
-
-/* INTERNAL */
-
-static void extract_value_from_style_table(gpointer key, gpointer value, gpointer user_data)
-{
- ItemFeatureValueData value_data;
- ZMapFeatureTypeStyle style;
- GQuark style_id;
-
- style_id = GPOINTER_TO_INT(key);
- style = ZMAP_FEATURE_STYLE(value);
- value_data = (ItemFeatureValueData)user_data;
-
- switch(value_data->param_id)
- {
- case ITEM_FEATURE_SET_BUMP_SPACING:
- case ITEM_FEATURE_SET_WIDTH:
- {
- double tmp_width, style_width;
-
- tmp_width = g_value_get_double(value_data->gvalue);
-
- g_object_get(G_OBJECT(style),
- value_data->spec_name, &style_width,
- NULL);
-
- if(style_width > tmp_width)
- g_value_set_double(value_data->gvalue, style_width);
- }
- break;
- case ITEM_FEATURE_SET_STRAND_SPECIFIC:
- case ITEM_FEATURE_SET_SHOW_WHEN_EMPTY:
- case ITEM_FEATURE_SET_DEFERRED:
- {
- gboolean style_version = FALSE, current;
-
- current = g_value_get_boolean(value_data->gvalue);
-
- if(!current)
- {
- g_object_get(G_OBJECT(style),
- value_data->spec_name, &style_version,
- NULL);
-
- if(style_version)
- g_value_set_boolean(value_data->gvalue, style_version);
- }
- }
- break;
- case ITEM_FEATURE_SET_FRAME_MODE:
- case ITEM_FEATURE_SET_VISIBLE:
- case ITEM_FEATURE_SET_BUMP_MODE:
- case ITEM_FEATURE_SET_DEFAULT_BUMP_MODE:
- {
- guint style_version = 0, current;
-
- current = g_value_get_uint(value_data->gvalue);
-
- if(!current)
- {
- g_object_get(G_OBJECT(style),
- value_data->spec_name, &style_version,
- NULL);
-
- if(style_version)
- g_value_set_uint(value_data->gvalue, style_version);
- }
- }
- break;
- case ITEM_FEATURE_SET_JOIN_ALIGNS:
- {
- guint style_version = 0, current;
-
- current = g_value_get_uint(value_data->gvalue);
-
- if(!current)
- {
- if(zMapStyleGetJoinAligns(style, &style_version))
- {
- g_value_set_uint(value_data->gvalue, style_version);
- }
- }
- }
- break;
- default:
- break;
- }
-
- return ;
-}
-
-static void reset_bump_mode_cb(gpointer key, gpointer value, gpointer user_data)
-{
- ZMapFeatureTypeStyle style;
-
- style = ZMAP_FEATURE_STYLE(value);
-
- zMapStyleResetBumpMode(style);
-
- extract_value_from_style_table(key, value, user_data);
-
- return ;
-}
-
-static void removeList(gpointer data, gpointer user_data_unused)
-{
- GList *user_hidden_items = (GList *)data ;
-
- g_list_free(user_hidden_items) ;
-
- return ;
-}
-
-static void queueRemoveFromList(gpointer queue_data, gpointer user_data)
-{
- GList *item_list = (GList *)queue_data;
- QueueFeature queue_feature = (QueueFeature)user_data;
- ListFeatureStruct list_feature;
-
- list_feature.list = item_list;
- list_feature.feature = (ZMapFeature)queue_feature->feature;
-
- g_list_foreach(item_list, listRemoveFromList, &list_feature);
-
- if(list_feature.list != item_list)
- zmap_g_queue_replace(queue_feature->queue, item_list, list_feature.list);
-
- return;
-}
-
-
-
-static void listRemoveFromList(gpointer list_data, gpointer user_data)
-{
- ListFeature list_feature = (ListFeature)user_data;
- ZMapFeature item_feature;
- FooCanvasItem *item;
-
- zMapAssert(FOO_IS_CANVAS_ITEM(list_data));
-
- item = FOO_CANVAS_ITEM(list_data);
- item_feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA);
- zMapAssert(item_feature);
-
- if(item_feature == list_feature->feature)
- list_feature->list = g_list_remove(list_feature->list, item);
-
- return ;
-}
-
-static void zmap_g_queue_replace(GQueue *queue, gpointer old, gpointer new)
-{
- int length, index;
-
- if((length = g_queue_get_length(queue)))
- {
- if((index = g_queue_index(queue, old)) != -1)
- {
- gpointer popped = g_queue_pop_nth(queue, index);
- zMapAssert(popped == old);
- g_queue_push_nth(queue, new, index);
- }
- }
- else
- g_queue_push_head(queue, new);
-
- return ;
-}
diff --git a/src/zmapWindow/zmapWindowItemFeatureSet.h b/src/zmapWindow/zmapWindowItemFeatureSet.h
deleted file mode 100755
index 878d2fb69..000000000
--- a/src/zmapWindow/zmapWindowItemFeatureSet.h
+++ /dev/null
@@ -1,119 +0,0 @@
-/* File: zmapWindowItemFeatureSet.h
- * Author: Roy Storey (rds@sanger.ac.uk)
- * Copyright (c) 2009: Genome Research Ltd.
- *-------------------------------------------------------------------
- * ZMap is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
- *-------------------------------------------------------------------
- * This file is part of the ZMap genome database package
- * originally written by:
- *
- * Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
- * Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
- *
- * Description:
- *
- * Exported functions: See XXXXXXXXXXXXX.h
- * HISTORY:
- * Last edited: May 7 22:36 2009 (rds)
- * Created: Fri Feb 6 15:32:46 2009 (rds)
- * CVS info: $Id: zmapWindowItemFeatureSet.h,v 1.10 2009-05-07 21:36:12 rds Exp $
- *-------------------------------------------------------------------
- */
-
-#ifndef __ZMAP_WINDOW_ITEM_FEATURE_SET_H__
-#define __ZMAP_WINDOW_ITEM_FEATURE_SET_H__
-
-#include <glib.h>
-#include <glib-object.h>
-
-
-#define ZMAP_TYPE_WINDOW_ITEM_FEATURE_SET (zmapWindowItemFeatureSetGetType())
-#define ZMAP_WINDOW_ITEM_FEATURE_SET(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_ITEM_FEATURE_SET, zmapWindowItemFeatureSetData))
-#define ZMAP_WINDOW_ITEM_FEATURE_SET_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_ITEM_FEATURE_SET, zmapWindowItemFeatureSetData const))
-#define ZMAP_WINDOW_ITEM_FEATURE_SET_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_WINDOW_ITEM_FEATURE_SET, zmapWindowItemFeatureSetDataClass))
-#define ZMAP_IS_WINDOW_ITEM_FEATURE_SET(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_WINDOW_ITEM_FEATURE_SET) || zmap_g_return_moan(__FILE__, __LINE__) )
-#define ZMAP_WINDOW_ITEM_FEATURE_SET_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_WINDOW_ITEM_FEATURE_SET, zmapWindowItemFeatureSetDataClass))
-
-
-/* Instance */
-typedef struct _zmapWindowItemFeatureSetDataStruct zmapWindowItemFeatureSetData, *ZMapWindowItemFeatureSetData;
-
-/* Class */
-typedef struct _zmapWindowItemFeatureSetDataClassStruct zmapWindowItemFeatureSetDataClass, *ZMapWindowItemFeatureSetDataClass ;
-
-
-gboolean zmap_g_return_moan(char *file, int line);
-
-
-/* Public funcs */
-GType zmapWindowItemFeatureSetGetType(void);
-
-
-ZMapWindowItemFeatureSetData zmapWindowItemFeatureSetCreate(ZMapWindow window,
- FooCanvasGroup *column_container,
- GQuark feature_set_unique_id,
- GQuark feature_set_original_id,
- GList *style_list,
- ZMapStrand strand,
- ZMapFrame frame);
-
-void zmapWindowItemFeatureSetAttachFeatureSet(ZMapWindowItemFeatureSetData set_data,
- ZMapFeatureSet feature_set_to_attach);
-ZMapFeatureSet zmapWindowItemFeatureSetRecoverFeatureSet(ZMapWindowItemFeatureSetData set_data);
-//ZMapWindowStats zmapWindowItemFeatureSetRecoverStats(ZMapWindowItemFeatureSetData set_data);
-ZMapFeatureTypeStyle zmapWindowItemFeatureSetStyleFromStyle(ZMapWindowItemFeatureSetData set_data,
- ZMapFeatureTypeStyle style2copy);
-ZMapFeatureTypeStyle zmapWindowItemFeatureSetStyleFromID(ZMapWindowItemFeatureSetData set_data,
- GQuark style_unique_id);
-GQuark zmapWindowItemFeatureSetColumnDisplayName(ZMapWindowItemFeatureSetData set_data);
-ZMapWindow zmapWindowItemFeatureSetGetWindow(ZMapWindowItemFeatureSetData set_data);
-ZMapStrand zmapWindowItemFeatureSetGetStrand(ZMapWindowItemFeatureSetData set_data);
-ZMapFrame zmapWindowItemFeatureSetGetFrame (ZMapWindowItemFeatureSetData set_data);
-
-ZMapFeatureTypeStyle zmapWindowItemFeatureSetGetStyle(ZMapWindowItemFeatureSetData set_data,
- ZMapFeature feature);
-
-
-double zmapWindowItemFeatureSetGetWidth(ZMapWindowItemFeatureSetData set_data);
-double zmapWindowItemFeatureGetBumpSpacing(ZMapWindowItemFeatureSetData set_data);
-
-gboolean zmapWindowItemFeatureSetGetMagValues(ZMapWindowItemFeatureSetData set_data,
- double *min_mag_out, double *max_mag_out);
-
-ZMapStyleColumnDisplayState zmapWindowItemFeatureSetGetDisplay(ZMapWindowItemFeatureSetData set_data);
-void zmapWindowItemFeatureSetDisplay(ZMapWindowItemFeatureSetData set_data, ZMapStyleColumnDisplayState state);
-
-gboolean zmapWindowItemFeatureSetShowWhenEmpty(ZMapWindowItemFeatureSetData set_data);
-ZMapStyle3FrameMode zmapWindowItemFeatureSetGetFrameMode(ZMapWindowItemFeatureSetData set_data);
-gboolean zmapWindowItemFeatureSetIsFrameSpecific(ZMapWindowItemFeatureSetData set_data,
- ZMapStyle3FrameMode *frame_mode_out);
-gboolean zmapWindowItemFeatureSetIsStrandSpecific(ZMapWindowItemFeatureSetData set_data);
-ZMapStyleBumpMode zmapWindowItemFeatureSetGetBumpMode(ZMapWindowItemFeatureSetData set_data);
-ZMapStyleBumpMode zmapWindowItemFeatureSetGetDefaultBumpMode(ZMapWindowItemFeatureSetData set_data);
-ZMapStyleBumpMode zmapWindowItemFeatureSetResetBumpModes(ZMapWindowItemFeatureSetData set_data);
-gboolean zmapWindowItemFeatureSetJoinAligns(ZMapWindowItemFeatureSetData set_data, unsigned int *threshold);
-gboolean zmapWindowItemFeatureSetGetDeferred(ZMapWindowItemFeatureSetData set_data);
-void zmapWindowItemFeatureSetFeatureRemove(ZMapWindowItemFeatureSetData item_feature_set,
- ZMapFeature feature);
-
-ZMapWindowItemFeatureSetData zmapWindowItemFeatureSetDestroy(ZMapWindowItemFeatureSetData item_feature_set);
-
-gboolean zmapWindowStyleListGetSetting(GList *list_of_styles,
- char *setting_name,
- GValue *value_in_out);
-
-
-#endif /* __ZMAP_WINDOW_ITEM_FEATURE_SET_H__ */
diff --git a/src/zmapWindow/zmapWindowItemFeatureSet_I.h b/src/zmapWindow/zmapWindowItemFeatureSet_I.h
deleted file mode 100755
index 513bf50c9..000000000
--- a/src/zmapWindow/zmapWindowItemFeatureSet_I.h
+++ /dev/null
@@ -1,108 +0,0 @@
-/* File: zmapWindowItemFeatureSet_I.h
- * Author: Roy Storey (rds@sanger.ac.uk)
- * Copyright (c) 2009: Genome Research Ltd.
- *-------------------------------------------------------------------
- * ZMap is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
- *-------------------------------------------------------------------
- * This file is part of the ZMap genome database package
- * originally written by:
- *
- * Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
- * Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
- *
- * Description:
- *
- * Exported functions: See XXXXXXXXXXXXX.h
- * HISTORY:
- * Last edited: Apr 27 11:46 2009 (edgrif)
- * Created: Fri Feb 6 11:49:03 2009 (rds)
- * CVS info: $Id: zmapWindowItemFeatureSet_I.h,v 1.7 2009-04-28 14:33:41 edgrif Exp $
- *-------------------------------------------------------------------
- */
-
-#ifndef __ZMAP_WINDOW_ITEM_FEATURE_SET_I_H__
-#define __ZMAP_WINDOW_ITEM_FEATURE_SET_I_H__
-
-#include <ZMap/zmapStyle.h>
-#include <zmapWindow_P.h>
-#include <zmapWindowItemFeatureSet.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)
-
-
-
-typedef struct _zmapWindowItemFeatureSetDataStruct
-{
- GObject __parent__;
-
- ZMapWindow window;
- ZMapStrand strand ;
- ZMapFrame frame ;
- GHashTable *style_table ;
-
- FooCanvasGroup *column_container;
-
- //GQuark style_id;
- GQuark unique_id;
-
- /* We keep the features sorted by position and size so we can cursor through them... */
- gboolean sorted ;
-
- /* Features hidden by user, should stay hidden. */
- GQueue *user_hidden_stack ;
-
- /* These fields are used for some of the more exotic column bumping. */
- gboolean hidden_bump_features ; /* Features were hidden because they
- * are out of the marked range. */
- GList *extra_items ; /* Match backgrounds etc. */
-
- GList *gaps_added_items ; /* List of features where gap data was added. */
-
- struct
- {
- unsigned int frame_mode : 1;
- unsigned int frame_specific : 1;
- unsigned int display_state : 1;
- unsigned int show_when_empty : 1;
- }lazy_loaded;
-
- struct
- {
- gboolean has_feature_set;
- gboolean has_stats;
- gboolean show_when_empty;
- gboolean frame_specific;
- gboolean strand_specific;
- ZMapStyle3FrameMode frame_mode;
- ZMapStyleColumnDisplayState display_state;
- ZMapStyleBumpMode bump_mode;
- ZMapStyleBumpMode default_bump_mode;
- }settings;
-
-} zmapWindowItemFeatureSetDataStruct;
-
-
-typedef struct _zmapWindowItemFeatureSetDataClassStruct
-{
- GObjectClass __parent__;
-
-} zmapWindowItemFeatureSetDataClassStruct;
-
-
-
-#endif /* __ZMAP_WINDOW_ITEM_FEATURE_SET_I_H__ */
--
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