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Commit 45a1427d authored by mh17's avatar mh17
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3F slice markers restored to former glory

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src/zmapWindow/items/zmapWindowBasicFeature.c
+ 20
− 6
View file @ 45a1427d
......@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Feb 15 14:20 2010 (edgrif)
* Created: Wed Dec 3 10:02:22 2008 (rds)
* CVS info: $Id: zmapWindowBasicFeature.c,v 1.14 2010-04-15 11:19:03 mh17 Exp $
* CVS info: $Id: zmapWindowBasicFeature.c,v 1.15 2010-05-18 09:45:47 mh17 Exp $
*-------------------------------------------------------------------
*/
......@@ -106,7 +106,7 @@ static FooCanvasItem *zmap_window_basic_feature_add_interval(ZMapWindowCanvasIte
gboolean interval_type_from_feature_type = TRUE; /* for now */
feature = basic->feature;
style = (ZMAP_CANVAS_ITEM_GET_CLASS(basic)->get_style)(basic);
double middle;
if(interval_type_from_feature_type)
{
......@@ -127,20 +127,34 @@ static FooCanvasItem *zmap_window_basic_feature_add_interval(ZMapWindowCanvasIte
case ZMAP_WINDOW_BASIC_GLYPH:
{
int which = 0;
gboolean rev_strand;
double origin = 0.0;
double min,max;
gboolean strand = FALSE;
double score = feature->score;
if (feature->flags.has_boundary)
{
basic->auto_resize_background = 1;
which = feature->boundary_type == ZMAPBOUNDARY_5_SPLICE ? 5 : 3;
rev_strand = !ZMAPFEATURE_FORWARD(feature);
// style is as configured or retrofitted in zMapStyleMakeDrawable()
// x and y coords are relative to main feature set up in CanvasItemCreate()
middle = zMapStyleGetWidth(style) / 2;
// we only have the fwd strand but need to flip-x when score is -ve
strand = score < 0.0;
if(score < 0.0)
score = -score;
min = zMapStyleGetMinScore(style);
max = zMapStyleGetMaxScore(style);
if(min < 0.0 && max > 0.0)
{
origin = zMapStyleGetWidth(style) * (-min / (max - min));
}
item = FOO_CANVAS_ITEM(zMapWindowGlyphItemCreate(FOO_CANVAS_GROUP(basic),
style, which, middle,0.0, feature->score,rev_strand));
style, which, origin,0.0, feature->score,strand));
// colour should be set by caller, esp if style is frame specific
}
......
src/zmapWindow/zmapWindowDraw.c
+ 73
− 69
View file @ 45a1427d
......@@ -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.
......@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Feb 15 11:52 2010 (edgrif)
* Created: Thu Sep 8 10:34:49 2005 (edgrif)
* CVS info: $Id: zmapWindowDraw.c,v 1.120 2010-03-04 15:12:50 mh17 Exp $
* CVS info: $Id: zmapWindowDraw.c,v 1.121 2010-05-18 09:45:47 mh17 Exp $
*-------------------------------------------------------------------
*/
......@@ -120,9 +120,9 @@ typedef struct
}SeparatorCanvasDataStruct, *SeparatorCanvasData;
static void preZoomCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
static void preZoomCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data) ;
static gboolean resetWindowWidthCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
static gboolean resetWindowWidthCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data);
......@@ -135,7 +135,7 @@ static void printQuarks(gpointer data, gpointer user_data) ;
static void hideColsCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
static void hideColsCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data) ;
static void featureInViewCB(void *data, void *user_data) ;
static void showColsCB(void *data, void *user_data) ;
......@@ -164,12 +164,16 @@ static void drawSeparatorFeatures(SeparatorCanvasData canvas_data, ZMapFeatureCo
void zMapWindowToggle3Frame(ZMapWindow window)
{
gpointer three_frame_id = NULL;
gpointer three_frame_Id = NULL; // capitalised!
zMapWindowBusy(window, TRUE) ;
// yuk...
three_frame_id = GUINT_TO_POINTER(zMapStyleCreateID(ZMAP_FIXED_STYLE_3FRAME));
three_frame_Id = GUINT_TO_POINTER(g_quark_from_string(ZMAP_FIXED_STYLE_3FRAME));
if(g_list_find(window->feature_set_names, three_frame_id))
if(g_list_find(window->feature_set_names, three_frame_id) ||
g_list_find(window->feature_set_names, three_frame_Id))
{
#ifndef RDS_REMOVED_STATS
/* Remove all col. configuration windows as columns will be destroyed/recreated and the column
......@@ -178,9 +182,9 @@ void zMapWindowToggle3Frame(ZMapWindow window)
/* The column configure widget can reload itself now. */
#endif
zmapWindowDrawRemove3FrameFeatures(window);
window->display_3_frame = !window->display_3_frame;
zmapWindowDraw3FrameFeatures(window);
}
else
......@@ -220,7 +224,7 @@ void zmapWindowCanvasGroupChildSort(FooCanvasGroup *group_inout)
/*
* some column functions....
* some column functions....
*/
......@@ -228,7 +232,7 @@ void zmapWindowCanvasGroupChildSort(FooCanvasGroup *group_inout)
* this may be easy (off or on) or may depend on current mag state/mark, frame state or compress
* state. If !new_col_state then the current column state is used to set the show/hide state,
* need this for setting up initial state of columns.
*
*
* */
void zmapWindowColumnSetState(ZMapWindow window, FooCanvasGroup *column_group,
ZMapStyleColumnDisplayState new_col_state, gboolean redraw_if_needed)
......@@ -263,7 +267,7 @@ void zmapWindowColumnSetState(ZMapWindow window, FooCanvasGroup *column_group,
gboolean mag_visible, frame_visible ;
mag_visible = zmapWindowColumnIsMagVisible(window, column_group) ;
frame_visible = zmapWindowColumnIs3frameVisible(window, column_group) ;
......@@ -315,7 +319,7 @@ void zmapWindowColumnSetState(ZMapWindow window, FooCanvasGroup *column_group,
zmapWindowFullReposition(window) ;
}
return ;
}
......@@ -331,10 +335,10 @@ void zmapWindowColumnSetMagState(ZMapWindow window, FooCanvasGroup *col_group)
container = (ZMapWindowContainerFeatureSet)col_group;
/* Only check the mag factor if the column is visible. (wrong) */
/*
/*
* This test needs to be thought about. We can't test if a column
* is visible as it'll never get shown on zoom in. We don't want to
* mess with the columns that have been hidden by the user though
* is visible as it'll never get shown on zoom in. We don't want to
* mess with the columns that have been hidden by the user though
* (as happens now). I'm not sure we have a record of this.
*/
......@@ -392,7 +396,7 @@ gboolean zmapWindowColumnIs3frameVisible(ZMapWindow window, FooCanvasGroup *col_
display = window->display_3_frame;
show_on_reverse = window->show_3_frame_reverse;
/*
/*
| WINDOW->... | REVERSE STRAND | FORWARD STRAND |
| DISPLAY|SHOW REV |NONE| 0 | 1 | 2 |NONE| 0 | 1 | 2 |
------------------------------------------------------
......@@ -401,21 +405,21 @@ gboolean zmapWindowColumnIs3frameVisible(ZMapWindow window, FooCanvasGroup *col_
| TRUE | TRUE | 0 | 1 | 1 | 1 | 0 | 1 | 1 | 1 |
| FALSE | TRUE | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
*/
frame_sens[ZMAPSTRAND_NONE] = &none[0];
frame_sens[ZMAPSTRAND_FORWARD] = &forward[0];
frame_sens[ZMAPSTRAND_REVERSE] = &reverse[0];
frame_sens[ZMAPSTRAND_NONE][ZMAPFRAME_NONE] = TRUE;
frame_sens[ZMAPSTRAND_NONE][ZMAPFRAME_0] = FALSE;
frame_sens[ZMAPSTRAND_NONE][ZMAPFRAME_1] = FALSE;
frame_sens[ZMAPSTRAND_NONE][ZMAPFRAME_2] = FALSE;
frame_sens[ZMAPSTRAND_FORWARD][ZMAPFRAME_NONE] = (!display);
frame_sens[ZMAPSTRAND_FORWARD][ZMAPFRAME_0] = display;
frame_sens[ZMAPSTRAND_FORWARD][ZMAPFRAME_1] = display;
frame_sens[ZMAPSTRAND_FORWARD][ZMAPFRAME_2] = display;
frame_sens[ZMAPSTRAND_REVERSE][ZMAPFRAME_NONE] = ((!display) || (display && !show_on_reverse));
frame_sens[ZMAPSTRAND_REVERSE][ZMAPFRAME_0] = (display && show_on_reverse);
frame_sens[ZMAPSTRAND_REVERSE][ZMAPFRAME_1] = (display && show_on_reverse);
......@@ -428,7 +432,7 @@ gboolean zmapWindowColumnIs3frameVisible(ZMapWindow window, FooCanvasGroup *col_
case ZMAPSTYLE_3_FRAME_ONLY_3:
case ZMAPSTYLE_3_FRAME_ONLY_1:
set_strand = zmapWindowContainerFeatureSetGetStrand(container);
visible = frame_sens[set_strand][set_frame];
if(frame_mode == ZMAPSTYLE_3_FRAME_ONLY_1)
{
......@@ -481,7 +485,7 @@ gboolean zmapWindowColumnIsMagVisible(ZMapWindow window, FooCanvasGroup *col_gro
double curr_bases ;
curr_bases = zMapWindowGetZoomMagAsBases(window) ;
if (zmapWindowContainerFeatureSetGetMagValues((ZMapWindowContainerFeatureSet)col_group,
&min_mag, &max_mag))
{
......@@ -491,7 +495,7 @@ gboolean zmapWindowColumnIsMagVisible(ZMapWindow window, FooCanvasGroup *col_gro
visible = FALSE ;
}
}
}
return visible ;
......@@ -502,7 +506,7 @@ gboolean zmapWindowColumnIsMagVisible(ZMapWindow window, FooCanvasGroup *col_gro
/* These next two calls should be followed in the user's code
* by a call to zmapWindowNewReposition()...
* Doing
* Doing
* g_list_foreach(columns_to_hide, call_column_hide, NULL);
* zmapWindowNewReposition(window);
* Is a lot quicker than putting the Reposition call in these.
......@@ -542,7 +546,7 @@ void zmapWindowColumnsCompress(FooCanvasItem *column_item, ZMapWindow window, ZM
zMapAssertNotReached() ;
block_container = zmapWindowContainerUtilsGetParentLevel(column_container, ZMAPCONTAINER_LEVEL_BLOCK) ;
compressed = zmapWindowContainerBlockRemoveCompressedColumns((ZMapWindowContainerBlock)block_container);
bumped = zmapWindowContainerBlockRemoveBumpedColumns((ZMapWindowContainerBlock)block_container);
......@@ -570,10 +574,10 @@ void zmapWindowColumnsCompress(FooCanvasItem *column_item, ZMapWindow window, ZM
/* If there is no mark or user asked for visible area only then do that. */
if (compress_mode == ZMAPWINDOW_COMPRESS_VISIBLE)
{
zmapWindowItemGetVisibleCanvas(window,
zmapWindowItemGetVisibleCanvas(window,
&wx1, &wy1,
&wx2, &wy2) ;
/* should really clamp to seq. start/end..... */
coords.start = (int)wy1 ;
coords.end = (int)wy2 ;
......@@ -607,7 +611,7 @@ void zmapWindowColumnsCompress(FooCanvasItem *column_item, ZMapWindow window, ZM
* to do it.
*
* It does what zmapWindowFullReposition does, but in the same
* cycle of recursion as the user's. Most calls to
* cycle of recursion as the user's. Most calls to
* zmapWindowContainerExecuteFull which had TRUE for the last
* parameter were missing doing this...
*
......@@ -706,22 +710,22 @@ void zmapWindowDrawZoom(ZMapWindow window)
/* Some features have different widths according to their score, this helps annotators
* guage whether something like an alignment is worth taking notice of.
*
*
* Currently we only implement the algorithm given by acedb's Score_by_width but it maybe
* that we will need to do others to support their display.
*
* I've done this because for James Havana DBs all methods that mention score have:
*
* Score_by_width
* Score_by_width
* Score_bounds 70.000000 130.000000
*
* (the bounds are different for different data sources...)
*
*
* The interface is slightly tricky here in that we use the style->width to calculate
* width, not (x2 - x1), hence x2 is only used to return result.
*
*
*/
void zmapWindowGetPosFromScore(ZMapFeatureTypeStyle style,
void zmapWindowGetPosFromScore(ZMapFeatureTypeStyle style,
double score,
double *curr_x1_inout, double *curr_x2_out)
{
......@@ -764,7 +768,7 @@ void zmapWindowGetPosFromScore(ZMapFeatureTypeStyle style,
dx = 0.25 ;
else if (dx > 1)
dx = 1 ;
*curr_x1_inout = mid_way - (half_width * dx) ;
*curr_x2_out = mid_way + (half_width * dx) ;
}
......@@ -773,7 +777,7 @@ void zmapWindowGetPosFromScore(ZMapFeatureTypeStyle style,
}
void zmapWindowDrawSeparatorFeatures(ZMapWindow window,
void zmapWindowDrawSeparatorFeatures(ZMapWindow window,
ZMapFeatureBlock block,
ZMapFeatureSet feature_set,
ZMapFeatureTypeStyle style)
......@@ -791,11 +795,11 @@ void zmapWindowDrawSeparatorFeatures(ZMapWindow window,
/* need to copy the block, */
block_cp = (ZMapFeatureBlock)zMapFeatureAnyCopy((ZMapFeatureAny)block);
/* ... the alignment ... */
align = (ZMapFeatureAlignment)zMapFeatureGetParentGroup((ZMapFeatureAny)block,
align = (ZMapFeatureAlignment)zMapFeatureGetParentGroup((ZMapFeatureAny)block,
ZMAPFEATURE_STRUCT_ALIGN) ;
align_cp = (ZMapFeatureAlignment)zMapFeatureAnyCopy((ZMapFeatureAny)align);
/* ... and the context ... */
context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)align,
context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)align,
ZMAPFEATURE_STRUCT_CONTEXT) ;
context_cp = (ZMapFeatureContext)zMapFeatureAnyCopy((ZMapFeatureAny)context);
......@@ -826,7 +830,7 @@ void zmapWindowDrawSeparatorFeatures(ZMapWindow window,
"style '%s' in strand separator.",
zMapStyleGetName(style));
else
zMapLogWarning("Feature set '%s' has no style!",
zMapLogWarning("Feature set '%s' has no style!",
g_quark_to_string(feature_set->original_id));
return;
......@@ -834,7 +838,7 @@ void zmapWindowDrawSeparatorFeatures(ZMapWindow window,
/*
/*
* Internal routines.
*/
......@@ -891,7 +895,7 @@ static void printItem(FooCanvasItem *item, int indent, char *prefix)
/* We need the window in here.... */
/* GFunc to call on potentially all container groups.
*/
static void preZoomCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
static void preZoomCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data)
{
switch(level)
......@@ -921,15 +925,15 @@ static void set_hlocked_scroll_region(gpointer key, gpointer value, gpointer use
ZMapWindow window = (ZMapWindow)key;
FooCanvasPoints *box = (FooCanvasPoints *)user_data;
zmapWindowSetScrollRegion(window,
&box->coords[0], &box->coords[1],
zmapWindowSetScrollRegion(window,
&box->coords[0], &box->coords[1],
&box->coords[2], &box->coords[3]) ;
return ;
}
/* A version of zmapWindowResetWidth which uses the points from the recursion to set the width */
static gboolean resetWindowWidthCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
static gboolean resetWindowWidthCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data)
{
ZMapWindow window = NULL;
......@@ -940,18 +944,18 @@ static gboolean resetWindowWidthCB(ZMapWindowContainerGroup container, FooCanvas
window = (ZMapWindow)user_data ;
zMapAssert(level == ZMAPCONTAINER_LEVEL_ROOT);
zmapWindowGetScrollRegion(window, &x1, &y1, &x2, &y2);
scr_reg_width = x2 - x1 + 1.0 ;
root_width = points->coords[2] - points->coords[0] + 1.0 ;
if (((root_width != scr_reg_width) &&
if (((root_width != scr_reg_width) &&
(window->curr_locking != ZMAP_WINLOCK_HORIZONTAL)))
{
double excess ;
excess = root_width - scr_reg_width ;
/* the spacing should be a border width from somewhere. */
x2 = x2 + excess + window->config.strand_spacing;
......@@ -959,7 +963,7 @@ static gboolean resetWindowWidthCB(ZMapWindowContainerGroup container, FooCanvas
/* Annoyingly the initial size of the canvas is an issue here on first draw */
if(y2 == ZMAP_CANVAS_INIT_SIZE)
y2 = window->max_coord;
zmapWindowSetScrollRegion(window, &x1, &y1, &x2, &y2) ;
}
else if(((window->curr_locking == ZMAP_WINLOCK_HORIZONTAL) &&
......@@ -967,47 +971,47 @@ static gboolean resetWindowWidthCB(ZMapWindowContainerGroup container, FooCanvas
{
double excess ;
FooCanvasPoints *box;
excess = root_width - scr_reg_width ;
/* the spacing should be a border width from somewhere. */
x2 = x2 + excess + window->config.strand_spacing;
/* Annoyingly the initial size of the canvas is an issue here on first draw */
if(y2 == 100.0)
y2 = window->max_coord;
box = foo_canvas_points_new(2);
box->coords[0] = x1;
box->coords[1] = y1;
box->coords[2] = x2;
box->coords[3] = y2;
zmapWindowSetScrollRegion(window, &x1, &y1, &x2, &y2) ;
/* We need to make the horizontal split & locked windows have
* the maximum width so that _all_ the features are
* accessible. Test: bump a column, split window, bump column
* another few columns and check the windows are scroolable
* another few columns and check the windows are scroolable
* to the full extent of columns. */
g_hash_table_foreach(window->sibling_locked_windows,
set_hlocked_scroll_region, box);
foo_canvas_points_free(box);
}
return result;
}
/*
/*
* 3 Frame Display functions.
*
*
* 3 frame display is complex in that some columns should only be shown in "3 frame"
* mode, whereas others are shown as a single column normally and then as the three
* "frame" columns in "3 frame" mode. This involves deleting columns, moving them,
* recreating them etc.
*
*
*/
......@@ -1017,7 +1021,7 @@ static gboolean resetWindowWidthCB(ZMapWindowContainerGroup container, FooCanvas
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
/*
/*
* debug functions, please leave here for future use.
*/
......@@ -1061,7 +1065,7 @@ static void printQuarks(gpointer data, gpointer user_data)
/* GFunc to call on potentially all container groups.
*/
static void hideColsCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
static void hideColsCB(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data)
{
VisCoords coord_data = (VisCoords)user_data ;
......@@ -1086,7 +1090,7 @@ static void hideColsCB(ZMapWindowContainerGroup container, FooCanvasPoints *poin
feature_set = zmapWindowContainerGetFeatureSet(container);
zMapAssert(feature_set);
if (!(coord_data->in_view)
&& (coord_data->compress_mode == ZMAPWINDOW_COMPRESS_VISIBLE
|| zmapWindowContainerFeatureSetGetDisplay((ZMapWindowContainerFeatureSet)container) != ZMAPSTYLE_COLDISPLAY_SHOW))
......@@ -1221,7 +1225,7 @@ static ZMapFeatureContextExecuteStatus draw_separator_features(GQuark key_id,
{
FooCanvasItem *align_hash_item;
canvas_data->curr_alignment =
canvas_data->curr_alignment =
zMapFeatureContextGetAlignmentByID(canvas_data->full_context,
feature_any->unique_id);
if((align_hash_item = zmapWindowFToIFindItemFull(window->context_to_item,
......@@ -1244,7 +1248,7 @@ static ZMapFeatureContextExecuteStatus draw_separator_features(GQuark key_id,
case ZMAPFEATURE_STRUCT_BLOCK:
{
FooCanvasItem *block_hash_item;
canvas_data->curr_block =
canvas_data->curr_block =
zMapFeatureAlignmentGetBlockByID(canvas_data->curr_alignment,
feature_any->unique_id);
......@@ -1260,9 +1264,9 @@ static ZMapFeatureContextExecuteStatus draw_separator_features(GQuark key_id,
block_parent = (ZMapWindowContainerGroup)(block_hash_item);
canvas_data->curr_block_group =
canvas_data->curr_block_group =
zmapWindowContainerGetFeatures(block_parent);
forward_strand = zmapWindowContainerBlockGetContainerStrand((ZMapWindowContainerBlock)block_parent,
ZMAPSTRAND_FORWARD);
canvas_data->curr_forward_group = zmapWindowContainerGetFeatures((ZMapWindowContainerGroup)forward_strand);
......@@ -1274,7 +1278,7 @@ static ZMapFeatureContextExecuteStatus draw_separator_features(GQuark key_id,
case ZMAPFEATURE_STRUCT_FEATURESET:
{
FooCanvasGroup *tmp_forward, *separator;
canvas_data->curr_set = zMapFeatureBlockGetSetByID(canvas_data->curr_block,
feature_any->unique_id);
if (zmapWindowCreateSetColumns(window,
......
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