void gt_graphics_cairo_draw_caret(GtGraphics *gg, double x, double y,
double width,double height,
ArrowStatus arrow_status, double arrow_width,
double stroke_width, GtColor stroke_color)
{
GtGraphicsCairo *g = gt_graphics_cairo_cast(gg);
gt_assert(g);
/* save cairo context */
cairo_save(g->cr);
cairo_rectangle(g->cr, g->margin_x, g->margin_y,
g->width-2*g->margin_x, g->height-2*g->margin_y);
cairo_clip(g->cr);
/* create caret path */
switch (arrow_status)
{
case ARROW_RIGHT:
if (gt_double_smaller_double(0, width - arrow_width))
{
width -= arrow_width;
cairo_move_to(g->cr, x, y + (height/2));
cairo_line_to(g->cr, x + (width/2), y);
cairo_line_to(g->cr, x + width, y + (height/2));
cairo_line_to(g->cr, x + width + arrow_width, y + (height/2));
/* add arrowhead */
cairo_move_to(g->cr, x + width, y);
cairo_line_to(g->cr, x + width + arrow_width, y + height / 2);
cairo_line_to(g->cr, x + width, y + height);
}
break;
case ARROW_LEFT:
if (gt_double_smaller_double(0, width - arrow_width))
{
width -= arrow_width;
/* draw arrowhead */
cairo_move_to(g->cr, x + arrow_width , y);
cairo_line_to(g->cr, x, y + (height/2));
cairo_line_to(g->cr, x + arrow_width, y + height);
cairo_move_to(g->cr, x, y + (height/2));
cairo_line_to(g->cr, x + arrow_width, y + (height/2));
cairo_line_to(g->cr, x + arrow_width + (width/2), y);
cairo_line_to(g->cr, x + arrow_width + width, y + (height/2));
}
break;
case ARROW_BOTH: /* XXX */
case ARROW_NONE:
cairo_move_to(g->cr, x, y + (height/2));
cairo_line_to(g->cr, x + (width/2), y);
cairo_line_to(g->cr, x + width, y + (height/2));
}
/* draw caret */
cairo_set_line_width(g->cr, stroke_width);
cairo_set_source_rgba(g->cr, stroke_color.red,
stroke_color.green,
stroke_color.blue,
stroke_color.alpha);
cairo_stroke(g->cr);
/* restore cairo context */
cairo_restore(g->cr);
}
int calculate_drawing_range(GtLineBreakerCaptions *lbc, GtDrawingRange *rng,
GtBlock* block, GtError *err)
{
double textwidth = 0.0;
GtDrawingRange drange;
gt_assert(block && lbc);
drange = gt_coords_calc_generic_range(gt_block_get_range(block),
gt_layout_get_range(lbc->layout));
drange.start *= lbc->width-2*lbc->margins;
drange.end *= lbc->width-2*lbc->margins;
if (gt_block_get_caption(block))
{
textwidth = gt_text_width_calculator_get_text_width(
gt_layout_get_twc(lbc->layout),
gt_str_get(gt_block_get_caption(block)),
err);
if (gt_double_smaller_double(textwidth, 0))
return -1;
if (gt_double_smaller_double(gt_drawing_range_length(drange), textwidth))
drange.end = drange.start + textwidth;
}
rng->start = drange.start;
rng->end = drange.end;
return 0;
}
int gt_drawing_range_compare(GtDrawingRange range_a, GtDrawingRange range_b)
{
gt_assert(range_a.start <= range_a.end && range_b.start <= range_b.end);
if (gt_double_equals_double(range_a.start, range_b.start) &&
gt_double_equals_double(range_a.end, range_b.end))
return 0; /* range_a == range_b */
if (gt_double_smaller_double(range_a.start, range_b.start) ||
(gt_double_equals_double(range_a.start, range_b.start)
&& gt_double_smaller_double(range_a.end, range_b.end)))
return -1; /* range_a < range_b */
return 1; /* range_a > range_b */
}
void gt_graphics_cairo_draw_dashes(GtGraphics *gg, double x, double y,
double width, double height,
ArrowStatus arrow_status, double arrow_width,
double stroke_width, GtColor stroke_color)
{
GtGraphicsCairo *g = gt_graphics_cairo_cast(gg);
double dashes[] = {2.0};
gt_assert(g);
/* save cairo context */
cairo_save(g->cr);
cairo_rectangle(g->cr, g->margin_x, g->margin_y,
g->width-2*g->margin_x, g->height-2*g->margin_y);
cairo_clip(g->cr);
cairo_set_line_width(g->cr, stroke_width);
cairo_set_source_rgba(g->cr, stroke_color.red,
stroke_color.green,
stroke_color.blue,
stroke_color.alpha);
/* create arrowhead path */
if (gt_double_smaller_double(0, width - arrow_width))
{
switch (arrow_status)
{
case ARROW_RIGHT:
cairo_move_to(g->cr, rnd_to_nhalf(x + width - arrow_width), y);
cairo_line_to(g->cr, rnd_to_nhalf(x + width), y + height / 2);
cairo_line_to(g->cr, rnd_to_nhalf(x + width - arrow_width), y + height);
/* draw arrowhead */
cairo_stroke(g->cr);
break;
case ARROW_LEFT:
cairo_move_to(g->cr, rnd_to_nhalf(x + arrow_width), y);
cairo_line_to(g->cr, rnd_to_nhalf(x), y + height / 2);
cairo_line_to(g->cr, rnd_to_nhalf(x + arrow_width), y + height);
/* draw arrowhead */
cairo_stroke(g->cr);
break;
case ARROW_BOTH:
cairo_move_to(g->cr, rnd_to_nhalf(x + width - arrow_width), y);
cairo_line_to(g->cr, rnd_to_nhalf(x + width), y + height / 2);
cairo_line_to(g->cr, rnd_to_nhalf(x + width - arrow_width), y + height);
cairo_move_to(g->cr, rnd_to_nhalf(x + arrow_width), y);
cairo_line_to(g->cr, rnd_to_nhalf(x), y + height / 2);
cairo_line_to(g->cr, rnd_to_nhalf(x + arrow_width), y + height);
cairo_stroke(g->cr);
break;
case ARROW_NONE: break;
}
}
/* draw dashes */
cairo_set_dash(g->cr, dashes, 1, (double) 0);
cairo_move_to(g->cr, rnd_to_nhalf(x), rnd_to_nhalf(y+(height/2)));
cairo_rel_line_to(g->cr, rnd_to_nhalf(width), 0);
cairo_stroke(g->cr);
/* restore cairo context */
cairo_restore(g->cr);
}
int gt_mathsupport_unit_test(GtError *err)
{
int had_err = 0;
double less_than_epsilon = 0.0000000000000001;
gt_error_check(err);
gt_ensure(had_err, !gt_double_equals_one(1.1));
gt_ensure(had_err, gt_double_equals_one(1));
gt_ensure(had_err, gt_double_equals_one(1+less_than_epsilon));
gt_ensure(had_err, !gt_double_equals_one(-1-less_than_epsilon));
gt_ensure(had_err, !gt_double_equals_double(1.0, 2.0));
gt_ensure(had_err, !gt_double_equals_double(-1.0, 1.0));
gt_ensure(had_err, !gt_double_equals_double(1.0, -1.0));
gt_ensure(had_err, !gt_double_equals_double(-1.0, 1+less_than_epsilon));
gt_ensure(had_err, !gt_double_equals_double(1.0, 1.1));
gt_ensure(had_err, gt_double_equals_double(1.0, 1+less_than_epsilon));
gt_ensure(had_err, gt_double_equals_double(1.0, 1.0));
gt_ensure(had_err, gt_double_equals_double(0.0, 0.0));
gt_ensure(had_err, gt_double_equals_double(-1.0, -1.0));
gt_ensure(had_err, gt_double_equals_double(-1.0+less_than_epsilon, -1.0));
gt_ensure(had_err, gt_double_equals_double(-1.0, -1.0+less_than_epsilon));
gt_ensure(had_err, gt_double_equals_double(1.0+less_than_epsilon, 1.0));
gt_ensure(had_err, gt_double_equals_double(1.0, 1.0+less_than_epsilon));
gt_ensure(had_err, gt_double_compare(1.0, 1.0) == 0);
gt_ensure(had_err, gt_double_compare(1.0, 1.1) < 0);
gt_ensure(had_err, gt_double_compare(1.1, 1.0) > 0);
gt_ensure(had_err, gt_double_compare(1.1, -1.0) > 0);
gt_ensure(had_err, gt_double_compare(-1.1, -1.0) < 0);
gt_ensure(had_err, gt_double_compare(1+less_than_epsilon, 1.0) == 0);
gt_ensure(had_err, gt_double_compare(1+less_than_epsilon, -1.0) > 0);
gt_ensure(had_err, gt_double_compare(-1+less_than_epsilon, -1.0) == 0);
gt_ensure(had_err, gt_double_compare(-1+less_than_epsilon, 1.0) < 0);
gt_ensure(had_err, gt_double_smaller_double(1.0, 1.1));
gt_ensure(had_err, gt_double_smaller_double(-1.0, 1.1));
gt_ensure(had_err, gt_double_smaller_double(-1.1, -1.0));
gt_ensure(had_err, !gt_double_smaller_double(-1.0, -1.1));
gt_ensure(had_err, !gt_double_smaller_double(1.0-less_than_epsilon, 1.0));
return had_err;
}
void gt_graphics_cairo_draw_curve_data(GtGraphics *gg, double x, double y,
GtColor color, double data[],
unsigned long ndata, GtRange valrange,
unsigned long height)
{
unsigned long i, rnglen;
double xpos;
GtGraphicsCairo *g;
g = gt_graphics_cairo_cast(gg);
xpos = (((double)g->width-2*g->margin_x)/((double)ndata-1));
rnglen = valrange.end - valrange.start;
cairo_save(g->cr);
cairo_move_to(g->cr,
x,
y+(1-(data[0]-valrange.start)/(double) rnglen)*height);
for (i=1;i<ndata;i++)
{
double val, pval;
if (gt_double_smaller_double(data[i], valrange.start)
|| gt_double_smaller_double(valrange.end, data[i]))
break;
val = (double) (data[i]-valrange.start)/(double) rnglen;
pval = (double) (data[i-1]-valrange.start)/(double) rnglen;
gt_assert(val <= 1 && val >= 0 && pval >= 0 && pval <= 1);
cairo_curve_to(g->cr,
x + ((i-0.5) * xpos),
y + (1-pval) * height,
x + ((i-0.5) * xpos),
y + (1-val) * height,
x + (i * xpos),
y + (1-val) * height);
}
cairo_set_source_rgba(g->cr, color.red,
color.green,
color.blue,
color.alpha);
cairo_stroke(g->cr);
cairo_restore(g->cr);
}
void gt_graphics_cairo_draw_text(GtGraphics *gg, double x, double y,
const char *text)
{
GtGraphicsCairo *g = gt_graphics_cairo_cast(gg);
cairo_text_extents_t ext;
gt_assert(g && text);
cairo_text_extents(g->cr, text, &ext);
if (gt_double_smaller_double(g->width, x+ext.width))
return;
cairo_set_source_rgb(g->cr, 0, 0, 0);
cairo_move_to(g->cr, x, y);
cairo_show_text(g->cr, text);
}
double gt_graphics_cairo_get_text_width(GtGraphics *gg, const char* text)
{
PangoRectangle rect;
GtGraphicsCairo *g = gt_graphics_cairo_cast(gg);
gt_assert(g && text && g->layout);
pango_layout_set_text(g->layout, text, -1);
/* get text extents */
pango_layout_get_pixel_extents(g->layout, &rect, NULL);
gt_assert(gt_double_smaller_double(0, rect.width));
return rect.width;
}
/* calculate divergence */
double gt_divergence(double E, /* relative error for divergence calculation */
double T, /* absolute error for exp shulen*/
double M, /* minimum for logarithm */
double threshold, /* abs error for divergence */
double shulen,
GtUword subjectLength,
double gc,
double *ln_n_fac,
GtUword n_s)
{
double p, q,
du, dl, dm, d, exp_shulen;
double *s1;
s1 = gt_calloc((size_t) n_s + 1, sizeof (double));
p = gc / 2;
q = (1.0 - gc) / 2.0;
du = 0.0;
dl = 1.0 - (2 * p * p + 2 * q * q); /* dl < 0.75 */
while (gt_double_smaller_double(threshold, (dl - du) / 2.0)) {
dm = (du + dl) / 2.0;
exp_shulen = expShulen(T, M, dm, p, subjectLength, ln_n_fac, s1, n_s);
if (gt_double_smaller_double(shulen, exp_shulen))
du = dm;
else
dl = dm;
/* test the relative error between du and dl; if it is smaller than some
* threshold, then break !! */
if (fabs (dl - du) / dl <= E)
break;
}
d = (du + dl) / 2.0;
gt_free(s1);
return d;
}
static int check_width(unsigned int width,
GtStyle *style,
GtError *err)
{
int had_err = 0;
double margins = MARGINS_DEFAULT;
(void) gt_style_get_num(style, "format", "margins", &margins, NULL);
if (gt_double_smaller_double(width - 2*margins, 0))
{
gt_error_set(err, "layout width must at least be twice the x-margin size "
"(2*%.1f=%.1f) but was %u",
margins,
2*margins,
width);
had_err = -1;
}
return had_err;
}
void gt_graphics_cairo_draw_text(GtGraphics *gg, double x, double y,
const char *text)
{
PangoRectangle ink;
GtGraphicsCairo *g = gt_graphics_cairo_cast(gg);
gt_assert(g && text && g->layout);
pango_layout_set_text(g->layout, text, -1);
/* get text extents */
pango_layout_get_pixel_extents(g->layout, &ink, NULL);
if (gt_double_smaller_double(g->width, x+ink.width))
return;
cairo_set_source_rgb(g->cr, 0, 0, 0);
cairo_move_to(g->cr, x, y-g->font_height);
pango_cairo_show_layout(g->cr, g->layout);
}
double gt_text_width_calculator_cairo_get_text_width(GtTextWidthCalculator *twc,
const char *text,
GT_UNUSED GtError *err)
{
GtTextWidthCalculatorCairo *twcc;
PangoRectangle rect;
gt_assert(twc && text);
twcc = gt_text_width_calculator_cairo_cast(twc);
/* redo layout */
pango_layout_set_text(twcc->layout, text, -1);
/* get extents */
pango_layout_get_pixel_extents(twcc->layout, &rect, NULL);
if (twcc->style)
cairo_restore(twcc->context);
gt_assert(gt_double_smaller_double(0, rect.width));
return rect.width;
}
/* This function orders GtElements by z-index or type. This enables the sketch
function to paint elements in a specific order based on their type
(painter's algorithm-like) */
static int elemcmp(const void *a, const void *b, void *data)
{
const char *type_a, *type_b;
double zindex_a = GT_UNDEF_DOUBLE, zindex_b= GT_UNDEF_DOUBLE;
GtStyle *sty = (GtStyle*) data;
GtElement *elem_a = *(GtElement**) a;
GtElement *elem_b = *(GtElement**) b;
type_a = gt_element_get_type(elem_a);
type_b = gt_element_get_type(elem_b);
/* same types are equal, no further action needed */
if (type_a == type_b)
return 0;
/* if not, then get z-index from style */
if (sty)
{
(void) gt_style_get_num(sty, type_a, "z_index", &zindex_a, NULL, NULL);
(void) gt_style_get_num(sty, type_b, "z_index", &zindex_b, NULL, NULL);
}
/* only one is set -> put types with set z-indices always on top of others*/
if (zindex_a == GT_UNDEF_DOUBLE && zindex_b != GT_UNDEF_DOUBLE)
return -1;
if (zindex_b == GT_UNDEF_DOUBLE && zindex_a != GT_UNDEF_DOUBLE)
return 1;
/* none is set, fall back to default alphabetic ordering */
if (zindex_a == GT_UNDEF_DOUBLE && zindex_b == GT_UNDEF_DOUBLE)
{
if (strcmp(type_a, type_b) < 0)
return 1;
return -1;
}
/* both z-indices are set */
if (gt_double_equals_double(zindex_a, zindex_b))
return 0;
if (gt_double_smaller_double(zindex_a, zindex_b))
return -1;
return 1;
}
int gt_block_get_max_height(const GtBlock *block, double *result,
const GtStyle *sty, GtError *err)
{
GtUword max_height = 0;
GtStyleQueryStatus rval = GT_STYLE_QUERY_OK;
GtUword i;
gt_assert(block && sty);
for (i=0;i<gt_array_size(block->elements);i++) {
GtElement *elem;
double height = 0;
elem = *(GtElement**) gt_array_get(block->elements, i);
/* get default or image-wide bar height */
rval = gt_style_get_num(sty, "format", "bar_height", &height, NULL, err);
switch (rval) {
case GT_STYLE_QUERY_ERROR:
return -1;
break; /* should never reach this */
case GT_STYLE_QUERY_NOT_SET:
height = BAR_HEIGHT_DEFAULT;
break;
default:
/* do nothing */
break;
}
/* try to get type-specific bar height */
rval = gt_style_get_num(sty, gt_element_get_type(elem), "bar_height",
&height, gt_element_get_node_ref(elem),
err);
if (rval == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_double_smaller_double(max_height, height))
max_height = height;
}
*result = max_height;
return 0;
}
void gt_firstcodes_spacelog_add(GtFirstcodesspacelog *fcsl,
int line,
const char *filename,
bool add,
const char *title,
bool work,
size_t size)
{
GtFirstcodespacelogentry *entry;
size_t logspace;
if (add)
{
entry = gt_spacelog_find(fcsl,title);
if (entry != NULL)
{
if (entry->size != 0)
{
fprintf(stderr,"existing entry for title \"%s\""
"(from file %s, line %d) "
"in spacelog entries must have size 0\n",
title,filename,line);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
gt_spacelog_updateaddentry(entry,filename,line,title,size,work);
} else
{
gt_spacelog_addentry(fcsl,filename,line,title,size,work);
}
if (work)
{
fcsl->workspace += size;
} else
{
fcsl->splitspace += size;
}
gt_firstcodes_updatemax(fcsl);
} else
{
entry = gt_spacelog_find(fcsl,title);
if (entry == NULL)
{
fprintf(stderr,"cannot find title \"%s\" (from file %s, line %d) "
"in spacelog entries\n",title,filename,line);
(void) gt_firstcodes_spacelog_showentries(stderr,fcsl);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
if ((entry->work && !work) || (!entry->work && work))
{
fprintf(stderr,"for title \"%s\" (from file %s, line %d) "
"in spacelog entries: inconsistent work/splitassignment\n",
title,filename,line);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
if (work)
{
if (entry->size > fcsl->workspace)
{
gt_firstcodes_subtract_error(title, filename, line, entry->size, true,
fcsl->workspace);
(void) gt_firstcodes_spacelog_showentries(stderr,fcsl);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
fcsl->workspace -= entry->size;
} else
{
if (entry->size > fcsl->splitspace)
{
gt_firstcodes_subtract_error(title, filename, line, entry->size, false,
fcsl->splitspace);
(void) gt_firstcodes_spacelog_showentries(stderr,fcsl);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
fcsl->splitspace -= entry->size;
}
if (size > 0)
{
gt_spacelog_updateaddentry(entry,filename,line,title,size,work);
if (work)
{
fcsl->workspace += size;
} else
{
fcsl->splitspace += size;
}
gt_firstcodes_updatemax(fcsl);
if (size > entry->size)
{
add = true;
size -= entry->size;
} else
{
size = entry->size - size;
}
} else
{
size = entry->size;
entry->size = 0;
}
}
logspace = fcsl->workspace+fcsl->splitspace;
gt_log_log(
#ifdef SKDEBUG
"file %s, line %d: "
#endif
"%s %s= %.2f, %s, w=%.2f, s=%.2f, sum=%.2f MB",
#ifdef SKDEBUG
filename,
line,
#endif
work ? "w" : "s",
add ? "+" : "-",
GT_MEGABYTES(size),
title,
GT_MEGABYTES(fcsl->workspace),
GT_MEGABYTES(fcsl->splitspace),
GT_MEGABYTES(logspace));
#ifdef SKDEBUG
if (gt_ma_bookkeeping_enabled())
{
unsigned long realspace = gt_ma_get_space_current() +
gt_fa_get_space_current();
gt_log_log("current space usage %.2f MB (%.2f+%.2f)",
GT_MEGABYTES(realspace),
GT_MEGABYTES(gt_ma_get_space_current()),
GT_MEGABYTES(gt_fa_get_space_current()));
if (fcsl->calc_difference)
{
double percent_difference;
if ((unsigned long) logspace > realspace)
{
fprintf(stderr,"overestimating logspace\n");
exit(GT_EXIT_PROGRAMMING_ERROR);
}
if (realspace >= 1000000UL)
{
/*
printf("realspace=%lu,logspace=%lu\n",realspace,
(unsigned long) logspace);
*/
percent_difference = 100.0 * (double) (realspace - logspace)/realspace;
if (gt_double_larger_double(percent_difference,3.0))
{
fprintf(stderr,"space difference of %.2f%% is too large\n",
percent_difference);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
if (gt_double_smaller_double(fcsl->max_percent_difference,
percent_difference))
{
fcsl->max_percent_difference = percent_difference;
}
}
}
}
#endif
}
int gt_canvas_cairo_visit_block(GtCanvas *canvas, GtBlock *block,
GtError *err)
{
int had_err = 0, arrow_status = ARROW_NONE;
GtRange block_range;
GtDrawingRange draw_range;
GtColor grey, fillcolor, strokecolor;
double block_start,
block_width,
bar_height = BAR_HEIGHT_DEFAULT,
min_len_block = MIN_LEN_BLOCK_DEFAULT,
arrow_width = ARROW_WIDTH_DEFAULT,
stroke_width = STROKE_WIDTH_DEFAULT;
const char *caption, *btype;
GtStrand strand;
double maxbarheight;
btype = gt_block_get_type(block);
gt_assert(canvas && block);
grey.red = grey.green = grey.blue = DEFAULT_GREY_TONE;
grey.alpha = 0.5;
strand = gt_block_get_strand(block);
block_range = gt_block_get_range(block);
if (gt_block_get_max_height(block, &maxbarheight, canvas->pvt->sty, err)) {
return -1;
}
if (gt_style_get_num(canvas->pvt->sty, "format", "bar_height", &bar_height,
NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_num(canvas->pvt->sty, "format", "min_len_block",
&min_len_block,NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_num(canvas->pvt->sty, "format", "arrow_width", &arrow_width,
NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_num(canvas->pvt->sty, "format", "stroke_width",
&stroke_width, NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_color_with_track(canvas->pvt->sty,
btype, "stroke", &strokecolor,
gt_block_get_top_level_feature(block),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (strand == GT_STRAND_REVERSE || strand == GT_STRAND_BOTH)
arrow_status = ARROW_LEFT;
if (strand == GT_STRAND_FORWARD || strand == GT_STRAND_BOTH)
arrow_status = (arrow_status == ARROW_LEFT ? ARROW_BOTH : ARROW_RIGHT);
/* calculate scaled drawing coordinates for this canvas */
draw_range = gt_coords_calc_generic_range(block_range,
canvas->pvt->viewrange);
draw_range.start *= canvas->pvt->width-2*canvas->pvt->margins;
draw_range.end *= canvas->pvt->width-2*canvas->pvt->margins;
block_start = draw_range.start + canvas->pvt->margins;
block_width = draw_range.end - draw_range.start;
/* draw block caption */
if (gt_block_caption_is_visible(block))
{
caption = gt_str_get(gt_block_get_caption(block));
if (caption)
{
double theight = gt_graphics_get_text_height(canvas->pvt->g),
captionspace = CAPTION_BAR_SPACE_DEFAULT;
if (gt_style_get_num(canvas->pvt->sty,
"format", "block_caption_space",
&captionspace, NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_num(canvas->pvt->sty,
"format", "block_caption_font_size",
&theight, NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
gt_graphics_set_font(canvas->pvt->g,
"Sans",
SLANT_NORMAL,
WEIGHT_NORMAL,
theight);
gt_graphics_draw_text_clip(canvas->pvt->g,
block_start,
canvas->pvt->y - bar_height/2
- captionspace,
caption);
}
}
/* do not draw further details in very small blocks */
if (!gt_block_has_only_one_fullsize_element(block)
&& gt_double_smaller_double(block_width, min_len_block))
{
/* optimise drawing for very narrow blocks,
if <= 1px/pt width, draw as simple lines */
if (canvas->pvt->bt && draw_range.end-draw_range.start <= 1.1)
{
if (!gt_bittab_bit_is_set(canvas->pvt->bt,
(unsigned long) draw_range.start)) {
gt_graphics_draw_vertical_line(canvas->pvt->g,
block_start,
canvas->pvt->y - bar_height/2,
strokecolor,
bar_height,
stroke_width);
gt_bittab_set_bit(canvas->pvt->bt, (unsigned long) draw_range.start);
}
} else {
if (gt_style_get_color_with_track(canvas->pvt->sty,
btype, "fill",
&fillcolor,
gt_block_get_top_level_feature(block),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
gt_graphics_draw_box(canvas->pvt->g,
block_start,
canvas->pvt->y - bar_height/2,
block_width,
bar_height,
fillcolor,
arrow_status,
arrow_width,
stroke_width,
strokecolor,
true);
/* draw arrowheads at clipped margins */
if (draw_range.clip == CLIPPED_LEFT || draw_range.clip == CLIPPED_BOTH)
gt_graphics_draw_arrowhead(canvas->pvt->g,
canvas->pvt->margins - 10,
canvas->pvt->y - 4,
grey,
ARROW_LEFT);
if (draw_range.clip == CLIPPED_RIGHT || draw_range.clip == CLIPPED_BOTH)
gt_graphics_draw_arrowhead(canvas->pvt->g,
canvas->pvt->width-canvas->pvt->margins
+ 10,
canvas->pvt->y - 4,
grey,
ARROW_RIGHT);
}
/* register coordinates in GtImageInfo object if available */
if (canvas->pvt->ii)
{
GtRecMap *rm = gt_rec_map_new(block_start,
canvas->pvt->y - bar_height/2,
block_start + block_width,
canvas->pvt->y + bar_height/2,
(GtFeatureNode*) /* XXX */
gt_block_get_top_level_feature(block));
gt_image_info_add_rec_map(canvas->pvt->ii, rm);
gt_rec_map_set_omitted_children(rm, true);
}
/* signal break */
return 1;
}
/* get stroke color */
if (gt_style_get_color(canvas->pvt->sty,
"format", "default_stroke_color",
&strokecolor, NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
/* draw parent block boundaries */
gt_graphics_draw_dashes(canvas->pvt->g,
block_start,
canvas->pvt->y - bar_height/2,
block_width,
bar_height,
ARROW_NONE,
arrow_width,
stroke_width,
strokecolor);
return had_err;
}
void gt_graphics_cairo_draw_box(GtGraphics *gg, double x, double y,
double width, double height,
GtColor fill_color, ArrowStatus arrow_status,
double arrow_width, double stroke_width,
GtColor stroke_color, bool dashed)
{
GtGraphicsCairo *g = gt_graphics_cairo_cast(gg);
double dashes[]={2.0};
bool widthdiff_geq0;
gt_assert(g);
/* save cairo context */
cairo_save(g->cr);
cairo_rectangle(g->cr, rnd_to_nhalf(g->margin_x), g->margin_y,
rnd_to_nhalf(g->width-2*g->margin_x),
g->height-2*g->margin_y);
cairo_clip(g->cr);
widthdiff_geq0 = gt_double_smaller_double(0, width - arrow_width);
/* construct shape of the box or arrow */
switch (arrow_status)
{
case ARROW_RIGHT:
cairo_move_to(g->cr, rnd_to_nhalf(x), rnd_to_nhalf(y));
if (widthdiff_geq0)
cairo_line_to(g->cr, x + width - arrow_width, rnd_to_nhalf(y));
cairo_line_to(g->cr, rnd_to_nhalf(x + width),
rnd_to_nhalf(y + height / 2));
if (widthdiff_geq0)
cairo_line_to(g->cr, x + width - arrow_width, rnd_to_nhalf(y + height));
cairo_line_to(g->cr, rnd_to_nhalf(x), rnd_to_nhalf(y + height));
cairo_close_path(g->cr);
break;
case ARROW_LEFT:
cairo_move_to(g->cr, rnd_to_nhalf(x + width), rnd_to_nhalf(y));
if (widthdiff_geq0) {
cairo_line_to(g->cr, rnd_to_nhalf(x + arrow_width), rnd_to_nhalf(y));
}
cairo_line_to(g->cr, rnd_to_nhalf(x), rnd_to_nhalf(y + height / 2));
if (widthdiff_geq0) {
cairo_line_to(g->cr, rnd_to_nhalf(x + arrow_width),
rnd_to_nhalf(y + height));
}
cairo_line_to(g->cr, rnd_to_nhalf(x + width), rnd_to_nhalf(y + height));
cairo_close_path(g->cr);
break;
case ARROW_BOTH:
cairo_move_to(g->cr, rnd_to_nhalf(x), rnd_to_nhalf(y + height/2));
if (gt_double_smaller_double(width, 2*arrow_width))
{
cairo_line_to(g->cr, rnd_to_nhalf(x + width/2), rnd_to_nhalf(y));
cairo_line_to(g->cr, rnd_to_nhalf(x + width),
rnd_to_nhalf(y + height/2));
cairo_line_to(g->cr, rnd_to_nhalf(x + width/2),
rnd_to_nhalf(y + height));
}
else
{
cairo_line_to(g->cr, rnd_to_nhalf(x + arrow_width), rnd_to_nhalf(y));
cairo_line_to(g->cr, rnd_to_nhalf(x + width - arrow_width),
rnd_to_nhalf(y));
cairo_line_to(g->cr, rnd_to_nhalf(x + width),
rnd_to_nhalf(y + height/2));
cairo_line_to(g->cr, rnd_to_nhalf(x + width - arrow_width),
rnd_to_nhalf(y + height));
cairo_line_to(g->cr, rnd_to_nhalf(x + arrow_width), y + height);
}
cairo_close_path(g->cr);
break;
case ARROW_NONE:
cairo_rectangle(g->cr, rnd_to_nhalf(x), rnd_to_nhalf(y), width, height);
}
/* fill area */
cairo_set_source_rgba(g->cr, fill_color.red,
fill_color.green,
fill_color.blue,
fill_color.alpha);
cairo_fill_preserve(g->cr);
/* draw outline */
cairo_set_line_width(g->cr, stroke_width);
cairo_set_source_rgba(g->cr, stroke_color.red,
stroke_color.green,
stroke_color.blue,
stroke_color.alpha);
if (dashed)
cairo_set_dash(g->cr, dashes, 1, (double) 0);
cairo_stroke(g->cr);
/* restore cairo context */
cairo_restore(g->cr);
}
static int gt_sketch_page_runner(GT_UNUSED int argc,
const char **argv,
int parsed_args,
void *tool_arguments,
GtError *err)
{
SketchPageArguments *arguments = tool_arguments;
int had_err = 0;
GtFeatureIndex *features = NULL;
GtRange qry_range, sequence_region_range;
GtStyle *sty = NULL;
GtStr *prog, *gt_style_file;
GtDiagram *d = NULL;
GtLayout *l = NULL;
GtBioseq *bioseq = NULL;
GtCanvas *canvas = NULL;
const char *seqid = NULL, *outfile;
unsigned long start, height, num_pages = 0;
double offsetpos, usable_height;
cairo_surface_t *surf = NULL;
cairo_t *cr = NULL;
GtTextWidthCalculator *twc;
gt_error_check(err);
features = gt_feature_index_memory_new();
if (cairo_version() < CAIRO_VERSION_ENCODE(1, 8, 6))
gt_warning("Your cairo library (version %s) is older than version 1.8.6! "
"These versions contain a bug which may result in "
"corrupted PDF output!", cairo_version_string());
/* get style */
sty = gt_style_new(err);
if (gt_str_length(arguments->stylefile) == 0)
{
prog = gt_str_new();
gt_str_append_cstr_nt(prog, argv[0],
gt_cstr_length_up_to_char(argv[0], ' '));
gt_style_file = gt_get_gtdata_path(gt_str_get(prog), err);
gt_str_delete(prog);
gt_str_append_cstr(gt_style_file, "/sketch/default.style");
}
else
{
gt_style_file = gt_str_ref(arguments->stylefile);
}
had_err = gt_style_load_file(sty, gt_str_get(gt_style_file), err);
outfile = argv[parsed_args];
if (!had_err)
{
/* get features */
had_err = gt_feature_index_add_gff3file(features, argv[parsed_args+1], err);
if (!had_err && gt_str_length(arguments->seqid) == 0) {
seqid = gt_feature_index_get_first_seqid(features);
if (seqid == NULL)
{
gt_error_set(err, "GFF input file must contain a sequence region!");
had_err = -1;
}
}
else if (!had_err
&& !gt_feature_index_has_seqid(features,
gt_str_get(arguments->seqid)))
{
gt_error_set(err, "sequence region '%s' does not exist in GFF input file",
gt_str_get(arguments->seqid));
had_err = -1;
}
else if (!had_err)
seqid = gt_str_get(arguments->seqid);
}
/* set text */
if (gt_str_length(arguments->text) == 0)
{
gt_str_delete(arguments->text);
arguments->text = gt_str_new_cstr(argv[parsed_args+1]);
}
if (!had_err)
{
/* set display range */
gt_feature_index_get_range_for_seqid(features, &sequence_region_range,
seqid);
qry_range.start = (arguments->range.start == GT_UNDEF_ULONG ?
sequence_region_range.start :
arguments->range.start);
qry_range.end = (arguments->range.end == GT_UNDEF_ULONG ?
sequence_region_range.end :
arguments->range.end);
/* set output format */
if (strcmp(gt_str_get(arguments->format), "pdf") == 0)
{
surf = cairo_pdf_surface_create(outfile,
mm_to_pt(arguments->pwidth),
mm_to_pt(arguments->pheight));
}
else if (strcmp(gt_str_get(arguments->format), "ps") == 0)
{
surf = cairo_ps_surface_create(outfile,
mm_to_pt(arguments->pwidth),
mm_to_pt(arguments->pheight));
}
gt_log_log("created page with %.2f:%.2f dimensions\n",
mm_to_pt(arguments->pwidth),
mm_to_pt(arguments->pheight));
offsetpos = TEXT_SPACER + arguments->theight + TEXT_SPACER;
usable_height = mm_to_pt(arguments->pheight)
- arguments->theight
- arguments->theight
- 4*TEXT_SPACER;
if (gt_str_length(arguments->seqfile) > 0) {
bioseq = gt_bioseq_new(gt_str_get(arguments->seqfile), err);
}
cr = cairo_create(surf);
cairo_set_font_size(cr, 8);
twc = gt_text_width_calculator_cairo_new(cr, sty);
for (start = qry_range.start; start <= qry_range.end;
start += arguments->width)
{
GtRange single_range;
GtCustomTrack *ct = NULL;
const char *seq;
single_range.start = start;
single_range.end = start + arguments->width;
if (had_err)
break;
d = gt_diagram_new(features, seqid, &single_range, sty, err);
if (!d) {
had_err = -1;
break;
}
if (bioseq) {
seq = gt_bioseq_get_sequence(bioseq, 0);
ct = gt_custom_track_gc_content_new(seq,
gt_bioseq_get_sequence_length(bioseq, 0),
800, 70, 0.4, true);
gt_diagram_add_custom_track(d, ct);
}
l = gt_layout_new_with_twc(d, mm_to_pt(arguments->width), sty, twc, err);
had_err = gt_layout_get_height(l, &height, err);
if (!had_err) {
if (gt_double_smaller_double(usable_height - 10 - 2*TEXT_SPACER
- arguments->theight, offsetpos + height))
{
draw_header(cr, gt_str_get(arguments->text), argv[parsed_args+1],
seqid, num_pages, mm_to_pt(arguments->pwidth),
mm_to_pt(arguments->pheight),
arguments->theight);
cairo_show_page(cr);
offsetpos = TEXT_SPACER + arguments->theight + TEXT_SPACER;
num_pages++;
}
canvas = gt_canvas_cairo_context_new(sty,
cr,
offsetpos,
mm_to_pt(arguments->pwidth),
height,
NULL,
err);
if (!canvas)
had_err = -1;
offsetpos += height;
if (!had_err)
had_err = gt_layout_sketch(l, canvas, err);
}
gt_canvas_delete(canvas);
gt_layout_delete(l);
gt_diagram_delete(d);
if (ct)
gt_custom_track_delete(ct);
}
draw_header(cr, gt_str_get(arguments->text), argv[parsed_args+1], seqid,
num_pages, mm_to_pt(arguments->pwidth),
mm_to_pt(arguments->pheight),
arguments->theight);
cairo_show_page(cr);
num_pages++;
gt_log_log("finished, should be %lu pages\n", num_pages);
gt_text_width_calculator_delete(twc);
cairo_destroy(cr);
cairo_surface_flush(surf);
cairo_surface_finish(surf);
cairo_surface_destroy(surf);
cairo_debug_reset_static_data();
if (bioseq)
gt_bioseq_delete(bioseq);
gt_style_delete(sty);
gt_str_delete(gt_style_file);
gt_feature_index_delete(features);
}
return had_err;
}
int gt_canvas_cairo_visit_element(GtCanvas *canvas, GtElement *elem,
GtError *err)
{
int had_err = 0, arrow_status = ARROW_NONE;
GtRange elem_range = gt_element_get_range(elem);
GtDrawingRange draw_range;
double elem_start = GT_UNDEF_DOUBLE,
elem_width = GT_UNDEF_DOUBLE,
stroke_width = STROKE_WIDTH_DEFAULT,
bar_height = BAR_HEIGHT_DEFAULT,
arrow_width = ARROW_WIDTH_DEFAULT;
GtColor elem_color, grey, fill_color;
const char *type;
GtStyleQueryStatus rval;
GtStr *style;
GtStrand strand = gt_element_get_strand(elem);
gt_assert(canvas && elem);
/* This shouldn't happen. */
if (!gt_range_overlap(&elem_range, &canvas->pvt->viewrange))
return -1;
type = gt_element_get_type(elem);
grey.red = grey.green = grey.blue = .85;
grey.alpha = 0.5;
/* get default or image-wide bar height */
if (gt_style_get_num(canvas->pvt->sty, "format", "bar_height", &bar_height,
NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
/* try to get type-specific bar height */
if (gt_style_get_num_with_track(canvas->pvt->sty, type, "bar_height",
&bar_height,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
/* get default or image-wide arrow width */
if (gt_style_get_num(canvas->pvt->sty, "format", "arrow_width", &arrow_width,
NULL, err)== GT_STYLE_QUERY_ERROR) {
return -1;
}
/* try to get type-specific arrow width */
if (gt_style_get_num_with_track(canvas->pvt->sty, type, "arrow_width",
&arrow_width,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if ((strand == GT_STRAND_REVERSE || strand == GT_STRAND_BOTH)
/*&& delem == gt_dlist_first(elems)*/)
arrow_status = ARROW_LEFT;
if ((strand == GT_STRAND_FORWARD || strand == GT_STRAND_BOTH)
/*&& gt_dlistelem_next(delem) == NULL*/)
arrow_status = (arrow_status == ARROW_LEFT ? ARROW_BOTH : ARROW_RIGHT);
gt_log_log("processing element from %lu to %lu, strand %d\n",
elem_range.start, elem_range.end, (int) strand);
draw_range = gt_coords_calc_generic_range(elem_range, canvas->pvt->viewrange);
draw_range.start *= (canvas->pvt->width-2*canvas->pvt->margins);
draw_range.end *= (canvas->pvt->width-2*canvas->pvt->margins);
elem_start = draw_range.start + canvas->pvt->margins;
elem_width = draw_range.end - draw_range.start;
gt_assert(elem_start != GT_UNDEF_DOUBLE && elem_width != GT_UNDEF_DOUBLE);
if (gt_element_is_marked(elem)) {
if (gt_style_get_color_with_track(canvas->pvt->sty, type, "stroke_marked",
&elem_color, gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_num_with_track(canvas->pvt->sty, "format",
"stroke_marked_width",
&stroke_width, gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
}
else {
if (gt_style_get_color_with_track(canvas->pvt->sty, type, "stroke",
&elem_color,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_num_with_track(canvas->pvt->sty, "format", "stroke_width",
&stroke_width,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_num_with_track(canvas->pvt->sty, type, "stroke_width",
&stroke_width,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
}
if (gt_style_get_color_with_track(canvas->pvt->sty, type, "fill",
&fill_color,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (canvas->pvt->bt &&
gt_double_smaller_double(draw_range.end-draw_range.start, 1.1))
{
if ((unsigned long) draw_range.start > gt_bittab_size(canvas->pvt->bt))
return had_err;
if (gt_bittab_bit_is_set(canvas->pvt->bt, (unsigned long) draw_range.start))
return had_err;
gt_graphics_draw_vertical_line(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_color,
bar_height,
stroke_width);
gt_bittab_set_bit(canvas->pvt->bt, (unsigned long) draw_range.start);
}
/* register coordinates in GtImageInfo object if available */
if (canvas->pvt->ii)
{
GtRecMap *rm = gt_rec_map_new(elem_start, canvas->pvt->y - bar_height/2,
elem_start+elem_width,
canvas->pvt->y+bar_height/2,
(GtFeatureNode*)
gt_element_get_node_ref(elem));
gt_image_info_add_rec_map(canvas->pvt->ii, rm);
}
if (canvas->pvt->bt && draw_range.end-draw_range.start <= 1.1)
{
return had_err;
}
gt_log_log("drawing element from %f to %f, arrow status: %d",
draw_range.start, draw_range.end, arrow_status);
/* draw each element according to style set in the style */
style = gt_str_new();
rval = gt_style_get_str_with_track(canvas->pvt->sty, type, "style", style,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err);
switch (rval) {
case GT_STYLE_QUERY_NOT_SET:
gt_str_set(style, "box"); /* default style */
break;
case GT_STYLE_QUERY_ERROR:
gt_str_delete(style);
gt_assert(gt_error_is_set(err));
return -1;
default:
break;
}
if (strcmp(gt_str_get(style), "box") == 0)
{
gt_graphics_draw_box(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_width,
bar_height,
fill_color,
arrow_status,
arrow_width,
stroke_width,
elem_color,
false);
}
else if (strcmp(gt_str_get(style), "rectangle") == 0)
{
gt_graphics_draw_box(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_width,
bar_height,
fill_color,
ARROW_NONE,
arrow_width,
stroke_width,
elem_color,
false);
}
else if (strcmp(gt_str_get(style), "caret") == 0)
{
gt_graphics_draw_caret(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_width,
bar_height,
ARROW_NONE,
arrow_width,
stroke_width,
elem_color);
}
else if (strcmp(gt_str_get(style), "dashes") == 0)
{
gt_graphics_draw_dashes(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_width,
bar_height,
arrow_status,
arrow_width,
stroke_width,
elem_color);
}
else if (strcmp(gt_str_get(style), "line") == 0)
{
gt_graphics_draw_horizontal_line(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_color,
elem_width,
1.0);
}
else
{
gt_graphics_draw_box(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_width,
bar_height,
fill_color,
arrow_status,
arrow_width,
stroke_width,
elem_color,
false);
}
gt_str_delete(style);
/* draw arrowheads at clipped margins */
if (draw_range.clip == CLIPPED_LEFT || draw_range.clip == CLIPPED_BOTH)
gt_graphics_draw_arrowhead(canvas->pvt->g,
canvas->pvt->margins - 10,
canvas->pvt->y - 4,
grey,
ARROW_LEFT);
if (draw_range.clip == CLIPPED_RIGHT || draw_range.clip == CLIPPED_BOTH)
gt_graphics_draw_arrowhead(canvas->pvt->g,
canvas->pvt->width-canvas->pvt->margins + 10,
canvas->pvt->y - 4,
grey,
ARROW_RIGHT);
return had_err;
}
