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added documentation of -opacity and -bump=>'overlap' values

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1 parent c2e5cd9 commit 1550c99dc02075129f457e9f7c8446f088566b26 @lstein lstein committed Jan 23, 2012
Showing with 23 additions and 5 deletions.
  1. +0 −1 lib/Bio/Graphics/Glyph/
  2. +23 −4 lib/Bio/Graphics/
@@ -36,7 +36,6 @@ sub draw {
# dynamic assignment of colors
if ($self->option('color_series')) {
- warn "setting color series!!";
my @color_series =
qw(red blue green yellow orange brown aqua black fuchsia green lime maroon navy olive purple silver teal magenta);
my $index = 0;
@@ -1925,6 +1925,9 @@ L<"GLYPH OPTIONS">). The following options are track-specific:
-glyph Glyph class to use. "generic"
+ -color_series Dynamically choose false
+ bgcolor.
-stylesheet Bio::Das::Stylesheet to none
use to generate glyph
classes and options.
@@ -1956,6 +1959,11 @@ object to the panel. This stylesheet will be called to determine both
the glyph and the glyph options. If both a stylesheet and direct
options are provided, the latter take precedence.
+The B<-color_series> argument, if true, causes the track to ignore
+the -bgcolor setting and instead to assign glyphs a series of
+contrasting colors. This is usually used in combination with
+-bump=>'overlap' in order to create overlapping features.
If successful, add_track() returns an Bio::Graphics::Glyph object.
You can use this object to add additional features or to control the
appearance of the track with greater detail, or just ignore it.
@@ -2150,6 +2158,11 @@ some are shared by all glyphs:
-font2color Secondary font color turquoise
+ -opacity Value from 0.0 (invisible) 1.0
+ to 1.0 (opaque) which
+ controls the translucency
+ of overlapping features.
-label Whether to draw a label false
-description Whether to draw a false
@@ -2320,11 +2333,17 @@ until there is room for them. A -bump value of -1 will cause
overlapping glyphs to bump upwards. You may also provide a -bump
value of +2 or -2 to activate a very simple type of collision control
in which each feature occupies its own line. This is useful for
-showing dense, nearly-full length features such as similarity hits.
-Finally, a bump of 3 or the string "fast" will turn on a faster
+showing dense, nearly-full length features such as similarity hits. A
+bump of 3 or the string "fast" will turn on a faster
collision-detection algorithm that only works properly with the
-default "left" sort order. The bump argument can also be a code reference; see
+default "left" sort order.
+Finally, a bump value of "overlap" will cause features to overlap each
+other and to made partially translucent (the translucency can be
+controlled with the -opacity setting). Features that are on opposite
+strands will bump, but those on the same strand will not.
+The bump argument can also be a code reference; see below.
For convenience and backwards compatibility, if you specify a -bump
of 1 and use the default sort order, the faster algorithm will be

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