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Revision history for Perl extension Bio::Graphics.
1.95 Sat May 30 18:07:21 EDT 2009
- In the substitution pattern rules, $id is replaced with the
output of either the feature_id or primary_id methods depending
on which one is implemented.
- The image.pm glyph will now render into SVG if a sufficiently-current
GD::SVG module is available.
- Some fixes to the segments glyph to work better with Bio::DB::Bam
rendering at the base pair level.
- The glyph_help.pl script can now create SVGs.
1.94 Wed Apr 29 05:59:02 EDT 2009
- Added a "fast" bumping option suitable for very dense tracks in which
all features have identical height. Activate it using -bump=>3 or
-bump=>'fast'.
- Fixed division by zero error in xyplot glyph when min_score==max_score.
1.93 Thu Apr 2 18:20:35 EDT 2009
- Many fixes to ideograph glyph to be more stable.
- Fixed minor display issues involving bumping and directional arrows.
- Continued documenting glyphs. About 75% done.
1.92 Tue Mar 31 00:38:16 EDT 2009
- Added documentation system for glyphs, but only half the glyphs are documented this way so far.
- Bug fixes for GBrowse on Windows.
1.91 Tue Mar 17 09:54:02 EDT 2009
- wiggle_density now supports local scaling
- wiggle loader now defaults to clipping at 2 stdev
- adjusted default smoothing parameters to do less smoothing
1.90 Sun Mar 15 01:11:28 EDT 2009
- Optimized Bio::Graphics::Wiggle to sample directly from disk when the desired visualization
size is significantly (less than 100 fold) smaller than the length of the region to
be sampled.
1.88 Sat Mar 14 23:31:46 EDT 2009
-Cleaned up calculation of min and max values for scaling and introduced the "autoscale" option.
1.87 Sat Mar 14 20:56:47 EDT 2009
-Fixed bug in xyplot visualization.
1.86 Sat Mar 14 12:22:50 EDT 2009
-Improved performance of wiggle xyplot drawing about 5-fold
-Added minor ticks to xyplots
1.83 Fri Jan 9 20:44:41 MST 2009
- Made #include directive case-insensitive.
1.80 December 2008
- Split off from Bio::Perl after a 6-year hiatus.
1.05 Fri Apr 12 20:53:42 EDT 2002
- Version 1.04 had a fatal bug. Do not use. 1.05 fixes this
and is identical to BioPerl 1.01.
1.04 Fri Apr 12 08:20:35 EDT 2002
- Take advantage of optimizations in Bio::DB::GFF::Feature so don't
have to retrieve subfeatures at low magnifications (when you can't
see 'em anyway).
1.03 Fri Apr 12 00:26:12 EDT 2002
- Fixes to handle case of a transcript glyph that is zoomed in so
far that only an intron shows (no exons).
1.02 Sun Mar 31 16:19:35 EST 2002
- Make the Bio::Graphics::Feature objects more-or-less compatible with
Bio::SeqFeatureI and Bio::LocationI. Slightly difficult because
this is a moving target.
- Minor bugfixes to support Generic Genome browser version 1.37
0.98 Fri Feb 22 14:02:11 EST 2002
-Fixed up the scale so that numbers don't (or shouldn't)
overlap.
0.97 Mon Feb 18 22:04:57 EST 2002
-Added the "dna" glyph, which supports display of raw DNA and a GC
content histogram.
0.96 Fri Jan 11 13:23:03 EST 2002
-Added support for displaying heterogeneous features, such as WABA similarities.
0.95 Thu Jan 3 08:50:01 EST 2002 (LS)
-Removed generic genome browser from project, it is now part of
Generic-Genome-Browser.
0.92 Sat Dec 8 23:28:19 EST 2001 (LS)
-Fixed up key glyph so that it correctly tracks what appears on screen
-Fixed wormbase_transcript glyph so that it uses the skinny arrow when
there isn't enough room to show the filled arrow.
0.91 Sun Nov 18 22:59:14 EST 2001 (LS)
-Modified Feature.pm to accept vanilla GFF format.
-Fixed Panel.pm so that empty tracks (height zero) do not take
up space in the map.
0.90 Sun Nov 18 21:46:46 EST 2001 (LS)
- Added the gbrowse genome browser script and supporting files
- Added a wormbase_transcript glyph for Wormbase's curated/uncurated genes.
0.85 Mon Oct 1 16:41:57 EDT 2001 (LS)
- Changed all instances of stop() to end() so that BioSeqFeatureI is supported
correctly.
0.82 Fri Jul 20 10:36:57 EDT 2001 (LS)
- Removed perl 5.6'isms.
- Added appropriate documentation to Feature.
0.81 Tue Jun 12 09:30:10 EDT 2001 (LS)
- Messed up sourceforge upload, so bumping version no
to clean up.
0.80 Tue Jun 12 09:10:15 EDT 2001 (LS)
- Basically functional
- examples in eg/
- Bio::Graphics::Panel documentation complete,
other documentation incomplete
0.01 Tue Jun 5 07:26:52 2001 (LS)
- original version; created by h2xs 1.20 with options
-n Bio::Graphics -A