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ChangeLog
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ChangeLog
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1.47 Tue Oct 8 14:44:44 EDT 2002
* Bug fix release.
* Fixed source sorting so that lowest alphabetically-sorted
configuration file is accepted by default. Otherwise,
the default is BioSQL, which is not installed on most
machines and causes an internal server error.
* Fixed the plugins so that they are not turned on by default.
* Changed the default empty track style from "suppress" to "key."
* Better error reporting.
* Changed passwd=>pass in all the sample config files.
1.46 Sun Oct 6 18:25:05 EDT 2002
* Major feature release.
* Internationalization support: French, Italian, Japanese, English.
* Some features need BioPerl 1.1; see patch file
* Flexible support for semantic zooming.
* Histograms in the overview and detailed views.
* Multiple labeled features in overview.
* Preliminary Oracle and BioSQL support.
* Revamped and simplified stylesheet.
* Hooks for adding HTML to display.
* Track labels can now be between tracks.
1.45 Sun Jul 7 17:32:08 EDT 2002
* Major feature release.
* Added conversion script for human genome annotations from NCBI.
* New CDS/reading frame glyph.
* New 3-frame translation glyph.
* FASTA dumper now dumps out decorated FASTA files.
* Sequence dumper supports output in GenBank, EMBL, GAME, BSML and other
formats (thanks to magic of Bio::SeqIO).
* Full set of restriction enzymes in restriction enzyme annotator plugin.
* Support for named external feature tracks in popup menu.
* External feature tracks are now highlighted in selection list.
* Fixed uploaded files so that they are persistent.
* Minor aesthetic improvements.
* REQUIRES: BioPerl 1.02.
* STILL PENDING: Internationalization/localization fixes
1.44 Mon May 6 19:14:45 EDT 2002
* Bug fix that caused keyword searches to fail on case mismatch.
* Number of matches now printed at top of multiple-match page.
1.43 Mon May 6 14:38:40 EDT 2002
* Bug fix to correct a server error that occurred when multiple
features match a search term.
* Added very preliminary support for using GBrowse as a
front end for GenBank and EMBL databases.
1.42 Sun May 5 11:35:22 EDT 2002
* Fixed a bad url in the help generated by gbrowse_img.
1.41 Sat May 4 16:19:20 EDT 2002
* Added gbrowse_img script; this allows local and remote HTML pages
to inline the images generated by gbrowse.
1.40 Fri Apr 12 20:49:50 EDT 2002
* Minor documentation fixes.
* Patch file now fixes a host of small display problems in bioperl 1.0
1.39 Fri Apr 12 00:18:10 EDT 2002
* Fixed problems compiling and installing on Solaris systems.
* Added the wormbase_gene aggregator. Useful for the c. elegans gff file.
* If you pick up the latest bioperl-live (or apply extras/bioperl-1.0.patch)
there are fixes in Bio::Graphics that prevent genes from disappearing
when zoomed all the way into an intron.
1.38 Mon Apr 8 21:16:12 EDT 2002
* Previous version would crash on vanilla Bioperl 1.0 installations.
This problem has been fixed, but at the cost of disabling wildcard
searches. To get wildcard searches, upgrade to Bioperl 1.01 using
CVS or the patch file in extras/bioperl-1.0.patch.
* Fixed aesthetic problems with a phantom "plugin:Restriction Sites"
entry appearing on the key even when restriction sites are turned
off.
* Fixed intermittent "Couldn't open database" errors.
* Fixed intermittent scrambling of user settings.
1.37 Sun Mar 31 16:10:11 EST 2002
* Plugin architecture completed see README-PLUGINS
* Sample plugins provided:
Restriction site annotator
Find regions by searching for oligos
GFF dumper
FASTA dumper
1.36 Sat Mar 23 23:28:10 EST 2002
* Completely reworked the way that track options are stored.
* Allow multiple files to be uploaded.
* Added online help documentation.
* Preparation for plug-in architecture.
1.35 Tue Mar 5 23:32:14 EST 2002
* Fixed mkpath bug in Browser.pm (wouldn't run without mods)
* Fixed typos in sample .conf files.
1.34 Tue Feb 19 14:22:31 EST 2002
* Fixed JavaScript code so that the popup zoom menu works correctly with konqueror
and old Netscape.
* Robustified in the face of server timeout errors.
1.33 Mon Feb 18 17:41:28 EST 2002
* Made the zoom/scroll navigation bar more intuitive (in my opinion)
* Zoom levels more configurable
* Cleaned up the GIF buttons (install will overwrite the old ones)
* Added GC and DNA content glyph to example config file
1.32 (intermediate version, do not use)
1.31 Thu Jan 24 15:44:40 EST 2002
* Fixed GFF and FASTA dumping problems.
* Version number is now printed at bottom of page.
1.30 Thu Jan 24 12:01:52 EST 2002
* Clarified the method for installing in non-standard locations
and gave an example for RedHat.
1.20 Mon Jan 21 17:43:06 EST 2002
* Fixed a bug that appeared with newer versions of Bio::DB::GFF
in which features with multiple locations showed up with the
same location repeated.
1.01 Fri Jan 11 13:12:36 EST 2002 Lincoln Stein <lstein@cshl.org>
* Better error reporting for when a database can't be opened
for whatever reason.
1.00 2002-01-02 Lincoln Stein <lstein@cshl.org>
* Made GGB a project separate from Bio::Graphics
* Wrote lots of documentation!