File Release Notes and Changelog
Notes:
Changes:
1.65 * Improved support for negative and fractional coordinates, such as those used
in some genetic maps.
* Added fixes to GFF.pm for GFF3 to BioPerl patches
* Fix the way that plugins are stored in mod_perl environment to prevent them from
appearing and disappearing haphazardly when switching between sources.
* Added a trace glyph
* Several fixes to the Chado adaptor, mostly to keep up with changes
to APIs
1.64 * Revamped state handling to use CGI::Session instead of cookies
* Added Russian and Polish language translations
* Fixed chado adaptor bug for older chado databases with both
SO and SOFA loaded
* Fixed bug to allow multple 'add' parameters
* Added an option to turn on and off the background grid.
* Fixed extraneous redirect when calling gbrowse_img.
1.63
* Added a new "region" panel which is intermediate in size between the overview
and the detail panels. Thanks to Barry Healy for coding this. Use the new
"region segment" configuration option to turn this feature on.
* Added ability to open and close sections with a JavaScript toggle.
* Added ability to group tracks logically.
* Added the "initial landmark" configuration option to bring up a
default region the first time user visits the web page.
* Added the "quicklink plugins" option to add selected plugins to
the links list underneath the instructions.
* Added compatibility with mod_perl version 2 (via ModPerl::Registry)
* Added the ability to highlight multiple features using URL arguments.
* Added the ability to highlight multiple sequence regions using URL arguments.
* Added the ability to turn off the autosearch feature which restores the previous
region when the user revisits the browser.
* Added sections on grouping tracks by category, defining
region panels, and loading Berkeleydb databases to tutorial.
* Added a "hide" option to use when semantic zooming should turn a track
off altogether.
* Added README-lucegene.pod, describing the Lucegene GFF adaptor
* The link option in the config file can now be used to override the built-in linking
rules from DAS sources.
* Moved plugins menu to a more prominent position.
* Uploaded features can now be placed in details panel, overview panel, or both panels.
* init_code subroutines and anonymous callbacks are now placed in the same package so that
one can refer to the other.
* The feature name search now no longer does a wildcard PREFIX search (*foo*), which was killing
performance. It still does a wildcard SUFFIX search (foo*).
* You can now use the parameters "enable" and "disable" to
selectively open or close a set of tracks without blowing
away the settings for all the other tracks the way "label" does.
* gbrowse_img now takes a "highlight" parameter that will highlight the indicated
named feature(s) in yellow.
* gbrowse_details will now evaluate URL options expressed as anonymous subroutines (contributed
by Cyril Pommier).
* gbrowse_details now accepts a general formatting rule syntax
that allows the formatting of each tag value to be precisely
controlled.
* Changed mainform submission method from POST to GET when MSIE detected,
in order to defeat evil "cache has expired" message. This hack is
under the control of the "msie hack" option, and is false by default.
1.62 Mon Apr 5 09:43:25 EDT 2004
* Added request timeout option for very long requests.
* Added additional padding to prevent scales of xyplot glyph from being
cut off.
* Added ability to search within external annotation files for uploaded
features. You will need to CVS update bioperl-live to get this feature.
* Fixed problem of external annotation files disappearing.
* Fixed the problem of three-frame translation glyph showing wrong
translation. HOWEVER, for the [x]flip feature to work properly,
you will need to CVS update bioperl-live.
* Fixed the problem of segments shrinking by 1 bp when the starting
segment length was an odd number.
* Fixed problem of gbrowse_img consuming all available memory
when displaying 3d party features in absolute coordinates.
* Fixed problem of only one feature being found during wildcard search
and identically-named matches are on different reference sequences.
* Fixed problem of track settings disappearing when "update image" is
pressed when the track checkboxes are hidden.
* Fixed cross-site scripting bug (security hole) reported by Toshiaki
Katayama.
* Added a pairwise_plot glyph for showing linkage disequilibrium,
paired blast scores, and other pairwise feature data.
* Use can now turn on and off the overview tracks.
* Fixed chado adaptor to properly render the gbrowse_details page.
* Patch from Eric Just to eliminate unecessary URL arguments.
* Fixes from Jack Chen to get colors in multiple alignments "just right."
* Several fixes, improvements to the chado adaptor.
* added code to the chado adaptor to allow it to generate
URLs to corresponding cmap features
1.61 Wed Mar 17 21:59:16 EST 2004
* Moved the BioSQL adaptor to 'experimental'. It is not guaranteed
to work.
* Really fixed the landmark problem (the 1.60 release was premature)
* Quashed warnings from the GeneFinder plugin
* Suppress warnings generated by coderefs in the link and window_target
options. See make_map() to turn this back on - it might not be the
greatest idea to turn off warnings
1.60 Tue Mar 16 16:36:45 EST 2004
* Fixed problem of some landmarks not being recognized using
the Class:Name syntax.
1.59 Mon Feb 16 13:56:46 EST 2004
* Fixed security hole related to track level security
* Fixed functioning related to arbitrary (non-base) units
* Fixed a bug that caused hanging when fetching reference sequences
* Updated BioSQL adaptor
* Updated ImportFeatures.pm and ExportFeatures.pm to better support
GFF3 and fascilitate Apollo import and export
* Added support for 3rd party DAS anotations
* Added a MOBY server
* Added a proof-of-concept filter module
* added allele_tower glyph
1.58 Wed Dec 31 10:49:20 EST 2003
* Fixed memory leak when used with mod_perl
* Fixed bug with link URL when the same feature type occurred in more
than one track
* Added SVG "Publication quality image" option; as a result, GD 2.07
is the minimum version of GD required.
* Added the ability to modify html display via callbacks utilizing
segment and page setting objects.
* Fixed alignment problems in gbrowse_details
* Fixed several items with the chado/gmod adaptor
* Added documentation for installing on MacOSX
* Added a simple MOBY browser (see CONFIGURE_HOWTO for configuring it).
* Fixed a long pathname bug with the Windows PPM install.
1.57 Sat Oct 4 21:59:19 EDT 2003
* Fixed formatting errors in gbrowse_details alignments.
* Fixed bug in generation of interspersed HTML that prevented one from
providing a code reference for the html1 option.
* New idiogram glyph for putting images of Giemsa-stained chromosomes
in the overview.
* Added Icelandic translation
* Updated French translation
* GET syntax for invoking gbrowse now changed from
http://localhost/cgi-bin/gbrowse?source=yeast
to
http://localhost/cgi-bin/gbrowse/yeast
This will allow restriction by data sources using Apache's standard
authentication/authorization techniques.
* Default time for cookie expiration reduced to 7 days. This will avoid
issues arising from previous change.
* Added mechanisms to restrict individual tracks by username and
password
or by host, domain, or IP address.
* Fixed ppm install utility script
* Updated documentation to reflect the new GET syntax
* Fixed sequence alignments in gbrowse_details when there are minus
strand sequences.
1.55
* Removed hard coded paths in install scripts
* Auto-open tracks that contain matches to the search term. This avoids
nasty behavior in which someone searches for "collagen" and never sees
what it was that matched.
* Support for highlighting the matched feature in yellow. Highlighted
feature is persistent across sessions (may annoy people - consider
a selectable option)
* Support for a "highlight" plugin class which will highlight features
based on matching attributes or other queries.
1.54 Thu Aug 28 12:08:15 EDT 2003
* Really fixed the security hole that was only partially fixed in 1.53.
* Fixed the config file associated with the tutorial.
* Fixed the install scripts so that they work on Windows.
* Added a patch to allow GBrowse to dump GenBank and EMBL formatted
files while using BioPerl 1.2.2.
* Modified GFFDumper to dump GFF from multiple sources, not just
what is in the primary data source. This functionality is still
experimental and not fully tested.
* Added more complete documentation for using GBrowse with GenBank
formated files
1.53 Thu Aug 21 14:40:54 EDT 2003
* Security hole that allowed the display of /etc/passwd and other
files fixed
* Documentation reworked as pod and which is converted to html on
install. That documentation is then available at
http://localhost/gbrowse
* Added an extensive tutorial, also available at http://localhost/gbrowse
* Added tools for making it easier to create a PPM package for Windows
* Added a 'nascent' synteny browser.
* Added gbrowse_details, a CGI that gives skeletal details on each feature
* Added an optional 'flip mode' to flip the orientation of the display
* Added a multiple alignment plugin
* Added a GeneFinder plugin
* Added support for the chado database schema
* Added support for the PostgreSQL database server
* Added a script for converting UCSC genome data to GFF3
* Added a script for loading Genbank/EMBL files to a GFF database
1.51 Thu Mar 6 13:40:09 EST 2003
* Number of search results returned by keyword search now configurable.
* Made it possible for same feature to belong to multiple tracks.
* Fixed HTML title so that Perl memory location of segment object won't
sometimes appear.
* Added new link to gbrowse_img, so that people can embed images of a region
in other HTML pages.
* Added option to hide the whole banner for those who prefer a minimal interface.
1.50 Thu Feb 27 09:05:37 EST 2003
* Added Dutch language support.
* Added missing POXIX.pm file that was causing bizarre behavior for some browsers.
* Fixed bug in label() subroutine that was causing crashes for some config files.
* Added human GFF processor to installed scripts.
* Fixed bug in htdocs_install.pl that created tmp directory with wrong permissions,
resulting in permission failures the first time gbrowse run.
1.49 Thu Feb 13 17:25:20 EST 2003
* Version 1.48 was missing some .pl files needed to successfully install.
1.48 Sun Feb 9 12:55:48 EST 2003
* Added ability to group related features with dotted lines.
* Added ability to pop up a new window when following links.
* Preliminary Chado database support.
* Added information on optimizing performance at SQL layer
(see INSTALL).
* Internationalization support: added Korean, Spanish, Chinese.
* Flybase/Gadfly conversion script now works on Release 3 data format.
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!
