webace release notes
====================

---------------------
release 2.0a5 23/3/98
---------------------

Fifth alpha release.

new features
------------

- documentation greatly enhanced, but still incomplete (user documentation
absent, setup documentation out of date)

- wspec/webace_view_ABCD.pl loaded instead of wspec/webace_view.pl by
webace running on WWW server running on port ABCD.  This is to
facilitate debugging/development of view settings by curators - by
running two WWW servers, one live and one test they can modify their
view settings privately on the test server, without having to
duplicate their acedb database.

- acedb 'query' processing enhanced: if query returns a single object, this
object is displayed directly.  If the object is a URL object, the page pointed
to by the URL is displayed.  This allows queries that are expected to return
a single result to be embedded as links on pages.  See documentation of the
API for examples.

- extra parameters, prequery and postquery are supported to allow a query to be
constructed from the combination of a user completed field in a form and
predefined text.

- sizes included on images for faster loading.

- where an FMAP or GMAP cannot be displayed, text version of object is
automatically displayed instead.

bug fixes
---------

- URL object markup handles nested URL structures correctly.

- &nocache parameter no works correctly for keysets.


---------------------
release 2.0a4 26/2/98
---------------------

Forth alpha release.

new features
------------

- Get Gene Features (GFF) format output mode added to fmap.

- Form method switched to 'GET' throughout so pages can be bookmarked

- Feature to import external header above 'Webace View of' added -
this is via a subroutine webace_header in a file
acelib/webace_header.pl.  This is to allow localization of webace on
server sites.  Static help pages are not modified since they are part
of distribution kit.

- Data in text view is highlighted in red if float, integer, text,
data or if to an object that is text or empty (i.e. unlinked).

- Debugging autodisabled unless on dev server

- Nocache qualifier now also works for text objects

- Generic webace_view.pl read if webace_view_db.pl does not exist
(avoids need to duplicate common settings for each db).

- External links are now defined (through links between feature labels
and URLs for external services) via external subroutine $external_link
in webace_view.pl for curator level control.

- Fmap/Gmap context sensitive help mode added, with links between
feature labels and help file defined via external subroutine
$external_help in webace_view.pl for curator level control.

- seme parameter syntax changed so information is in qualifier rather
than parameter name (semeX=1&semeY=2 -> seme=X.Y).

- html'ised introductory help, release notes, API

bug fixes
---------

- Trapped missing view error for map displays (should only happen when
an db administrator gets things wrong)

- Changed caching of begin/end to deal with decimal/integer mix in maps.

- fixed bug where overwriting a cache file caused a link error.


---------------------
release 2.0a3 13/2/98
---------------------

Third alpha release.

new features
------------

- View control added for both maps and sequence displays.  View
control is controlled by the acedb server administrator, via either a
webace_view.pl file in the wspec directory or via a
webace_view_dbname.pl file in the cgi-bin/acelib/ directory (only one
is used and former by default).  The file is a perl script which is
evaluated by main display code each time a graphic is displayed.  If
the script is absent or does not parse correctly now views are
displayed - the syntax of the file can be with 'perl -c filename' to
avoid these errors.  The mechanism is different for gmap and fmap
control although to the user the appearence is identical.  For gmap, a
set of view names are defined which map to view names already defined
inside the relevant acedb.  A subroutine is this file can be edited to
automatically select between a number of alternative views according
to properties such as objectname.  The mechanism for fmap is similar
except that the 'views' themselves are defined in this file as a set
of column on/off states - it is therefore required to list all methods
that you want control off and define if they should be on or off for
any given view.  In fact the view is calculated relative to default
state, so this must also be stored, although in practice this is not
difficult (any user defined method is on, some acedb hardwired methods
are on and some are off).  Both fmap and gmap setups also allow the
definition of $fmap_head and $fmap_key respectively, which will be
printed as html at the top and bottom of the page respectively.  Icons
for each acedb defined colour can be found in /webace/I/colour.gif and
can be used to build keys.

- Reports error gracefully if aceserver is down, instead of web error.

- Added feature which causes cache regeneration if '&nocache=1' is
added to url string

- URL class WWW_URL supported (even though it is not in the models
file).  Tags with value E_mail are also parsed into mailto: links.

- External URL links are distinguished by italics (i.e. URL objects,
links specified by global_markup.pl or markup.pl [except any url in
these files containing 'webace' or 'display' which are assumed to be
internal]).  Italics is used instead of colour since it is impossible
to selectively colour hyperlinks - alternative would be red brackets
around the hyperlink or something like that, which looks horrible.

- Fmap display has new mouseclick mode 'show external entry'.  When
this is selected clicking on an embl/protein entry jumps straight to
swissprot/embl entry page.

bug fixes
---------

- Fixed missing reset buttons.

- Bug giving javascript errors with mouseover titles containing '''
fixed.


---------------------
release 2.0a2 30/1/98
---------------------

Second alpha release.

- URL objects are now partially supported: tags Url (simple Url) and
Prepend (full URL is completed by object name) are recognised.

- Added count of objects above any keyword search result.

- Improved descriptions of functions on display pages.

- Fixed bug which causes fatal error if gif cannot be drawn.
Implements a page with a link to get text version.

- Fixed bug resulting in 'empty object' (caused by // being
incorrectly recognised as a comment when actually part of an http
entry in an object).


---------------------
release 2.0a1 23/1/98
---------------------

First numbered release of webace2.

- First unified version, supporting java, javascript and
non-java/javascript browsers via a single set of scripts, with
clickable gifs accessible to all browsers.

- Added caching of html pages of text objects and associated code to
allow expand/contract functionality for such pages.

- Added caching of querykeysets.  Did not add caching of classes as
seems to be a very fasta acedb query.

- Added cookie system to save parameters for individual users.  Cookie
set automatically if it doesn't exist.

- Added graphics labelling option for objects/features on clickable
images to aid the keeping of printed records.

- Added dna output option for objects/features on clickable images.

- Added explicit keyword search function on all pages (via acedb grep
function).

- Added unified webace page header with configure and help options.

- Reset button added to lists allowing multiple selection

- Javascript extension for 'selection button for lists' prevents a
query if no object selected.

- Background colour white throughout.


---------------------------------------
release from Sean Walsh following Ace97
---------------------------------------

Code used for UK cropnet (http://synteny.nott.ac.uk/db.html) around
11/97.

- Added java implementation of 'mouseover' functionality.

- Implementation of 'dna' and 'homology list' functions in fmap.

- Regularized cachename scheme


----------------------
release prior to Ace97
----------------------

Code released for Ace97 workshop.  Major features only listed, for
historical interest, compared to original version of webace from NAL.

- display rewritten to use gifaceserver instead of giface; cache gif
and box files; provide 'mouseover' functionality via javascript.


--------------
KnownBugs/ToDo
--------------

- model, and other scripts need regularizing

- any reference to a sub_class should default to class if query cannot
be satisfied at sub_class level (e.g. 'view genome_sequence model').

- qbe and qb do not work on humace (but do work for exprace)

- view error for map should allow mail to be sent to db administrator:
email should be encoded in dbinfo.

- titles of pages should show range

- Added label option to 'mouseover off' displays.

- Mouseover button changed to default on, and parsing through webace
script improved.

- Mouseover labels objects in order of size, if too many rather than
just switching off.

- Added caching of classes: although this is a fast query, caching it
means we do not have to wait for gifaceserver to start up.  Issues an
'activate' request to gifaceserver anyway though so subsequent queries
will be faster.

- Improved consistency of use of different netscape windows

- Cleanup of code so when debugging off there are no error messages
written to web log files, and no temp debug files written.

- Cleanup of string passing, building in display

- Controlled order for classes [??]

- canned queries

- reactivate zoom boxes in js display

- view not passed back as variable in display

- display not passed back to webace as variable

- manual/auto error in box file [js,click different cache file]