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Commit f74f2b12 authored by zmap's avatar zmap
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new zmap release notes for 9 January 2009

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<!-- File automatically generated. Do not edit. --!>
<!--#set var="banner" value="ZMap Release Notes For ' 9 January 2009'" -->
<!--#include virtual="/perl/header" -->
<!--#set var="author" value="edgrif@sanger.ac.uk" -->
<!-- The release version, etc... --!>
<h5>Release Version: ZMap 0.1.57 </h5>
<h5>Release Date: 9 January 2009</h5>
<p>
(Last release was on 14/11/2008)
</p>
<h5>Request Tracker Tickets Resolved</h5>
<br />
<!-- Now the resolved tickets... --!>
<!-- Finished getting the resolved request tracker tickets --!>
<fieldset><legend>zmap</legend>
<ul>
<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=46564">46564</a>, Resolved (Thu Nov 20 14:32:41 2008)
<p>Configuration Manager Widget</p>
<p>rds@sanger.ac.uk</p>
</li>
<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=67581">67581</a>, Resolved (Tue Dec 02 15:10:14 2008)
<p>evidence missing in zmap window - actually a problem with Blixem</p>
<p>mpind@cc.umanitoba.ca</p>
</li>
<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=67903">67903</a>, Resolved (Tue Dec 02 15:04:58 2008)
<p>Horizontal guide tooltip follows cursor off screen</p>
<p>rds@sanger.ac.uk</p>
</li>
<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=69688">69688</a>, Resolved (Thu Nov 20 14:33:32 2008)
<p>Saving Preferences across sessions...</p>
<p>jel@sanger.ac.uk, rds@sanger.ac.uk</p>
</li>
<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=87526">87526</a>, Resolved (Thu Nov 20 14:48:40 2008)
<p>zmap crash</p>
<p>ib2@sanger.ac.uk</p>
</li>
</ul>
</fieldset><br />
<!-- End of tickets --!>
<fieldset>
<legend>ZMap Changes/Fixes [from cvs]</legend>
<ul>
<li><!-- --- Start editing ZMap changes here... --- --!>
<a href="http://cvs.internal.sanger.ac.uk/cgi-bin/viewcvs.cgi/ZMap/?root=zmap">Browse CVS</a>
</li>
<li> src/zmapFeature/zmapStyle.c: Fix mac build
</li>
<li> src/zmapWindow/zmapWindow.c: Make sure we only continuous scroll
when the center on position is in correct 'sense'
</li>
<li> src/zmapWindow/zmapWindowNavigator.c: Fix the navigator to handle
all (really?) the possible expose/initialisation orders...
</li>
<li> src/zmapWindow/zmapWindowNavigatorMenus.c: Fix the Show loci
variants search...
</li>
<li> src/zmapWindow/zmapWindowNavigator_P.h: Add expose handler ids...
</li>
<li> src/zmapWindow/zmapWindowNavigator.c: remove debug info
</li>
<li> doc/Release_notes/release_notes.2008_11_14.shtml: new zmap
release notes for 14 November 2008
</li>
<li> src/include/ZMap/zmapWebPages.h: update release notes file to
release_notes.2008_11_14.shtml
</li>
<li> doc/Release_notes/LAST_RELEASE_DATE.txt: update last release
notes to 14/11/2008
</li>
<li> src/zmapUtils/zmapUtils_P.h:
/var/tmp/zmap.9696/ZMap/scripts/versioner run by zmap
</li>
<li> src/: include/ZMap/zmapStyle.h, zmapFeature/zmapStyle.c: if enum
property is set to XXX_INVALID this now resets the field_set.XXXX
to FALSE now.
</li>
<li> src/include/ZMap/zmapUtilsLog.h: add log macro for internal logic
errors.
</li>
<li> src/zmapWindow/zmapWindowDrawFeatures.c: strand divide colour
</li>
<li> src/zmapConfig/zmapConfigIni.c: Config code to set values.
</li>
<li> src/: zmapUtils/zmapGUINotebook.c, include/ZMap/zmapUtilsGUI.h:
Update to add save and edit callbacks
</li>
<li> src/zmapUtils/zmapGUIutils.c: allow addition of extra widgets to
the file chooser dialog
</li>
<li> src/zmapView/zmapViewCallBlixem.c: - update for edit and saving
in notebook code. - save to config file
</li>
<li> src/zmapWindow/zmapWindowDNA.c: use stock items...
</li>
<li> src/zmapWindow/zmapWindowList.c: we might need to set the genomic
offset. here's some code that might help.
</li>
<li> src/zmapWindow/zmapWindowUtils.c: Some extra code to test
notebook saving code. Not sure of it's worth to users.
</li>
<li> src/zmapControl/zmapControlPreferences.c: Fix typo Some extra
code to test notebook saving code. Not sure of it's worth to
users.
</li>
<li> src/: zmapConfig/zmapConfigIni.c, include/ZMap/zmapWindow.h,
include/ZMap/zmapConfigIni.h, zmapView/zmapViewCallBlixem.c:
compiler warning
</li>
<li> src/libpfetch/: libpfetch.c, libpfetch_I.h, libpfetch_P.h: added
protection against misbehaving sub processes...
</li>
<li> src/: zmapFeature/zmapFeatureOutput.c, zmapGFF/zmapGFF2Dumper.c:
Support for dumping ranges...
</li>
<li> src/zmapWindow/: zmapWindowMenus.c, zmapWindowFeature.c: Support
for dumping marked area...
</li>
<li> src/zmapWindow/zmapWindowSearch.c: compiler warning
</li>
<li> src/libpfetch/libpfetch.c: use POSIX code
</li>
<li> src/zmapWindow/zmapWindow.c: make capital P do the same as p
</li>
<li> src/zmapDraw/zmapDraw.c: Finally fix rt ticket #67903
</li>
<li> src/zmapWindow/zmapWindowMenus.c: Finally fix rt ticket #67581
</li>
<li> src/zmapServer/: zmapServer.c, zmapServer.h: correct a couple of
func prototypes so all funcs return a ZMapServerResponseType. Fix
return code from close ruotine.
</li>
<li> src/: include/ZMap/zmapServerProtocol.h,
zmapServer/zmapServerProtocolHandler.c: remove openserverload,
add functions to allocate/destroy requests, add proper support
for all requests, handle 'unsupported' requests properly.
</li>
<li> src/zmapThreads/: zmapSlave.c, zmapThreadsUtils.c,
zmapThreads_P.h: add call to return error and data because latter
has request details which should be reported.
</li>
<li> src/zmapServer/: das/dasServer.c, zmapServerPrototype.h: fix
destroy func to return a ZMapServerResponseType
</li>
<li> src/zmapServer/file/fileServer.c: fix err msg memory leak, fix
destroy func bug when no file, fix destroy to return a
ZMapServerResponseType
</li>
<li> src/zmapServer/acedb/acedbServer.c: Fix connect and destroy func
return codes, fix err_msg memory leak
</li>
<li> src/zmapView/: zmapViewUtils.c, zmapView_P.h: add package to
manage a set of connections.
</li>
<li> src/include/ZMap/zmapView.h: remove redundant load func.
</li>
<li> src/zmapView/zmapView.c: major change from issuing one openload
command to stepping through all stages one by one. Remove
openload, change all requests to use new step interface. fix bug
in terminate code.
</li>
<li> src/zmapWindow/zmapWindowStats.c: chnage fatal asset to critical
warning...much better...
</li>
<li> src/zmapFeature/zmapFeatureTypes.c: fix stupid bug, show_reverse
implies strand specific.
</li>
<li> src/zmapServer/zmapServerProtocolHandler.c: don't set drawable
here...it's now the wrong place.
</li>
<li> src/zmapView/zmapView.c: setting style mode at wrong place +
needed makedrawable code from server to be done here.
</li>
<li> src/include/ZMap/zmapServerProtocol.h: rename struct fields to be
more meaningful.
</li>
<li> src/: zmapFeature/zmapFeatureTypes.c, include/ZMap/zmapStyle.h:
add merge type to merge call to control how merging is done.
</li>
<li> src/zmapFeature/zmapFeature.c: add merge type to styles merge
call.
</li>
<li> src/zmapFeature/zmapFeatureOutput.c: fix trivial struct init
bugs.
</li>
<li> src/zmapView/zmapViewUtils.c: add code to handle when a user
callback reports an error.
</li>
<li> src/zmapServer/zmapServerProtocolHandler.c: change to new
protocol struct names + add new merge type for styles merge.
</li>
<li> src/zmapView/zmapView.c: add new request struct names, add styles
mode call and styles drawable call.
</li>
<li> src/zmapView/zmapView_P.h: tidy up dispatch and process
prototypes
</li>
<li> src/zmapControl/: zmapControl.c, zmapControlViews.c: fix destroy
of info panel hash, needs to check that it's widget has not
already been destroyed.
</li>
<li> src/: zmapFeature/zmapFeature.c,
zmapView/zmapViewRemoteReceive.c: Hack to fix up styles
</li>
<li> src/zmapFeature/zmapFeature.c: Hack to fix up styles
</li>
<li> src/zmapWindow/: zmapWindowUtils.c, zmapWindow_P.h: add function
to show a style in a text window for a feature or a column.
</li>
<li> src/zmapWindow/zmapWindowFeature.c: fix some compiler cast
warnings, add a show style menu item for a features.
</li>
<li> src/zmapWindow/zmapWindowDrawFeatures.c: add a show style menu
item for columns.
</li>
<li> src/zmapUtils/zmapGUIutils.c: trivial layout changes.
</li>
<li> src/zmapServer/zmapServerProtocolHandler.c: document style print
change for debugging.
</li>
<li> src/zmapFeature/zmapStyleUtils.c: move style print into this file
and tidy up formatting.
</li>
<li> src/zmapFeature/zmapFeatureTypes.c: move style print to
zmapStyleUtils.c.
</li>
<li> src/include/ZMap/zmapStyle.h: add dest parameter to style print
so it can output to terminal or a string.
</li>
<li> src/zmapFeature/zmapFeatureUtils.c: no changes, cvs somehow
thinks it's out....
</li>
<li> src/: include/ZMap/zmapUtils.h, lib/Makefile.am,
zmapUtils/zmapUtilsUsers.c: add some user-related utils for
set/get developer status.
</li>
<li> src/zmapApp/zmapAppwindow.c: add call to set up user status, e.g.
developer or not.
</li>
<li> src/zmapWindow/: zmapWindowMenus.c, zmapWindow_P.h: add developer
only menu.
</li>
<li> src/zmapWindow/: zmapWindowDrawFeatures.c, zmapWindowFeature.c:
add developer only menu to columns and features.
</li>
<li> src/zmapControl/zmapControl.c: change name of guimsg call for new
Utils msg calls.
</li>
<li> src/zmapControl/zmapControlWindowMenubar.c: add 'set developer
status' option + change 'new sequence' code to use new msg calls.
</li>
<li> src/include/ZMap/zmapUtilsGUI.h: unify several message routines
into one.
</li>
<li> src/zmapUtils/zmapGUIutils.c: Unify several message functions
into one, add call to get text from user.
</li>
<li> src/: include/ZMap/zmapView.h, zmapView/zmapView.c,
zmapView/zmapView_P.h: do stateconnection check for all zmap
states. Return view information to destroyCB
</li>
<li> src/zmapControl/zmapControlRemoteSend.c: small format change.
</li>
<li> src/zmapControl/zmapControlRemoteReceive.c: add code to handle a
'close_view' request.
</li>
<li> src/zmapControl/zmapControl_P.h: add func dec for common remove
view call.
</li>
<li> src/zmapControl/zmapControl.c: handle dying state in interface
functions, clear up view dying handlers to be more robust.
</li>
<li> src/zmapApp/zmapApp_P.h: increase exit timeout for linux + add
exit rc and msg to appcontext.
</li>
<li> src/zmapApp/zmapAppremote.c: replace finalise message with call
to _signal_ zmap app to die, finalise must come later.
</li>
<li> src/zmapApp/zmapAppwindow.c: completely rejig exit code, now we
wait until all threads have quit before sending finalise and exit
comes in widget destroy.
</li>
<li> src/zmapApp/zmapAppwindow.c: more tidying up of exit routines,
correct now I think.
</li>
<li> src/zmapControl/remote/zmapXRemote_P.h: real no-op
</li>
<li> src/zmapControl/remote/zmapXRemote.c: Fixes for:
- BadWindow errors in tk, not being caught by it's error handler.
(nested zmapXTrapError calls!) - DeleteNotify events in queue
from old windows erroneously causing window destroyed messages.
- Object creation logic
</li>
<li> src/zmapApp/zmapAppwindow.c: fix small bug with issuing finalise
</li>
<li> src/zmapXML/zmapXMLParse.c: Fixes for uninitialised variable!
</li>
<li> src/zmapApp/zmapAppwindow.c: add comment, remove def'd out code.
<!-- --- End editing ZMap changes here... --- --!>
</li>
</ul>
</fieldset>
<br />
<fieldset>
<legend>Aceb Changes/Fixes [from cvs]</legend>
<ul>
<li><!-- --- Start editing ACeDB changes here... --- --!>
<a href="http://cvs.internal.sanger.ac.uk/cgi-bin/viewcvs.cgi/acedb/?root=acedb">Browse CVS</a>
<!-- --- End editing ACeDB changes here... --- --!>
</li>
</ul>
</fieldset>
<br />
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