diff --git a/doc/Release_notes/release_notes.2008_10_13.shtml b/doc/Release_notes/release_notes.2008_10_13.shtml new file mode 100755 index 0000000000000000000000000000000000000000..7b5da6687af5d7e994d2fc97d23e7c2664b2001f --- /dev/null +++ b/doc/Release_notes/release_notes.2008_10_13.shtml @@ -0,0 +1,565 @@ +<!-- File automatically generated. Do not edit. --!> + +<!--#set var="banner" value="ZMap Release Notes For '13 October 2008'" --> +<!--#include virtual="/perl/header" --> +<!--#set var="author" value="edgrif@sanger.ac.uk" --> + +<!-- The release version, etc... --!> + +<h5>Release Version: ZMap 0.1.55 </h5> + + +<h5>Release Date: 13 October 2008</h5> + + +<p> +(Last release was on 04/09/2008) +</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=25156">25156</a>, Resolved (Fri Oct 10 17:22:20 2008) +<p>Marked region adjusters</p> +<p>jgrg@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=70729">70729</a>, Resolved (Fri Oct 10 17:29:40 2008) +<p>marking of a zoomed in area broken</p> +<p>ib2@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=72829">72829</a>, Resolved (Fri Oct 10 17:31:52 2008) +<p>cannot open zmap because server connections died</p> +<p>lw2@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=75016">75016</a>, Resolved (Mon Sep 15 14:58:09 2008) +<p>zmap and lace crash</p> +<p>ib2@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=76121">76121</a>, Resolved (Thu Sep 04 16:51:03 2008) +<p>Unbump all features</p> +<p>mt4@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=80814">80814</a>, Resolved (Fri Oct 10 09:42:47 2008) +<p>locale settings break various bits of code</p> +<p>rds@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=80886">80886</a>, Resolved (Fri Oct 10 17:38:07 2008) +<p>zmap can't connect to server</p> +<p>gdr@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=83480">83480</a>, Resolved (Fri Oct 10 08:09:58 2008) +<p>consistent zmap (test_otterlace) crash when saving changed transcript</p> +<p>lw2@sanger.ac.uk</p> +</li> +</ul> + +</fieldset><br /> + +<fieldset><legend>acedb</legend> + +<ul> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=61970">61970</a>, Resolved (Wed Oct 01 15:56:59 2008) +<p>acedb panel query - different since debian upgrade</p> +<p>mt3@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/libcurlobject/libcurlobject.c: minor update, response code + from curl + + + </li> + <li> src/zmapUtils/: zmapConfigDir.c, zmapConfigDir_P.h: removed some + old code and added support for pending config (ini) changes. + + + </li> + <li> src/zmapUtils/zmapGUINotebook.c: zMapAssert change to help with + RT #79387 + + + </li> + <li> src/zmapUtils/zmapGUITreeView.c: minor code reorganisation + + + </li> + <li> src/zmapWindow/: zmapWindow.c, zmapWindowColBump.c, + zmapWindowColConfig.c, zmapWindowDraw.c, + zmapWindowDrawFeatures.c, zmapWindowMenus.c, + zmapWindowNavigator.c, zmapWindowNavigatorMenus.c, + </li> + <li> typo - + Implement unbump all columns (RT #76121) + + + </li> + <li> doc/Release_notes/release_notes.2008_09_04.shtml: new zmap + release notes for 4 September 2008 + + + </li> + <li> src/include/ZMap/zmapWebPages.h: update release notes file to + release_notes.2008_09_04.shtml + + + </li> + <li> doc/Release_notes/LAST_RELEASE_DATE.txt: update last release + notes to 04/09/2008 + + + </li> + <li> src/zmapUtils/zmapUtils_P.h: + /var/tmp/zmap.12944/ZMap/scripts/versioner run by zmap + + + </li> + <li> doc/Release_notes/LAST_RELEASE_DATE.txt: Stepping back to get all + release notes after dodgy build... + + + </li> + <li> doc/Release_notes/release_notes.2008_09_04.shtml: new zmap + release notes for 4 September 2008 + + + </li> + <li> doc/Release_notes/LAST_RELEASE_DATE.txt: update last release + notes to 04/09/2008 + + + </li> + <li> src/zmapUtils/zmapUtils_P.h: + /var/tmp/zmap.28205/ZMap/scripts/versioner run by zmap + + + </li> + <li> src/include/ZMap/zmapConfigStrings.h: simple #define addition for + locale string + + + </li> + <li> src/zmapApp/zmapApp_P.h: simple addition to struct for locale + + + </li> + <li> src/zmapApp/zmapAppwindow.c: setup locale in an attempt to fix + problems with parsing strings when locale is not C or POSIX... + See RT ticket #80814 for details. It's possible we'll need to + change this as I foresee a few issues appearing + + + </li> + <li> src/include/ZMap/zmapStyle.h: add 3 frame variations. rationalise + bump names. add calls to set strand, frame. + + + </li> + <li> src/zmapFeature/zmapFeature.c: change to new bump name. + + + </li> + <li> src/zmapFeature/zmapFeatureTypes.c: add new strand/frame + functions for setting/printing. Parse bump string better. Add + frame stuff to inherited styles. + + + </li> + <li> src/zmapFeature/zmapStyle.c: Add functions to check styles are + drawable and make them drawable. Fix bump modes. Add gobject + frame/strand stuff. + + + </li> + <li> src/zmapFeature/zmapStyle_I.h: add new frame/strand state. + + + </li> + <li> src/zmapServer/: zmapServer.c, zmapServer.h: add new + style/feature set calls to interface. + + + </li> + <li> src/zmapServer/zmapServerProtocolHandler.c: Add code to check + feature sets and styles + + + </li> + <li> src/zmapServer/zmapServerPrototype.h: add new prototypes for + getting feature sets and styles. + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: Add new calls to support + using methods as feature sets and having separate style objects. + parse new frame tags. parse bump stuff better. Sort out column + group stuff. + + + </li> + <li> src/zmapServer/acedb/acedbServer_P.h: bump up server version. Add + new child tag. + + + </li> + <li> src/zmapServer/: das/dasServer.c, file/fileServer.c: add new + feature set calls. + + + </li> + <li> src/zmapView/zmapView.c: don't merge navigator style names into + main style list, all predefined now. + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: add rationalised bump names. + + + </li> + <li> src/zmapWindow/zmapWindowColOrder.c: use new frame calls. + + + </li> + <li> src/zmapWindow/zmapWindowDraw.c: fix bug in 3 frame state + setting, add func to properly set column state according to mag. + etc. Add 3 frame handling funcs using new start/frame states. + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: add new column + visibility state call. + + + </li> + <li> src/zmapWindow/zmapWindowItem.c: fix small logic bug causing seg. + violation. + + + </li> + <li> src/zmapWindow/zmapWindowMenus.c: once again try to rationalise + col. bumping. + + + </li> + <li> src/zmapWindow/zmapWindow_P.h: add new func. prototypes. + + + </li> + <li> src/zmapWindow/zmapWindowUtils.c: remove over zealous assert. + + + </li> + <li> doc/ZMAP_LACE_XML.README: add column type info. + + + </li> + <li> src/zmapFeature/zmapFeatureTypes.c: minor change to style + printing code. + + + </li> + <li> src/include/ZMap/zmapConfigStrings.h: remove acedb specific + def...put in acedb code. + + + </li> + <li> src/zmapServer/acedb/: acedbServer.c, acedbServer_P.h: make + styles the default, not methods and move method keyword for + source into here. + + + </li> + <li> src/zmapView/zmapView.c: remove uneeded use of config style + keyword. + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: forgot to change def name for + use methods flag. + + + </li> + <li> src/zmapServer/zmapServerProtocolHandler.c: fix bad bit of error + handling giving faulty error message. + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: fix stupid debug messages and + also defaulting of use_methods.... + + + </li> + <li> src/zmapFeature/zmapFeatureTypes.c: remove debug statement. + + + </li> + <li> src/include/ZMap/zmapConfigStrings.h: More config strings + + + </li> + <li> src/include/ZMap/zmapThreads.h: remove (now) unused define + + + </li> + <li> src/: zmapApp/zmapAppwindow.c, zmapConfig/zmapConfig.c, + zmapFeature/zmapFeatureTypes.c, zmapUtils/zmapLogging.c, + zmapUtils/zmapUtilsConfig.c: move to [ini] style config files + + + </li> + <li> src/: zmapView/zmapView.c, zmapView/zmapViewCallBlixem.c, + zmapView/zmapView_P.h, zmapWindow/zmapWindowDrawFeatures.c: move + to [ini] style config files + + + </li> + <li> src/zmapWindow/zmapWindow.c: move to [ini] style config files + + busy cursor + + + </li> + <li> src/zmapWindow/zmapWindowItem.c: fix I forgot to put in ages + ago... + + + </li> + <li> src/zmapWindow/: zmapWindowPreferences.c, zmapWindowPrint.c: move + to [ini] style config files + + + </li> + <li> src/: include/ZMap/zmapConfigIni.h, + include/ZMap/zmapConfigLoader.h, + include/ZMap/zmapConfigStanzaStructs.h, include/Makefile.am, + zmapConfig/zmapConfigIni.c, lib/Makefile.am: move to [ini] style + config files + + + </li> + <li> src/: include/Makefile.am, zmapUtils/zmapConfigLoader.c: move to + [ini] style config files + + + </li> + <li> src/: zmapView/zmapView.c, include/ZMap/zmapConfigIni.h: move to + [ini] style config files + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: move to [ini] style config + files + + + </li> + <li> src/zmapUtils/zmapConfigLoader.c: move to [ini] style config + files + + + </li> + <li> src/: zmapView/zmapView.c, include/ZMap/zmapConfigLoader.h: free + what we no longer need + + + </li> + <li> src/zmapWindow/zmapWindowItemFactory.c: further exclusion of + zmapasserts to stop crashing... see rt ticket # 79058 + + + </li> + <li> src/zmapWindow/zmapWindow.c: fix stupid copy/paste error... hmm I + think I need to rethink the interface... + + + </li> + <li> doc/Project_notes/Strategy_Autumn_2008.shtml: first version + + + </li> + <li> src/zmapWindow/zmapWindowFeatureList.c: Move from storing the + feature for each row to storing a serialised version of it. + This way we fix the issue in RT ticket #83480, although the + list shown is incomplete it does not result in a crash. + + + </li> + <li> src/zmapWindow/zmapWindowFeatureList.h: Move from storing the + feature for each row to storing a serialised version of it. + This way we fix the issue in RT ticket #83480, although the + list shown is incomplete it does not result in a crash. + + -Added some documentation too. + + + </li> + <li> src/zmapWindow/zmapWindowList.c: - runing of old/broken code - + fix the issue in RT ticket #83480, + + + </li> + <li> src/include/ZMap/zmapGUITreeView.h: brief documentation + + + </li> + <li> src/zmapConfig/zmapConfigIni.c: protect against glib + warning/empty strings + + + </li> + <li> src/zmapUtils/zmapGUITreeView.c: attempt to protect against gtk + warnings "failed to convert to text from pointer" + + + </li> + <li> src/zmapUtils/zmapConfigLoader.c: include logging group + + + </li> + <li> src/: zmapConfig/zmapConfigIni.c, include/ZMap/zmapConfigDir.h: + compiler warning + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: stop an endless loop + + + </li> + <li> src/zmapConfig/zmapConfigIni.c: get the correct order for + overwriting to work + + + </li> + <li> src/zmapWindow/zmapWindowList.c: Add context menu code for rows. + context menu includes visit url item when feature has url. + + <!-- --- 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> + + </li> + <li> w4/command.c: fix uninitialised variable (status) error. + + + </li> + <li> w6/smap.c: fix small bug in smapdump for when root has no parent. + + + </li> + <li> w3/gifacemain.c, w3/tacemain.c, w3/taqlmain.c, w3/xacemain.c, + wsocket/serverace.c: fix locale bug, we only handle straight C + + + </li> + <li> w3rdparty/libpfetch/: Makefile, libcurlobject.c, libcurlobject.h, + libcurlobject_I.h, libpfetch-cmarshal.c, libpfetch-cmarshal.h, + libpfetch-cmarshal.list, libpfetch-utils.c, libpfetch.c, + libpfetch.h, libpfetch_I.h, libpfetch_P.h: initial version of + pfetch package. + + + </li> + <li> w3rdparty/libpfetch/.deps/: libcurlobject_a-libcurlobject.Po, + libpfetch_a-libpfetch-cmarshal.Po, + libpfetch_a-libpfetch-utils.Po, libpfetch_a-libpfetch.Po: compile + dependencies + + + </li> + <li> w3rdparty/libpfetch/: libpfetch-cmarshal.c, libpfetch-cmarshal.h: + remove libpfetch-cmarshal.c libpfetch-cmarshal.h, they are + generated by the make. + + + </li> + <li> w3rdparty/libpfetch/: Makefile, README: first versions. + + + </li> + <li> w4/: commandmenu.c, command.c: add neighbours command to mirror + find neighbours in keyset window. + + + </li> + <li> w3rdparty/libpfetch/Makefile: fix up to use acedb DEFs files to + build on different machines. + + + </li> + <li> w4/command.c: remove duplicate objects found message. + + + </li> + <li> wh/command.h: add a find neighbours command. + + + </li> + <li> wmake/DARWIN_4_DEF: fix up ar command, compiler commands. + + + </li> + <li> wmake/DARWIN_UNIVERSAL_DEF: fix up universal binary options, ar + options. + + + </li> + <li> wmake/: LINUX_4_DEF, LINUX_64_DEF: fix up pkgconfig options, ar + options. + + + </li> + <li> wmake/makefile: remove unsupported code from all target, + rationalise defines so we only build main progs. + + + </li> + <li> wmake/truemake: fix ar options, fix pfetch defines. + + + </li> + <li> w6/smap_.h: add debug flag to allow per smap setting from + debugger. + + + </li> + <li> w6/smap.c: add error handling to smapaddnode(), used to silently + fail. + + + </li> + <li> wmake/makefile: provide standard build for acedb build system. + + + </li> + <li> wnq/aceversion.c: update to 47 + + <!-- --- End editing ACeDB changes here... --- --!> + </li> +</ul> +</fieldset> +<br /> + +<!--#include virtual="/perl/footer" --> +