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Commit b6fcd6df authored by zmap's avatar zmap
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new zmap release notes for 24 April 2007

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<!--#set var="banner" value="ZMap Release Notes For 24 April 2007"-->
<!--#include virtual="/perl/header"-->
<!--#set var="author" value="edgrif@sanger.ac.uk" -->
<h3>Release Version: ZMap 0.1.21</h3>
<h3>Release Date: 24 April 2007</h3>
<P>
(Last release was on 29/03/2007)
<h3>Request Tracker Tickets Resolved</h3>
<h4>ZMap</h4>
<PRE>
id: ticket/8400
Subject: Column Smart Bump selection on feature/ background
Requestors: jgrg@sanger.ac.uk
Resolved: Wed Apr 18 10:50:24 2007
id: ticket/20193
Subject: Bumping ordering
Requestors: rds@sanger.ac.uk
Resolved: Wed Apr 18 10:59:42 2007
id: ticket/20194
Subject: Export/Show Sequence "Highlight" Exons
Requestors: rds@sanger.ac.uk
Resolved: Fri Apr 20 15:28:43 2007
id: ticket/24079
Subject: Bumping Inconsistencies
Requestors: lw2@sanger.ac.uk
Resolved: Wed Apr 18 10:45:24 2007
id: ticket/24523
Subject: bump sorting
Requestors: lw2@sanger.ac.uk
Resolved: Wed Apr 18 10:42:18 2007
id: ticket/25692
Subject: Rev-comp dataset with gaps causes alignment problems in Blixem
Requestors: jpa@sanger.ac.uk
Resolved: Wed Apr 18 10:48:23 2007
id: ticket/27451
Subject: logging improvements
Requestors: edgrif@sanger.ac.uk
Resolved: Wed Apr 18 10:20:26 2007
</PRE>
<h4>Acedb</h4>
<PRE>
id: ticket/23903
Subject: sgifaceserver normal exit on fatal error when cache2 is filled
Requestors: jel@sanger.ac.uk
Resolved: Mon Apr 02 10:48:30 2007
id: ticket/27755
Subject: Invisible PhastCons
Requestors: rcg@sanger.ac.uk
Resolved: Tue Apr 17 09:36:20 2007
</PRE>
<h3>ZMap Changes/Fixes</h3>
<p> doc/Release_notes/LAST_RELEASE_DATE.txt: tmp commit to manually
make release notes!
<p> doc/Release_notes/LAST_RELEASE_DATE.txt: update last release
<p> src/include/ZMap/zmapWebPages.h: update release notes file to
duplicate runs...
<p> src/zmapWindow/zmapWindowFeature.c: remove a whole load of unused
code and compiler warnings!
<p> src/zmapDraw/zmapDraw.c: remove over zealous assert, we can have
invisible boxes !
<p> src/zmapFeature/zmapFeatureTypes.c: fix compiler warning and
remove redundant style mode.
<p> src/zmapFeature/zmapFeatureUtils.c: fix compiler warning.
<p> src/: zmapServer/acedb/acedbServer.c, zmapServer/das/dasServer.c,
include/ZMap/zmapStyle.h: remove redundant style mode.
<p> src/zmapWindow/zmapWindowItem.c: fix compiler warnings.
<p> src/zmapWindow/zmapWindowItemFactory.c: fix my own bugs in
selecting draw method.
<p> src/zmapWindow/zmapWindowFeature.c: some testing of gtk_tooltips
on enter/leave of foo_canvas_items. Needs more work before it'd
be useful.
<p> src/zmapWindow/zmapWindowNavigator.c: silly mistake in choice of
span that compressed all the text into the wrong area when the
32k limit was in force.
<p> src/canvas_choice/long_item_test.c: commit test of new cvs...
code might not compile...
<p> src/perl/X11-XRemote-0.01/X11/XRemote/Changes: Changes -
move/rename TO ../../Changes
<p> src/perl/X11-XRemote-0.01/Changes: ../../Changes - move/rename
FROM Changes
<p> src/perl/X11-XRemote-0.01/X11/XRemote/MANIFEST: MANIFEST -
move/rename TO ../../../MANIFEST
<p> src/perl/MANIFEST: ../../../MANIFEST - move/rename FROM MANIFEST
<p> src/perl/X11-XRemote-0.01/X11/XRemote/Makefile.PL: Makefile.PL -
move/rename TO ../../../Makefile.PL
<p> src/perl/Makefile.PL: ../../../Makefile.PL - move/rename FROM
Makefile.PL
<p> src/perl/X11-XRemote-0.01/X11/XRemote/README: README -
move/rename TO ../../../README
<p> src/perl/README: ../../../README - move/rename FROM README
<p> src/perl/Makefile.PL: Makefile.PL - move/rename TO
X11-XRemote-0.01/Makefile.PL
<p> src/perl/X11-XRemote-0.01/Makefile.PL:
X11-XRemote-0.01/Makefile.PL - move/rename FROM Makefile.PL
<p> src/perl/README: README - move/rename TO X11-XRemote-0.01/README
<p> src/perl/X11-XRemote-0.01/README: X11-XRemote-0.01/README -
move/rename FROM README
<p> src/perl/MANIFEST: MANIFEST - move/rename TO
X11-XRemote-0.01/MANIFEST
<p> src/perl/X11-XRemote-0.01/MANIFEST: X11-XRemote-0.01/MANIFEST -
move/rename FROM MANIFEST
<p> src/perl/X11-XRemote-0.01/X11/XRemote/typemap: typemap -
move/rename TO ../../typemap
<p> src/perl/X11-XRemote-0.01/typemap: ../../typemap - move/rename
FROM typemap
<p> src/perl/X11-XRemote-0.01/X11/XRemote/tk_test.pl: tk_test.pl -
move/rename TO ../../tk_test.pl
<p> src/perl/X11-XRemote-0.01/tk_test.pl: ../../tk_test.pl -
move/rename FROM tk_test.pl
<p> src/perl/X11-XRemote-0.01/X11/XRemote/test.pl: test.pl -
move/rename TO ../../test.pl
<p> src/perl/X11-XRemote-0.01/test.pl: ../../test.pl - move/rename
FROM test.pl
<p> src/perl/X11-XRemote-0.01/X11/XRemote/test.c: test.c -
move/rename TO ../../test.c
<p> src/perl/X11-XRemote-0.01/test.c: ../../test.c - move/rename FROM
test.c
<p> src/perl/X11-XRemote-0.01/X11/XRemote/test: test - move/rename TO
../../test
<p> src/perl/X11-XRemote-0.01/test: ../../test - move/rename FROM
test
<p> src/perl/X11-XRemote-0.01/X11/XRemote/debug_test.pl:
debug_test.pl - move/rename TO ../../debug_test.pl
<p> src/perl/X11-XRemote-0.01/debug_test.pl: ../../debug_test.pl -
move/rename FROM debug_test.pl
<p> src/perl/X11-XRemote-0.01/X11/XRemote/compile_test.sh:
compile_test.sh - move/rename TO ../../compile_test.sh
<p> src/perl/X11-XRemote-0.01/compile_test.sh: ../../compile_test.sh
- move/rename FROM compile_test.sh
<p> src/perl/X11-XRemote-0.01/X11/XRemote/XRemote.xs: XRemote.xs -
move/rename TO ../../XRemote.xs
<p> src/perl/X11-XRemote-0.01/XRemote.xs: ../../XRemote.xs -
move/rename FROM XRemote.xs
<p> src/perl/X11-XRemote-0.01/X11/XRemote/XRemote.pm: XRemote.pm -
move/rename TO ../XRemote.pm
<p> src/perl/X11-XRemote-0.01/X11/XRemote.pm: ../XRemote.pm -
move/rename FROM XRemote.pm
<p> src/zmapFeature/zmapFeature.c: merge styles when merging a
context.
<p> src/include/ZMap/zmapStyle.h: add new bumping type for fmap like
bump only better.
<p> src/zmapApp/: zmapApp_P.h, zmapAppwindow.c: fix bug in code that
aborted when we timed out on exit.
<p> src/zmapWindow/: zmapWindowItem.c, zmapWindow_P.h: add functions
to examine a compound feature item and its children.
<p> src/zmapWindow/zmapWindowMenus.c: add menu item for testing new
fmap bump style.
<p> src/zmapServer/zmapServerProtocolHandler.c: try to fix style
bug....still bugged for column_group's
<p> src/zmapWindow/zmapWindowDraw.c: add new fmap like (but better)
bumping.
<p> src/perl/X11-XRemote-0.01/XRemote.xs: XRemote.xs - move/rename TO
X11/XRemote.xs
<p> src/perl/X11-XRemote-0.01/X11/XRemote.xs: X11/XRemote.xs -
move/rename FROM XRemote.xs
<p> src/perl/X11-XRemote-0.01/: MANIFEST, Makefile.PL: File moves to
make more like std. CPAN module, and better error handling in
Makefile.PL
<p> src/perl/X11-XRemote-0.01/X11/XRemote.pm: X11/XRemote.pm -
move/rename TO lib/X11/XRemote.pm
<p> src/perl/X11-XRemote-0.01/lib/X11/XRemote.pm: lib/X11/XRemote.pm
- move/rename FROM X11/XRemote.pm
<p> src/perl/X11-XRemote-0.01/X11/XRemote.xs: X11/XRemote.xs -
move/rename TO lib/X11/XRemote.xs
<p> src/perl/X11-XRemote-0.01/lib/X11/XRemote.xs: lib/X11/XRemote.xs
- move/rename FROM X11/XRemote.xs
<p> src/perl/X11-XRemote-0.01/: MANIFEST, Makefile.PL: [no log
message]
<p> src/perl/X11-XRemote-0.01/lib/X11/XRemote.xs: lib/X11/XRemote.xs
- move/rename TO ./XRemote.xs
<p> src/perl/X11-XRemote-0.01/XRemote.xs: ./XRemote.xs - move/rename
FROM lib/X11/XRemote.xs
<p> src/perl/X11-XRemote-0.01/: MANIFEST, Makefile.PL: [no log
message]
<p> src/zmapApp/: zmapApp_P.h, zmapAppwindow.c: remove logger object,
now a hidden global singleton object.
<p> src/: include/ZMap/zmapUtilsLog.h, zmapUtils/zmapLogging.c: allow
switching off of code details in log record, clean up logging
calls and code.
<p> src/include/ZMap/zmapUtils.h: Improve code message formatting.
<p> src/zmapApp/zmapAppremote.c: - additional logging information -
change timing for removal of property notify handler
<p> src/zmapFeature/zmapFeatureContext.c: upcase exons for unspliced
dump.
<p> src/zmapServer/zmapServerProtocolHandler.c: fix bug whereby some
styles from acedb methods did not have a mode set from their
features.
<p> src/zmapWindow/: zmapWindowDraw.c, zmapWindowFeature.c: fix bug
in bump menu display of bump state.
<p> src/zmapFeature/zmapFeatureTypes.c: fix minor bug in assert
behaviour, too strict.
<p> src/zmapGFF/gffparser.c: get roys test app up to date with zmap
libs.
<p> src/runconfig: added Xlinker to make gtk2.10 compile easier.
<p> src/: include/ZMap/zmapUtilsLog.h, zmapUtils/zmapLogging.c: fix
compiler warning.
<p> src/zmapApp/zmapAppwindow.c: change fatal to critical log, fatal
ends up calling abort which we don't want here.
<p> src/zmapFeature/zmapFeatureTypes.c: add new bump type for my new
bumping.
<p> src/: zmapServer/acedb/acedbServer.c, zmapWindow/zmapWindow.c:
make new smart bump the default one for acedb cluster bump.
<p> src/zmapWindow/zmapWindowDraw.c: make new smart bump the default
one for acedb cluster bump.
<p> src/zmapWindow/zmapWindowContainer.c: add some debugging
messages.
<p> src/zmapWindow/zmapWindowLongItems.c: add more debugging.
<p> src/zmapWindow/zmapWindowMark.c: add property to range overlay.
<p> src/zmapWindow/zmapWindowMenus.c: make new bump the default and
rearrange column menu a bit.
<p> src/zmapUtils/zmapUtils_P.h: reset version number.
<h3>Acedb Changes/Fixes</h3>
<p> w2/graphcon.c, w2/graphsub.c, wh/graph.h: add new bounds calls to
graph.
<p> w7/gmapconvert.c: fix code to reflect changes in 2 point data
model.
<p> w7/smapconvert.c: fix my own bug in read pair recording of
homologies, fix small bug in assembly tag stuff.
<p> wtools/aceSetReleaseDir: fix where perl is.
<p> w7/dnacpt.c: formatting only, to improve readability + fix a
compiler warning.
<p> w3/: gifacemain.c, tacemain.c: rationalise quitting to use
aceQuit() only.
<p> wnq/acelib.c: add crash exit call so log gets correct message on
crash.
<p> w4/session.c, wh/session.h: sort out crashes giving a 'normal'
exit message in the log.
<p> w3/xacemain.c, w6/treedisp.c, wh/tree.h: add cmdline option to
disable treeview editting.
<p> wnq/aceversion.c: increment update level.
<!--#include virtual="/perl/footer"-->
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