new zmap release notes for 30 November 2009

doc/Release_notes/release_notes.2009_11_30.shtml

+<!-- File automatically generated. Do not edit. --!>
+
+<!--#set var="banner" value="ZMap Release Notes For '30 November 2009'" -->
+<!--#include virtual="/perl/header" -->
+<!--#set var="author" value="edgrif@sanger.ac.uk" -->
+
+<!-- The release version, etc... --!>
+
+<h5>Release Version: ZMap 0.1.72 </h5>
+
+
+<h5>Release Date: 30 November 2009</h5>
+
+
+<p>
+(Last release was on 23/10/2009)
+</p>
+
+<h5>Request Tracker Tickets Resolved</h5>
+<br />
+<!-- Now the resolved tickets... --!>
+
+<!-- Finished getting the resolved request tracker tickets --!>
+
+<!-- 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> doc/Release_notes/release_notes.2009_10_23.shtml: new zmap
+	  release notes for 23 October 2009
+
+
+  </li>
+  <li> src/include/ZMap/zmapWebPages.h: update release notes file to
+	  release_notes.2009_10_23.shtml
+
+
+  </li>
+  <li> doc/Release_notes/LAST_RELEASE_DATE.txt: update last release
+	  notes to 23/10/2009
+
+
+  </li>
+  <li> src/zmapUtils/zmapUtils_P.h:
+	  /var/tmp/zmap.4393/ZMap/scripts/versioner run by zmap
+
+
+  </li>
+  <li> src/zmapFeature/zmapFeatureContext.c: replace local revcompdna
+	  func with utils copy.
+
+
+  </li>
+  <li> src/zmapUtils/zmapDNA.c: redo recomp function to be much simpler.
+
+
+  </li>
+  <li> src/zmapWindow/items/zmapWindowTextItem.c: fix bad, bad bug,
+	  calling destroy twice results in slice chain corruption.
+
+
+  </li>
+  <li> src/zmapFeature/zmapFeatureTypes.c: fix up predefined styles so
+	  that dna and peptide sequence are only drawn on the forward
+	  strand.
+
+
+  </li>
+  <li> src/zmapManager/zmapManager.c: change logic so if no views
+	  connect then zmap window is destroyed.
+
+
+  </li>
+  <li> src/zmapUtils/zmapConfigLoader.c: add missing convertor for frame
+	  mode.
+
+
+  </li>
+  <li> src/zmapView/zmapView.c: improved error handling when config file
+	  contains no feature sets.
+
+
+  </li>
+  <li> src/zmapWindow/zmapWindowDrawFeatures.c: fix logic for making
+	  columns for different frames.
+
+
+  </li>
+  <li> src/zmapWindow/zmapWindowItem.c: fix bug where we thought dna was
+	  displayed but it wasn't.
+
+
+  </li>
+  <li> src/zmapWindow/zmapWindowState.c: need to test if col is _shown_
+	  not just whether its strand specific.
+
+
+  </li>
+  <li> src/zmapWindow/items/: zmapWindowContainerFeatureSet.c,
+	  zmapWindowContainerFeatureSet.h,
+	  zmapWindowContainerFeatureSet_I.h: add code to test for reverse
+	  strand display.
+
+
+  </li>
+  <li> src/zmapWindow/items/zmapWindowSequenceFeature.c: fix bug for
+	  when there is no dna in peptide func.
+
+
+  </li>
+  <li> src/zmapFeature/zmapFeatureContext.c: fix missing intialiser for
+	  string.
+
+
+  </li>
+  <li> src/: include/ZMap/zmapUtils.h, zmapUtils/zmapCoords.c: add new
+	  coords functions and file.
+
+
+  </li>
+  <li> src/zmapApp/zmapAppwindow.c: add code to check for start/end
+	  separately from sequence.
+
+
+  </li>
+  <li> src/zmapUtils/Makefile.am: add zmapCoords.c to build.
+
+
+  </li>
+  <li> src/: include/ZMap/zmapFeature.h,
+	  zmapFeature/zmapFeatureContext.c: remove redundant context param
+	  from dna calls, fix bug where object is partly off end of dna,
+	  make calls return NULL for no dna.
+
+
+  </li>
+  <li> src/zmapUtils/zmapDNA.c: fix rubbish compiler warnings.
+
+
+  </li>
+  <li>
+	  bug.
+
+
+  </li>
+  <li> src/zmapWindow/: zmapWindowFeature.c, zmapWindowMenus.c: handle
+	  NULL return from dna routines.
+
+
+  </li>
+  <li> src/zmapWindow/items/zmapWindowSequenceFeature.c: change args to
+	  fit new ones for getting dna.
+
+
+  </li>
+  <li> src/zmapWindow/zmapWindowItemText.c: fix up dna call, now returns
+	  NULL like it always should have.
+
+
+  </li>
+  <li> src/zmapServer/pipe/README:
+	  file created
+
+
+  </li>
+  <li> src/zmapServer/pipe/pipeServer.c: file created from fileServer.c;
+	  file replaced by pipe
+
+
+  </li>
+  <li> src/zmapServer/pipe/pipeServer_P.h: file created from
+	  fileServer_P.h; file replaced by pipe
+
+
+  </li>
+  <li> src/zmapServer/pipe/Makefile.am: file created
+
+
+  </li>
+  <li> src/zmapServer/Makefile.am: pipeServer library added
+
+
+  </li>
+  <li> src/zmapServer/Makefile.am: took out pipe directory as this would
+	  break the build for others
+
+
+  </li>
+  <li> src/: zmapServer/Makefile.am, zmapServer/zmapServer.c,
+	  zmapServer/zmapServer.h, zmapServer/zmapServerPrototype.h,
+	  zmapServer/zmapServer_P.h, zmapUtils/zmapUrl.c,
+	  include/ZMap/zmapUrl.h: updated to test build scripts - warning:
+	  incompleted work
+
+
+  </li>
+  <li> src/configure.ac: added zmapServer/pipe directory
+
+
+  </li>
+  <li> src/README.zmap:
+	  added comment about adding directories to the build
+
+
+  </li>
+  <li> src/zmapMake/README: added instructions on how to add directories
+	  to the build
+
+
+  </li>
+  <li> src/zmapServer/pipe/pipeServer.c: fixed errors on build, still
+	  incomplete
+
+
+  </li>
+  <li> src/zmapUtils/zmapLogging.c: add zmap version info to log
+	  start/stop messages.
+
+
+  </li>
+  <li> src/zmapFeature/zmapFeatureContext.c: fix stupid assert bug.
+
+
+  </li>
+  <li> src/include/ZMap/zmapUtilsLog.h: add macros to do gtk like
+	  'return_if_fail' testing.
+
+
+  </li>
+  <li> src/zmapWindow/zmapWindowDrawFeatures.c: fix ghastly
+	  uninitialised variable bug and rationalise some of the code.
+
+
+  </li>
+  <li> src/zmapUtils/zmapConfigLoader.c: added scripts-dir to [ZMap]
+	  ...configKeyEntryStruct
+
+
+  </li>
+  <li> src/zmapGFF/zmapGFF_P.h: add code to allow separate parsing of
+	  sequence from file.
+
+
+  </li>
+  <li> src/zmapGFF/zmapGFF2parser.c: add code to parse sequence
+	  separately and simplify handling of parser state/errors.
+
+
+  </li>
+  <li> src/zmapGFF/gffparser.c: fix up create call for new params.
+
+
+  </li>
+  <li> src/include/ZMap/zmapGFF.h: create parser without args now, add
+	  feature args later.
+
+
+  </li>
+  <li> src/zmapServer/pipe/pipeServer.c: fix up code for new GFF parser
+	  args.
+
+
+  </li>
+  <li> src/zmapServer/acedb/acedbServer.c: fix up for new GFF parser
+	  args.
+
+
+  </li>
+  <li> src/zmapServer/file/fileServer.c: fix up context call, was wrong,
+	  also sequence getting call, but this is still bugged cvs diff
+	  zmapServer/file/fileServer.c double free somewhere.
+
+
+  </li>
+  <li> src/zmapServer/zmapServerProtocolHandler.c: do return an error if
+	  getting dna is unsupported, just return a message.
+
+
+  </li>
+  <li> src/zmapWindow/zmapWindowColBump.c: fix bump handling when bump
+	  not set yet.
+
+
+  </li>
+  <li> src/zmapWindow/zmapWindowFeature.c: remove faulty setting of
+	  sequence size, it is _not_ the window size.
+
+
+  </li>
+  <li> src/zmapWindow/zmapWindowItemFactory.c: fix bug in feature
+	  sizing, must be _relative_ to block.
+
+
+  </li>
+  <li> src/zmapWindow/items/zmapWindowTextFeature.c: fix text colouring
+	  for text.
+
+
+  </li>
+  <li> src/include/ZMap/zmapConfigStrings.h: fix missing dec.
+
+    <!-- --- 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> wmake/: DARWIN_BLXNEW_DEF, LINUX_BLXNEW_DEF: add files to compile
+	  new blixem from SeqTools subdir instead of w9
+
+
+  </li>
+  <li> w1/: getopt.c, getopt1.c: remove getopt files, these functions
+	  are now part of the Std C library so they are no longer required.
+
+
+  </li>
+  <li> wmake/truemake: remove getopt files from build, no longer
+	  required as getoptNNN are in Std C library.
+
+
+  </li>
+  <li> wh/fmapsegdump.h: moving file to w7
+
+
+  </li>
+  <li> w7/fmapsegdump.h: moved from wh
+
+
+  </li>
+  <li> wmake/: DARWIN_BLXNEW_DEF, LINUX_BLXNEW_DEF: add comment about
+	  new blixem build from SeqTools.
+
+
+  </li>
+  <li> w1/acein.c: two small formatting changes, thought I was going to
+	  do more.
+
+
+  </li>
+  <li> wh/gff.h: superceded by w7/fmapsegdump.h
+
+
+  </li>
+  <li> w4/gifcommand.c: fix bug caused by wrong number of command
+	  options in array..ugh.
+
+
+  </li>
+  <li> w7/fmap_.h: move some decs to fmapsegdump.h.
+
+
+  </li>
+  <li> w7/fmapsegdump.h: use KEY instead of strings, still more to do on
+	  func. prototype once gffv3 requirements clearer.
+
+
+  </li>
+  <li> w7/fmapsegdumpdas.c: add new args to dumping function.
+
+
+  </li>
+  <li> w7/fmapcontrol.c: add new params to dumpgff call and tidy up
+	  headers.
+
+
+  </li>
+  <li> w7/fmapsegdump.c: add parent/child flags to dump call, add new
+	  params to dumpseg code.
+
+
+  </li>
+  <li> w7/fmapsegdumpgff.c: not finished, waiting for wormgroup
+	  decisions, set up so->so_id tables, add parent/child/multiline
+	  flags and code, get basic worm support going.
+
+
+  </li>
+  <li> w7/smapconvert.c: record parent seg type where we need it for
+	  later seg dumping.
+
+
+  </li>
+  <li> w4/dump.c: minor format changes, was waiting for user to
+	  reproduce dumping error.
+
+
+  </li>
+  <li> w9/: blixem_.h, blxFetch.c, blxparser.c, blxview.c: Fixed a bug
+	  where blixem didn't work if sequences were the wrong case (RT
+	  148580)
+
+
+  </li>
+  <li> w9/dotterng.c: Used for non-graphic dotter version, contains
+	  place-holder graphic funcs.
+
+    <!-- --- End editing ACeDB changes here... --- --!>
+  </li>
+</ul>
+</fieldset>
+<br />
+
+<!--#include virtual="/perl/footer" -->
+