From 48a239b74c130d5c2056ae4b5c2b5ebb9a00c9b9 Mon Sep 17 00:00:00 2001 From: zmap <zmap> Date: Mon, 18 May 2009 14:07:48 +0000 Subject: [PATCH] new zmap release notes for 18 May 2009 --- .../release_notes.2009_05_18.shtml | 1994 +++++++++++++++++ 1 file changed, 1994 insertions(+) create mode 100755 doc/Release_notes/release_notes.2009_05_18.shtml diff --git a/doc/Release_notes/release_notes.2009_05_18.shtml b/doc/Release_notes/release_notes.2009_05_18.shtml new file mode 100755 index 000000000..27ddf6fc3 --- /dev/null +++ b/doc/Release_notes/release_notes.2009_05_18.shtml @@ -0,0 +1,1994 @@ +<!-- File automatically generated. Do not edit. --!> + +<!--#set var="banner" value="ZMap Release Notes For '18 May 2009'" --> +<!--#include virtual="/perl/header" --> +<!--#set var="author" value="edgrif@sanger.ac.uk" --> + +<!-- The release version, etc... --!> + +<h5>Release Version: ZMap 0.1.58 </h5> + + +<h5>Release Date: 18 May 2009</h5> + + +<p> +(Last release was on 09/01/2009) +</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=68249">68249</a>, Resolved (Wed Apr 15 14:28:36 2009) +<p>Failed checking MarkIsSet [restoring bumping]</p> +<p>ib2@sanger.ac.uk, th2@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=72782">72782</a>, Resolved (Tue Feb 10 09:42:59 2009) +<p>columns hiding</p> +<p>jm12@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=91972">91972</a>, Resolved (Mon Jan 12 17:16:33 2009) +<p>zmap will not zoom to minus strand features</p> +<p>jgrg@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=93011">93011</a>, Resolved (Mon Jan 12 17:15:54 2009) +<p></p> +<p>jpa@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=94781">94781</a>, Resolved (Mon Jan 12 17:15:32 2009) +<p>ZMAP crashed, now cannot save recovered session</p> +<p>jpa@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=94924">94924</a>, Resolved (Mon Jan 12 10:11:22 2009) +<p>Same problem as Friday: Cannot save my otterlace session after lace crash</p> +<p>jpa@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=95007">95007</a>, Resolved (Mon Jan 12 17:23:35 2009) +<p>locator bar panel cannot be revealed</p> +<p>lw2@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=97791">97791</a>, Resolved (Wed Feb 11 18:44:41 2009) +<p>Remove highlighting and clipboard selection for text entry boxes</p> +<p>lw2@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=97917">97917</a>, Resolved (Thu Feb 12 14:56:38 2009) +<p>Remote query for marked region</p> +<p>jgrg@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=98873">98873</a>, Resolved (Thu Feb 12 11:43:08 2009) +<p>Show Translation Amino Acid Coords</p> +<p>jel@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=103166">103166</a>, Resolved (Wed Apr 15 14:43:51 2009) +<p>Wrong name and missing score for the ensembl_solexa_intron in Zmap</p> +<p>ml6@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=107182">107182</a>, Resolved (Wed Apr 15 14:27:41 2009) +<p>Zmap features disappeared after reverse complementing,showing: Failed checking MarkIsSet.</p> +<p>ca1@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=24542">24542</a>, Resolved (Mon Mar 09 13:54:33 2009) +<p>Xace bug: Display CDS translation in protein window</p> +<p>mms@sanger.ac.uk, pad@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=45499">45499</a>, Resolved (Fri Feb 13 14:27:36 2009) +<p>Bad redrawing of fmap and table maker buttons</p> +<p>mt3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=58519">58519</a>, Resolved (Tue Mar 03 09:23:16 2009) +<p>Travelling right bug</p> +<p>mt3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=66566">66566</a>, Resolved (Fri Feb 13 14:26:03 2009) +<p>which window I am in when clicking "to select and object"</p> +<p>mt3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=71103">71103</a>, Resolved (Fri Mar 13 08:59:46 2009) +<p>Protein window display issues.</p> +<p>pad@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=71767">71767</a>, Resolved (Fri Mar 13 09:11:01 2009) +<p>geneace : window focus</p> +<p>mt3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=74533">74533</a>, Resolved (Tue Mar 03 15:32:23 2009) +<p>Reproducible bug that causes xace to crash.</p> +<p>pad@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=74832">74832</a>, Resolved (Fri Feb 13 14:24:08 2009) +<p>current db fatal error.</p> +<p>mt3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=85054">85054</a>, Resolved (Fri Feb 13 14:22:52 2009) +<p>geneace crash.</p> +<p>mt3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=86412">86412</a>, Resolved (Tue Mar 03 15:48:15 2009) +<p>Xace crash and burn FATAL ERROR.</p> +<p>pad@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=87981">87981</a>, Resolved (Mon Mar 09 13:53:24 2009) +<p>Xace bug: genefinder features get re-selected on Fmap</p> +<p>pad@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=90779">90779</a>, Resolved (Fri Feb 13 14:21:43 2009) +<p>geneace crash</p> +<p>mt3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=95807">95807</a>, Resolved (Fri Feb 13 14:20:28 2009) +<p>Genetic Map freeze WS201</p> +<p>mt3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=96548">96548</a>, Resolved (Fri Feb 13 14:32:41 2009) +<p>display bug in acedb</p> +<p>mh6@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=96617">96617</a>, Resolved (Fri Mar 20 14:31:14 2009) +<p>Blixem error message when dottering</p> +<p>gdr@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=98944">98944</a>, Resolved (Fri Mar 06 10:08:59 2009) +<p>genefeatures</p> +<p>gw3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=98953">98953</a>, Resolved (Mon Mar 09 13:52:31 2009) +<p>FMAP goes blue</p> +<p>gw3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=100964">100964</a>, Resolved (Mon Mar 02 12:36:58 2009) +<p>sgifaceserver asks "Do you wish to see further errors?"</p> +<p>jgrg@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=102438">102438</a>, Resolved (Mon Mar 09 13:51:09 2009) +<p>geneace crash</p> +<p>mt3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=102440">102440</a>, Resolved (Mon Mar 09 13:49:12 2009) +<p>window focus</p> +<p>mt3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=102442">102442</a>, Resolved (Mon Mar 09 13:48:17 2009) +<p>tabbing</p> +<p>mt3@sanger.ac.uk</p> +</li> +<li>Ticket No.<a href="https://rt.sanger.ac.uk/rt/Ticket/Display.html?id=102704">102704</a>, Resolved (Wed Mar 11 10:43:08 2009) +<p>xremote on deskpro machines.</p> +<p>pad@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> doc/Release_notes/release_notes.2009_01_09.shtml: new zmap + release notes for 9 January 2009 + + + </li> + <li> src/include/ZMap/zmapWebPages.h: update release notes file to + release_notes.2009_01_09.shtml + + + </li> + <li> doc/Release_notes/LAST_RELEASE_DATE.txt: update last release + notes to 09/01/2009 + + + </li> + <li> src/zmapUtils/zmapUtils_P.h: + /var/tmp/zmap.21614/ZMap/scripts/versioner run by zmap + + + </li> + <li> src/zmapUtils/zmapBase.c: Temporary fix for base object thread + issues... + + + </li> + <li> src/zmapUtils/: zmapBase.c, zmapBase_I.h: More permanent fix for + base object thread issues... + + + </li> + <li> src/zmapUtils/zmapBase.c: Fix a few warnings... + + + </li> + <li> src/: zmapApp/zmapAppwindow.c, + zmapControl/zmapControlWindowMenubar.c, + zmapWindow/zmapWindowSearch.c: change message calls to use new + extended params list. + + + </li> + <li> src/: include/ZMap/zmapUtilsGUI.h, zmapUtils/zmapGUIutils.c: add + code to message funcs to allow timeout for modal dialogs + add + non-modal blocking dialog code. + + + </li> + <li> src/runconfig: Add -fPIC to resolve issue building X11::XRemote + on 64bit machines + + + </li> + <li> src/zmapDocs/ZMapMainPage.c: update version number and author + information. + + + </li> + <li> src/zmapWindow/zmapWindowNavigator.c: Attempt at a fix for RT + ticket # 95659. Needs more testing... + + + </li> + <li> src/zmapView/zmapViewRemoteReceive.c: Fix for RT ticket # 95659. + + The Locus features being edited (when saving transcripts) were + using feature->type not style->mode. + + New code copies style->mode into feature->type if style has mode. + + zMapFeatureAnyForceStyleMode should catch the rest... + + + </li> + <li> src/zmapView/zmapViewRemoteReceive.c: Fix for RT ticket # 95659. + + The Locus features being edited (when saving transcripts) were + using feature->type not style->mode. + + New code copies style->mode into feature->type if style has mode. + + zMapFeatureAnyForceStyleMode should catch the rest... + + + </li> + <li> src/zmapFeature/: zmapStyle_I.h, zmapStyle.c: Correct get and set + property functions for access to mode_data union. + + + </li> + <li> src/include/ZMap/zmapStyle.h: add text-font property + + + </li> + <li> src/zmapWindow/zmapWindow.c: Fix issue where canvasWindowEventCB + is attached too early. i.e. before data load. Various asserts + can fail if events are triggered before data load! + + + </li> + <li> src/zmapWindow/zmapWindowStats.c: Temporary fix for RT ticket + #97093 + + + </li> + <li> src/zmapWindow/zmapWindowStats.c: Temporary fix for RT ticket + #97093 + + + </li> + <li> src/: include/ZMap/zmapFeature.h, zmapFeature/zmapFeature.c, + zmapFeature/zmapFeatureUtils.c, zmapServer/acedb/acedbServer.c, + zmapView/zmapViewRemoteReceive.c, zmapWindow/zmapWindowDNA.c, + zmapWindow/zmapWindowDraw.c, zmapWindow/zmapWindowDrawFeatures.c, + zmapWindow/zmapWindowFeature.c, zmapWindow/zmapWindowItem.c, + zmapWindow/zmapWindowItemText.c, zmapWindow/zmapWindowMenus.c, + zmapWindow/zmapWindowNavigator.c, + zmapWindow/zmapWindowRemoteReceive.c, zmapWindow/zmapWindow_P.h: + removal of styles from feature set struct + + + </li> + <li> src/zmapFeature/zmapStyle.c: fix for incorrect implied mode + setting during get/set + + + </li> + <li> src/zmapView/zmapViewRemoteReceive.c: add new param for + forcemodestyles call, needs finishing... + + + </li> + <li> src/zmapView/zmapView_P.h: add styles field to view struct. + + + </li> + <li> src/include/ZMap/zmapFeature.h: add style_id to feature, remove + styles, change func. prototypes to take style lists. + + + </li> + <li> src/include/ZMap/zmapStyle.h: add align_error to gapped call. + + + </li> + <li> src/zmapFeature/zmapFeature.c: remove feature->style usage. + + + </li> + <li> src/zmapFeature/zmapFeatureContext.c: remove feature->style usage + + + </li> + <li> src/zmapGFF/zmapGFF2parser.c: remove need to reference style in + feature. + + + </li> + <li> src/zmapFeature/zmapFeatureXML.c: See warning! + + + </li> + <li> src/zmapFeature/zmapFeatureXML.c: See warning! + + + </li> + <li> src/zmapWindow/zmapWindowStats.c: fix missing style modes. + + + </li> + <li> src/: zmapGFF/zmapGFF2Dumper.c, include/ZMap/zmapGFF.h: replace + references to features style ptr with calls find names style. + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: fix some comments...more + work to be done to pass in correct styles. + + + </li> + <li> src/zmapWindow/zmapWindowRemoteReceive.c: fix revcomp call to + include a style. + + + </li> + <li> src/zmapWindow/zmapWindow_P.h: add styles to window struct and + merge context + + + </li> + <li> src/zmapWindow/zmapWindow.c: part way changes to support removing + style ptr from feature. + + + </li> + <li> src/include/ZMap/zmapFeature.h: add styles to calls for dumping + etc. + + + </li> + <li> src/include/ZMap/zmapWindow.h: add data to command callback to + support dyn. loading. + + + </li> + <li> src/zmapFeature/zmapFeature.c: remove style ptr from feature, add + styles to dumping calls. + + + </li> + <li> src/zmapFeature/zmapFeatureOutput.c: add styles to calls to dump, + supports removing style ptr from feature. + + + </li> + <li> src/zmapFeature/zmapFeatureTypes.c: add function to copy a set of + styles. + + + </li> + <li> src/zmapFeature/zmapStyle.c: add code to set deferred properly. + + + </li> + <li> src/zmapServer/acedb/: acedbServer.c, acedbServer_P.h: add code + to support dyn. loading of subsets of features. + + + </li> + <li> src/zmapView/zmapView.c: add code to support dyn. loading of + features, more to be done. + + + </li> + <li> src/zmapFeature/zmapFeatureUtils.c: Remove zMapFeatureGetStyle + + + </li> + <li> src/zmapView/zmapViewRemoteReceive.c: Style rationalisation + + + </li> + <li> src/zmapWindow/: zmapWindowDrawFeatures.c, zmapWindowFeature.c, + zmapWindowFeatureShow.c, zmapWindowItem.c, + zmapWindowItemFactory.c, zmapWindowRemoteReceive.c, + zmapWindow_P.h: Style rationalisation + + + </li> + <li> src/zmapWindow/zmapWindow.c: fix reference to style from feature. + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: fix refs from feature to + style. + + + </li> + <li> src/: zmapWindow/zmapWindow.c, zmapWindow/zmapWindowColBump.c, + zmapWindow/zmapWindowMenus.c, zmapServer/das/dasServer.c, + zmapWindow/zmapWindowSearch.c, zmapWindow/zmapWindowStats.c, + zmapWindow/zmapWindow_P.h: Style rationalisation + + + </li> + <li> src/zmapFeature/zmapFeature.c: fix bug in referencing user_data + in callback. + + + </li> + <li> src/zmapFeature/zmapFeature.c: fix compiler warning + + + </li> + <li> src/zmapWindow/zmapWindow.c: only minor comment changes. + + + </li> + <li> src/zmapWindow/zmapWindowFeature.c: fix look up of style, should + be ok to use read only list of styles. + + + </li> + <li> src/zmapFeature/zmapStyle.c: Style object fix + + + </li> + <li> src/zmapWindow/: zmapWindowRemoteReceive.c, zmapWindowSearch.c: + Styles rationalisation + + + </li> + <li> src/include/ZMap/zmapFeature.h: remove styles from context, + remove redundant accessor function. + + + </li> + <li> src/include/ZMap/zmapServerProtocol.h: add styles to get + sequence/features requests. + + + </li> + <li> src/: include/ZMap/zmapStyle.h, zmapFeature/zmapStyleUtils.c: add + func to print styles to stdout. + + + </li> + <li> src/zmapFeature/zmapFeature.c: comment out loads of refs to + context styles...now needs testing. + + + </li> + <li> src/zmapFeature/zmapFeatureContext.c: remove usage of styles ptr + in context and feature. + + + </li> + <li> src/zmapFeature/zmapFeatureUtils.c: remove use of context styles. + + + </li> + <li> src/zmapServer/: zmapServer.c, zmapServer.h, + zmapServerPrototype.h: add styles to getfeatures/sequence calls. + + + </li> + <li> src/zmapServer/zmapServerProtocolHandler.c: call sequence/feature + funcs with styles. + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: remove usage of context + styles. + + + </li> + <li> src/zmapServer/: das/dasServer.c, das/dasServer_P.h, + file/fileServer.c: remove usage of context styles, add + getfeaturs/sequence styles param. + + + </li> + <li> src/zmapWindow/zmapWindowNavigator.c: Styles rationalisation + + + </li> + <li> src/zmapView/zmapView.c: remove usage of context styles, add + debug info. + + + </li> + <li> src/zmapView/zmapViewRemoteReceive.c: remove usage of context + styles. + + + </li> + <li> src/zmapWindow/zmapWindow.c: fix info. display of style name, add + debug info. + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: fix minor compiler msg. + + + </li> + <li> src/zmapWindow/zmapWindowDNA.c: remove unused context styles ref. + + + </li> + <li> src/zmapWindow/: zmapWindowDraw.c, zmapWindowDrawFeatures.c, + zmapWindowFeature.c, zmapWindowItem.c: replace use of context + styles with view usage. + + + </li> + <li> src/: include/ZMap/zmapWindowNavigator.h, zmapView/zmapView.c: + Styles rationalisation + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: fix dna feature set retrieval + + + </li> + <li> src/zmapView/zmapView.c: add modes and drawable to view style + list. + + + </li> + <li> src/zmapWindow/: zmapWindowDraw.c, zmapWindowDrawFeatures.c, + zmapWindowFeature.c, zmapWindowItem.c, zmapWindow_P.h: need + styles passed into create col. + + + </li> + <li> src/include/ZMap/zmapWindow.h: add styles to redraw call. + + + </li> + <li> src/zmapView/zmapView.c: remove debug stuff, set deferred load in + master styles list. Add styles to redraw. + + + </li> + <li> src/zmapWindow/zmapWindow.c: add styles to redraw. + + + </li> + <li> src/zmapWindow/zmapWindowDraw.c: add styles to set drawing. + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: remove debug, fix bug in + style table copying. + + + </li> + <li> src/zmapWindow/zmapWindowFeature.c: add style to draw featuer + call. + + + </li> + <li> src/zmapWindow/zmapWindowUtils.c: change table add to do the + style copy itself. + + + </li> + <li> src/zmapWindow/zmapWindow_P.h: add styles to draw calls, change + table add to table copy. + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: remove debug info. + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: fix bug in logic in + styles/columns setting. + + + </li> + <li> src/: include/ZMap/zmapWindow.h, zmapView/zmapView.c, + zmapWindow/zmapWindow.c: add styles to copy window calls. + + + </li> + <li> src/: zmapControl/remote/zmapXRemote.c, + zmapFeature/zmapFeature.c, zmapFeature/zmapFeatureUtils.c, + zmapUtils/zmapUtils.c, zmapView/zmapViewRemoteReceive.c, + zmapWindow/zmapWindowItemText.c, zmapWindow/zmapWindowList.c, + zmapWindow/zmapWindowMenus.c: fix minor compiler warning. + + + </li> + <li> src/zmapWindow/: zmapWindow.c, zmapWindowColBump.c, + zmapWindowColConfig.c, zmapWindowColOrder.c, + zmapWindowContainer.c, zmapWindowDraw.c, + zmapWindowDrawFeatures.c, zmapWindowFeature.c, + zmapWindowItemFeatureSet.c, zmapWindowItemFeatureSet.h, + zmapWindowItemFeatureSet_I.h, zmapWindowMenus.c, + zmapWindowNavigator.c, zmapWindowState.c, zmapWindow_P.h: Removal + of style from "Item Feature Set Data". + + Not complete, but a good start. + + + </li> + <li> src/zmapWindow/zmapWindowItemFeatureSet.c: silly mistake in + switch + + + </li> + <li> src/zmapFeature/: zmapFeature.c, zmapFeatureUtils.c: Keep sanity + checks up to date + + + </li> + <li> src/zmapFeature/zmapFeature.c: fix setting of style mode, + accidentally commented out. + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: fix bug in width of column. + still more work to do here for multiple styles in one column. + + + </li> + <li> src/zmapUtils/zmapCmdLineArgs.c: make sure we parse gtk args as + well. + + + </li> + <li> src/zmapWindow/zmapWindowNavigatorMenus.c: remove compiler + warning + + + </li> + <li> src/zmapWindow/: zmapWindowColOrder.c, zmapWindowDraw.c, + zmapWindowItemFeatureSet.c, zmapWindowItemFeatureSet.h, + zmapWindowItemFeatureSet_I.h: item feature set frame changes + + + </li> + <li> src/zmapView/zmapView.c: copy styles for _each_ window being + redrawn + + + </li> + <li> src/zmapWindow/: zmapWindowItemFeatureSet.c, + zmapWindowItemFeatureSet.h: more functions to access set data + + + </li> + <li> src/zmapWindow/: zmapWindowItemFactory.c, + zmapWindowDrawFeatures.c, zmapWindow.c, zmapWindowColBump.c, + zmapWindowFeature.c: use set data code + + + </li> + <li> src/zmapWindow/zmapWindowDraw.c: fix bug in showing 3 frame + single column. + + + </li> + <li> src/zmapWindow/zmapWindowDraw.c: use set data functions + + + </li> + <li> src/zmapWindow/: zmapWindowDNA.c, zmapWindowDNAChoose.c, + zmapWindowSearch.c: Fix RT ticket #97791 + + + </li> + <li> src/zmapWindow/zmapWindowRemoteReceive.c: Implement James' + request (RT ticket #97917) + + + </li> + <li> src/zmapControl/remote/xremote_gui_test.c: Unify the start zmap + code + + + </li> + <li> src/: include/ZMap/zmapFeature.h, zmapFeature/zmapFeature.c: add + code to detect when a merge doesn't work because there are no new + features. + + + </li> + <li> src/zmapWindow/zmapWindow.c: add code to update styles lists + properly. + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: styles for display now + come from widnow struct. + + + </li> + <li> src/zmapWindow/zmapWindowUtils.c: add function to update window + styles tables. + + + </li> + <li> src/zmapWindow/zmapWindow_P.h: store display styles in window. + + + </li> + <li> src/zmapView/zmapView_P.h: improve styles comments. + + + </li> + <li> src/zmapView/zmapView.c: handle styles list better, window now + makes a copy of them. Handle merge when nothing changes. + + + </li> + <li> src/zmapView/: zmapView.c, zmapView_P.h: make load features a + package level zmapView function. + + + </li> + <li> src/: include/ZMap/zmapWindow.h, zmapView/zmapView.c, + zmapView/zmapViewCallBlixem.c, zmapView/zmapView_P.h: + implementing feature in RT ticket #95467 + + + </li> + <li> src/zmapWindow/: zmapWindow.c, zmapWindowFeature.c, + zmapWindowMenus.c: implementing feature in RT ticket #95467 + + + </li> + <li> src/zmapFeature/zmapStyle_I.h: define set_data string for + returning property set/get status code. + + + </li> + <li> src/: include/ZMap/zmapStyle.h, zmapFeature/zmapStyle.c: add + set/get functions which return a boolean to say if they worked. + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: Make parseStyle look for + description not remark. + + + </li> + <li> src/zmapUtils/zmapConfigLoader.c: fix missing defines for + property strings. + + + </li> + <li> src/include/ZMap/zmapConfigStrings.h: change all underscores to + dashes to be consistent in property names. + + + </li> + <li> src/: include/ZMap/zmapWindow.h, + zmapWindow/zmapWindowZoomControl.c, + zmapWindow/zmapWindowZoomControl_P.h: add function to report zoom + in number of bases per line. + + + </li> + <li> src/zmapWindow/zmapWindowFeature.c: fix bug in displaying + feature/style description. + + + </li> + <li> src/zmapWindow/zmapWindowDraw.c: make mag stuff work on number of + bases per line + + + </li> + <li> src/zmapWindow/zmapWindowItemFeatureSet.c: fix bug in testing mag + factors. + + + </li> + <li> src/zmapFeature/: zmapStyle.c, zmapStyle_I.h: fix bug in mode + checking when we are doing a style copy not a straight set/get. + + + </li> + <li> src/zmapServer/zmapServerProtocolHandler.c: make return codes + from server on create/open fail to be SERVERDIED + + + </li> + <li> src/: include/ZMap/zmapThreads.h, zmapThreads/zmapSlave.c, + zmapThreads/zmapThreads.c, zmapThreads/zmapThreads_P.h: split out + close/destroy into separate handler funcs for abnormal thread + exit. + + + </li> + <li> src/: include/ZMap/zmapServerProtocol.h, + zmapServer/zmapServerProtocolHandler.c: add destroy func for new + thread abnormal termination. + + + </li> + <li> src/zmapView/: zmapViewUtils.c, zmapView_P.h: add new delete all + connections from step list function. + + + </li> + <li> src/zmapView/zmapView.c: clean up handling of when a server dies + during feature loading. + + + </li> + <li> src/zmapControl/remote/zmap_crash_handler.c: Better solution + became apparent + + + </li> + <li> src/lib/Makefile.am: remove zmap_crash_handler, no longer needed. + + + </li> + <li> src/zmapWindow/: zmapWindowItemFeatureBlock.c, + zmapWindowItemFeatureBlock.h, zmapWindowItemFeatureBlock_I.h: + Item Feature Block code + + + </li> + <li> src/zmapUtils/zmapSeqBitmap.c: Crude bitmap + + + </li> + <li> src/zmapDAS/Makefile.am: automake makefile + + + </li> + <li> src/: configure.ac, Makefile.common, Makefile.am, + lib/Makefile.am, libcurlobject/Makefile.am, + libpfetch/Makefile.am, zmapApp/Makefile.am, + zmapConfig/Makefile.am, zmapControl/Makefile.am, + zmapDAS/.cvsignore, zmapDraw/Makefile.am: moving to libtool for + building convenience libraries + + + </li> + <li> src/: zmapFeature/Makefile.am, zmapGFF/Makefile.am, + zmapManager/Makefile.am: moving to libtool for building + convenience libraries + + + </li> + <li> src/: zmapServer/Makefile.am, zmapServer/acedb/Makefile.am, + zmapServer/das/Makefile.am, zmapServer/file/Makefile.am, + zmapThreads/Makefile.am, zmapUtils/Makefile.am, + zmapView/Makefile.am, zmapWindow/Makefile.am, + zmapXML/Makefile.am: moving to libtool for building convenience + libraries + + + </li> + <li> src/include/ZMap/zmapSeqBitmap.h: Crude bitmap code + + + </li> + <li> src/zmapFeature/Makefile.am: tests isn't there yet... + + + </li> + <li> src/configure.ac: tests isn't there yet... + + + </li> + <li> src/libpfetch/libpfetch.c: - correct status on failed fetch - + call the closed signal for pipe handles + + + </li> + <li> src/libpfetch/libpfetch-utils.c: ref/unref the object during + emit_signal + + + </li> + <li> src/: Makefile.am, configure.ac, libpfetch/Makefile.am, + zmapFeature/Makefile.am, libpfetch/tests/Makefile.am, + libpfetch/tests/Makefile.in, libpfetch/tests/check_libpfetch.c, + libpfetch/tests/check_libpfetch.h, zmapFeature/tests/.cvsignore, + zmapFeature/tests/Makefile.am, + zmapFeature/tests/check_zmapFeature.c, + zmapFeature/tests/check_zmapFeature.h, + zmapFeature/tests/check_zmapFeature_P.c, + zmapFeature/tests/check_zmapFeature_P.h, + zmapFeature/tests/check_zmapStyle.c, + zmapFeature/tests/check_zmapStyle.h, + zmapFeature/tests/check_zmapStyle_P.c, + zmapFeature/tests/check_zmapStyle_P.h, + libpfetch/tests/.cvsignore: beginnings of unit testing using + 'check' and make check + + + </li> + <li> src/tests/: .cvsignore, Makefile.am, check_zmapmain.c, + zmapCheck.h, zmapSuites.h: beginnings of unit testing using + 'check' and make check + + + </li> + <li> src/zmapWindow/zmapWindow_P.h: remove duplicate struct + + + </li> + <li> src/zmapView/zmapView.c: unset deferred flag on styles correctly + + + </li> + <li> src/zmapFeature/zmapFeature.c: [no log message] + + + </li> + <li> src/zmapWindow/zmapWindowColConfig.c: Addition of deferred + columns tab + + + </li> + <li> src/zmapWindow/zmapWindowColOrder.c: Fix for frame sensitive + columns and location of 3 frame columns + + + </li> + <li> src/zmapWindow/zmapWindowDraw.c: - moved 3 frame drawing to + windowDrawContextCB - fixed single function to determine + visibility of columns in 3 frame mode + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: - moved 3 frame drawing + to windowDrawContextCB + + + </li> + <li> src/zmapWindow/zmapWindowItemFactory.c: - removed stats + temporarily... MUST BE FIXED + + + </li> + <li> src/zmapWindow/: zmapWindowItemFeatureSet.c, + zmapWindowItemFeatureSet_I.h, zmapWindowItemFeatureSet.h: Column + data + + + </li> + <li> src/zmapWindow/zmapWindowNavigator.c: updating to keep up with + changes + + + </li> + <li> src/zmapWindow/zmapWindow.c: - bug fix for signal_handler_find - + deferred columns handling code + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: draw 3 frame only 1 + columns too. + + + </li> + <li> src/zmapWindow/zmapWindowDraw.c: - draw 3 frame only 1 columns + too. - make sure frame columns don't get shown/hidden by zoom + code + + + </li> + <li> src/zmapManager/Makefile.am: typo! + + + </li> + <li> src/libpfetch/: libpfetch.h, libpfetch_I.h: Fix universal compile + on mac + + + </li> + <li> src/zmapUtils/: zmapUrl.c, zmapUrlOptions.h: Fix universal + compile on mac + + + </li> + <li> src/lib/Makefile.am: No longer needed + + + </li> + <li> src/zmapUtils/zmapLogging.c: signal handler returns now for core + dumping. + + + </li> + <li> src/share/ZMap/ZMap: make check support + + + </li> + <li> src/: include/ZMap/zmapUtils.h, zmapUtils/zmapUtils.c: add + trivial func to convert single digit to char representation. + + + </li> + <li> src/: include/ZMap/zmapGLibUtils.h, zmapUtils/zmapGLibUtils.c: + improve quark list printing function. + + + </li> + <li> src/tests/zmapCheck.h: Do we need a timeout... + + + </li> + <li> src/: tests/check_zmapmain.c, tests/zmapSuites.h, + zmapUtils/tests/.cvsignore, zmapUtils/tests/Makefile.am, + zmapUtils/tests/check_zmapConfigLoader.c, + zmapUtils/tests/check_zmapConfigLoader.h, zmapUtils/Makefile.am, + configure.ac: more tests + + + </li> + <li> src/Makefile.am: more tests + + + </li> + <li> src/zmapUtils/tests/Makefile.am: chmod test/example config file + for make check to work. + + + </li> + <li> src/zmapWindow/zmapWindowState.c: not all columns have feature + sets now + + + </li> + <li> src/: include/ZMap/zmapFeature.h, zmapFeature/zmapFeature.c, + zmapFeature/zmapFeatureOutput.c: change 'text' to 'description' + and add source text/name fields. + + + </li> + <li> src/zmapGFF/zmapGFF2Dumper.c: change 'text' to 'description' + + + </li> + <li> src/: include/ZMap/zmapGFF.h, zmapGFF/zmapGFF2parser.c, + zmapGFF/zmapGFF_P.h: add source id/text and style hashes to + parser so it can look them up. + + + </li> + <li> src/zmapView/zmapView.c: removed redundant header include + + + </li> + <li> src/include/ZMap/zmapServerProtocol.h: improve comments. + + + </li> + <li> src/zmapServer/acedb/: acedbServer.c, acedbServer_P.h: completely + rework column_tags/styles code to use new/better tags. + + + </li> + <li> src/zmapWindow/: zmapWindowItemFactory.c, zmapWindowItemText.c: + feature struct text changed to description. + + + </li> + <li> src/zmapWindow/zmapWindowFeature.c: fix calls to get + feature/featureset description/text. + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: get feature_set + description displayed rather than style description. + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: fix code to display + feature_set text for columns. + + + </li> + <li> src/zmapControl/zmapControlWindowInfoPanel.c: fix info panel + display, column only was bugged. + + + </li> + <li> src/zmapWindow/: zmapWindow.c, zmapWindow_P.h: fix text for + column to be feature set text, NOT style text. + + + </li> + <li> src/: include/ZMap/zmapStyle.h, zmapFeature/zmapStyle.c, + zmapFeature/zmapStyle_I.h: add blixem disp. and allow misalign + options. + + + </li> + <li> src/zmapUtils/zmapLogging.c: reset _the_ signal handler to + default, rather than just SEGV! Doh! + + + </li> + <li> src/zmapUtils/zmapLogging.c: typo! time to go home. + + + </li> + <li> src/configure.ac: abs_top_srcdir substitution + + + </li> + <li> src/zmapUtils/tests/Makefile.am: use abs_top_srcdir as top_srcdir + is different for linked program + + + </li> + <li> src/zmapGFF/zmapGFF2parser.c: add code to fix up data for our + inbuilt locus type. + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: remove debug output. + + + </li> + <li> src/zmapWindow/zmapWindowNavigator.c: set the navigator columns + to visible to make them easier to see. + + + </li> + <li> src/zmapGFF/zmapGFF2parser.c: fix bug in looking for feature set + styles. + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: Partial fix for column + creation without styles... + + + </li> + <li> src/zmapWindow/: zmapWindowItemFeatureSet_I.h, + zmapWindowItemFeatureSet.c: Add strand specific + + + </li> + <li> src/include/ZMap/zmapUtils.h: SWAP Macro + + + </li> + <li> src/zmapWindow/zmapWindowMark.c: Fix RT # 107182 and 68249 + + + </li> + <li> src/: include/ZMap/zmapGLibUtils.h, zmapUtils/zmapGLibUtils.c: + add functions to manage a hash of GQuark -> Glist's of GQuarks + + + </li> + <li> src/zmapGFF/zmapGFF2parser.c: remove redundant column tag and + style parsing code. + + + </li> + <li> src/zmapUtils/zmapSeqBitmap.c: add missing system header include. + + + </li> + <li> src/zmapServer/: das/dasServer.c, file/fileServer.c: update + getfeaturesetnames() signature for new hash param. + + + </li> + <li> src/: include/ZMap/zmapServerProtocol.h, zmapServer/zmapServer.c, + zmapServer/zmapServer.h, zmapServer/zmapServerProtocolHandler.c, + zmapServer/zmapServerPrototype.h: add new featureset/style hash + param. + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: add code to support returning + a mapping of column names to style names. + + + </li> + <li> src/zmapView/: zmapView.c, zmapView_P.h: add code to support new + featureset to styles mapping. + + + </li> + <li> src/: include/ZMap/zmapWindow.h, zmapWindow/zmapWindow.c, + zmapWindow/zmapWindow_P.h: add code to support new hash of + featuresets to styles for columns. + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: fix one trivial compiler + warning and remove debug stuff. + + + </li> + <li> src/zmapControl/remote/zmapXRemote.c: compiler warning + + + </li> + <li> src/zmapWindow/: zmapWindowItemFeatureBlock.c, + zmapWindowItemFeatureBlock.h, zmapWindowItemFeatureBlock_I.h, + zmapWindowItemFeatureSet.c, zmapWindowItemFeatureSet.h, + zmapWindowItemFeatureSet_I.h, zmapWindowDrawFeatures.c: compiler + warning + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: compiler warning + + + </li> + <li> src/zmapWindow/zmapWindowItemFeatureBlock.c: Move away from + styles + + + </li> + <li> src/zmapWindow/: zmapWindowItemFeatureSet.c, + zmapWindowItemFeatureSet.h, zmapWindowItemFeatureSet_I.h: Require + a styles list for creation + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: Require a styles list + for creation of columns + + + </li> + <li> src/zmapWindow/zmapWindowNavigator.c: Require a styles list for + creation of columns + + + </li> + <li> src/zmapWindow/zmapWindowColConfig.c: use column display name + function + + + </li> + <li> src/zmapWindow/zmapWindowUtils.c: function to get list of styles + for a column + + + </li> + <li> src/zmapWindow/zmapWindow.c: Set data unique id + + + </li> + <li> src/zmapFeature/zmapStyle.c: protect mode_data union access + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: remove dependence on column + style + + + </li> + <li> src/zmapWindow/: zmapWindowItemFeatureSet.c, + zmapWindowItemFeatureSet.h: Added function for bumping support + + + </li> + <li> src/canvas_choice/.cvsignore: ignore Makefile + + + </li> + <li> src/canvas_choice/Makefile.am: libtoolised + + + </li> + <li> src/canvas_choice/Makefile.am: typo! + + + </li> + <li> src/canvas_choice/Makefile.am: re-organised again... + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: Fix use of uninitialised + style. Use one from column table. + + + </li> + <li> src/include/ZMap/zmapConfigStyleDefaults.h: Add predefined + assembly path style. + + + </li> + <li> src/: include/ZMap/zmapGLibUtils.h, zmapUtils/zmapGLibUtils.c: + add print func for hashlist package + fix bad bug when inserting. + + + </li> + <li> src/zmapFeature/zmapFeatureFormatInput.c: add assembly_path to + list of non-standard gffv2 sources. + + + </li> + <li> src/zmapFeature/zmapFeatureTypes.c: add assembly_path as a + predefined style. + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: move some tests and + critical warnings. + + + </li> + <li> src/zmapWindow/zmapWindowUtils.c: changed place of test for + finding feature set. + + + </li> + <li> src/zmapWindow/zmapWindowItemFeatureSet.c: Added more functions + for bumping and warning for old function + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: fix bug in column groups + collection of styles for features sets. + + + </li> + <li> src/zmapWindow/zmapWindowState.c: Fix incorrect use of style + + + </li> + <li> src/zmapWindow/: zmapWindowDrawFeatures.c, zmapWindow.c: move to + accessing column computed style property + + + </li> + <li> src/zmapWindow/: zmapWindowColBump.c, zmapWindowState.c: move to + accessing column computed style property + + + </li> + <li> src/zmapWindow/zmapWindowMenus.c: move to accessing column + computed style property + + + </li> + <li> src/zmapWindow/zmapWindowContainer.c: move to accessing column + computed style property + + + </li> + <li> src/zmapWindow/: zmapWindowDrawFeatures.c, + zmapWindowItemFeatureSet.c, zmapWindowItemFeatureSet.h, + zmapWindowNavigator.c: move to accessing column computed style + property + + + </li> + <li> src/zmapWindow/items/: zmapWindowAlignmentFeature.c, + zmapWindowAlignmentFeature.h, zmapWindowAlignmentFeature_I.h, + zmapWindowBasicFeature.c, zmapWindowBasicFeature.h, + zmapWindowBasicFeature_I.h, zmapWindowCanvasItem.c, + zmapWindowCanvasItem.h, zmapWindowCanvasItem_I.h, + zmapWindowCollectionFeature.c, zmapWindowCollectionFeature.h, + zmapWindowCollectionFeature_I.h, zmapWindowGlyphItem.c, + zmapWindowGlyphItem.h, zmapWindowGlyphItem_I.h, + zmapWindowSequenceFeature.h, zmapWindowSequenceFeature_I.h, + zmapWindowTextFeature.c, zmapWindowTextFeature.h, + zmapWindowTextFeature_I.h, zmapWindowTranscriptFeature.c, + zmapWindowTranscriptFeature.h, zmapWindowTranscriptFeature_I.h: A + set of FooCanvasItem subclasses which act as FooCanvasGroups + to contain base FooCanvasItems to draw features, both + compound and non-compound. + + CanvasItem is the first subclass, with an interface, which the + rest of the set inherit from. + + Status: Currently work in progress, with some missing + functionality in Glyph, Text and Sequence Features + + + </li> + <li> src/zmapUtils/zmapUtilsUsers.c: Now possible to be a developer... + + + </li> + <li> src/include/ZMap/zmapGFF.h: add missing func. dec. + + + </li> + <li> src/zmapGFF/zmapGFF2Dumper.c: refactor slightly. + + + </li> + <li> src/zmapWindow/zmapWindow.c: def out unused func. + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: def out unused func + fix + compiler warning. + + + </li> + <li> src/zmapWindow/zmapWindowItemFeatureSet.c: fix compiler warning. + + + </li> + <li> src/zmapWindow/zmapWindowMenus.c: reinstate developer menu show + style code + + + </li> + <li> src/zmapWindow/zmapWindowList.c: fix missing param to dump call ! + + + </li> + <li> src/zmapWindow/zmapWindowSearch.c: fix compiler warnings + + + </li> + <li> src/zmapWindow/zmapWindow_P.h: add missing func decs. + + + </li> + <li> src/zmapWindow/zmapWindow_P.h: moved #include to top of file + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: Fix a few inconsistencies + + + </li> + <li> src/include/ZMap/zmapEnum.h: add support for short/long + description strings for enums. + + + </li> + <li> src/include/ZMap/zmapServerProtocol.h: add to type enums, need + dummy short/long text entries. + + + </li> + <li> src/include/ZMap/zmapStyle.h: change 'overlap' to 'bump' for + bumping, add short/long text to bump enums. + + + </li> + <li> src/zmapFeature/: zmapFeature.c, zmapFeatureTypes.c, + zmapStyleUtils.c, zmapStyle_I.h: add Fixed to styles, change + overlap to bump and change code to fit new bump names. + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: change bump reading code to + fit new bump names. + + + </li> + <li> src/zmapUtils/zmapConfigLoader.c: change to new bump properties. + + + </li> + <li> src/zmapWindow/: zmapWindow.c, zmapWindowColBump.c, + zmapWindowDraw.c, zmapWindowDrawFeatures.c, zmapWindowFeature.c, + zmapWindowItemFeatureSet.c, zmapWindowItemFeatureSet.h, + zmapWindowItemFeatureSet_I.h, zmapWindowMenus.c, + zmapWindowNavigator.c, zmapWindowNavigatorMenus.c, + zmapWindowNavigator_P.h: change calls/names for new bumping + names/options. + + + </li> + <li> src/zmapWindow/: zmapWindowState.c, zmapWindow_P.h: change + calls/names for new bumping names/options. + + + </li> + <li> src/: zmapFeature/zmapStyle.c, zmapServer/acedb/acedbServer.c: + remove debug printfs.... + + + </li> + <li> src/zmapServer/acedb/models.wrm: keep up to date with bump + changes + + + </li> + <li> src/zmapWindow/items/: zmapWindowAlignmentFeature.c, + zmapWindowBasicFeature.c, zmapWindowCanvasItem.c, + zmapWindowCanvasItem.h, zmapWindowCanvasItem_I.h, + zmapWindowCollectionFeature.c, zmapWindowCollectionFeature.h, + zmapWindowGlyphItem.c, zmapWindowTextFeature.c, + zmapWindowTranscriptFeature.c: Remove style from the items... + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: fix faulty error handling in + finding method lists, add bump_fixed tag support. + + + </li> + <li> src/include/ZMap/zmapStyle.h: Make sure last really is last + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: inspect properties that were + set not, those that were ignored. + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: fix offset problem in gff + dumping, we need to set -refseq. + + + </li> + <li> src/include/ZMap/zmapFeature.h: sequence type in features + + + </li> + <li> src/include/ZMap/zmapSeqBitmap.h: compiler issues + + + </li> + <li> src/zmapWindow/zmapWindow.c: Pass through the featureset to + styles hash when reverse complementing + + + </li> + <li> src/zmapWindow/zmapWindow.c: reverse comp before doing load data + + + </li> + <li> src/zmapView/zmapView.c: handle hashes in featureset name request + + + </li> + <li> src/zmapUtils/zmapGLibUtils.c: handle hashes in featureset name + request + + + </li> + <li> src/zmapWindow/: zmapWindow.c, zmapWindowColConfig.c, + zmapWindowUtils.c, zmapWindow_P.h: fix reverse complemented + issues and a few compiler complaints + + + </li> + <li> src/zmapWindow/Makefile.am: [no log message] + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: Add an Immediate keyword for + deferred loading so it can be set to FALSE. + + + </li> + <li> src/zmapWindow/: zmapWindowItemFeatureSet.c, + zmapWindowItemFeatureSet.h: function to get style properties from + a list of styles. + + + </li> + <li> src/zmapWindow/zmapWindow_P.h: function prototype + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: Correct creation of + columns from feature sets Better error handling too + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: fix bad mistake in tag + string, just wrong. + + + </li> + <li> src/zmapServer/acedb/models.wrm: Keep model in step + + + </li> + <li> src/zmapWindow/zmapWindowDrawFeatures.c: fix for multiple drawing + of non frame specific features + + + </li> + <li> src/: zmapFeature/Makefile.am, zmapFeature/zmapFeature.c, + zmapFeature/zmapFeature3FrameTranslation.c, + zmapFeature/zmapFeatureContext.c, zmapFeature/zmapFeatureDNA.c, + zmapFeature/zmapFeatureUtils.c, zmapServer/acedb/acedbServer.c: + DNA and 3 Frame Translation feature code + + + </li> + <li> src/zmapFeature/zmapStyle.c: Fix some style drawable omissions + + + </li> + <li> src/zmapWindow/zmapWindowItem.c: DNA and 3 Frame Translation + feature code + + + </li> + <li> src/zmapWindow/zmapWindowItemFactory.c: DNA and 3 Frame + Translation feature code + + + </li> + <li> src/zmapWindow/: zmapWindowFeature.c, zmapWindow_P.h: add funcs + to get feature set and source names/description. + + + </li> + <li> src/zmapWindow/zmapWindow.c: return feature set _and_feature + source information. + + + </li> + <li> src/zmapControl/: zmapControlWindowInfoPanel.c, zmapControl_P.h: + display both feature set and source info. + + + </li> + <li> src/include/ZMap/zmapFeature.h: add fields for separate set and + source info. to feature description. + + + </li> + <li> src/zmapServer/acedb/models.wrm: insert all the missing stuff + from the original styles doc. + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: some cleaning up, some + factorising functions and data structures. trying to find + initial bump issues... + + + </li> + <li> src/include/ZMap/zmapFeature.h: compiler warnings etc + + + </li> + <li> src/libpfetch/libpfetch.c: fix for problems running pfetch + + + </li> + <li> src/zmapUtils/zmapIOOut.c: Simple new create file function + + + </li> + <li> src/zmapWindow/zmapWindowColBump.c: Fix for bump spacing which + relied on correct returns from item_get_bounds. Well now it'll + return the correct numbers! + + + </li> + <li> src/: include/ZMap/zmapFeature.h, zmapFeature/zmapFeature.c: add + structs and calls to handle new assembly path feature type. + + + </li> + <li> src/include/ZMap/zmapStyle.h: add new assembly path mode. + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: add code to parse new + assembly path mode for style. + + + </li> + <li> src/zmapWindow/zmapWindowItem.c: add new colour for assembly path + + + </li> + <li> src/zmapWindow/zmapWindowItemFactory.c: add assembly path mode. + + + </li> + <li> src/zmapGFF/zmapGFF2parser.c: add code to parse out assembly path + features. + + + </li> + <li> src/zmapServer/acedb/models.wrm: add new assembly mode. + + + </li> + <li> src/zmapServer/acedb/acedbServer.c: Support acedb methods as we + as zmap styles, missing feature set to style id stuff only. + + <!-- --- 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/parse.c: fix bug whereby renaming an object to an already + existing but empty object caused a crash. + + + </li> + <li> wh/command.h: add setinteraction command. + + + </li> + <li> w4/command_.h: add state for no interaction. + + + </li> + <li> w4/command.c: add command for no interaction, change dna calls to + turn off user intervention. + + + </li> + <li> wh/smap.h: improve comments on smapdna codes. + + + </li> + <li> wsocket/serverace.c: add call to turn off user interaction for + commands. + + + </li> + <li> w6/smap.c: turn off errors by default. + + + </li> + <li> wh/dna.h: add error action codes to control what happens with + mismatch. + + + </li> + <li> w7/fmapcontrol.c: add code to keep original sequence start/end + when fetching a subset of features. + + + </li> + <li> w6/treedisp.c: add code to make moving around boxes correct when + adding data. Add debug function to show BS neighbours. + + + </li> + <li> w6/dnasubs.c: add/modify functions to continue, query or fail for + mismatch errors. + + + </li> + <li> w7/gmapconvert.c: improve error message for 2 point data. + + + </li> + <li> w7/gmapdatacol.c: format change. + + + </li> + <li> w6/smap.c: add better args checking to smapmapalign + + + </li> + <li> w4/sigsubs.c: add acedb info. to sig message, replace our sig + text with portable glib one. + + + </li> + <li> w6/smap.c: remove the source_exons code I put into length call, + messes it all up. + + + </li> + <li> w7/fmapcontrol.c: fix highlighting bug, if obj. goes off screen, + only highlight siblings if original had a parent. + + + </li> + <li> w7/fmapgene.c: fix bugs: stop reselection of unselected splices, + fix copy of method on fixing gene. + + + </li> + <li> w7/smapconvert.c: bug: must only process exons if parent obj was + created ok. + + + </li> + <li> w7/gmapconvert.c: agh....fix my own cut/paste error in 2_point + tag code. + + + </li> + <li> w7/gmapdata.c: formatting/debugging changes. + + + </li> + <li> w4/parse.c: fix horrible bug in writeaccesschange code whereby it + calls a null routine. + + + </li> + <li> w3rdparty/libpfetch/: libcurlobject.c, libcurlobject_I.h, + libpfetch-utils.c, libpfetch.c, libpfetch.h: update for Roys fix + for variants. + + + </li> + <li> w1/utils.c, wh/regular.h: add small function to translate a + single digit int to the corresponding char. + + + </li> + <li> w7/smapconvert.c: output the phase of all exons, coding or not, + may need revisiting. + + + </li> + <li> w7/: gff.c, fmap_.h: add new data field to segs, we need more + data per seg. + + + </li> + <li> w3rdparty/libpfetch/: libcurlobject.c, libcurlobject.h, + libpfetch_I.h, libpfetch_P.h: these seem not to have been + committed properly last time. + + + </li> + <li> wnq/aceversion.c: update to update number 48 + + + </li> + <li> wtools/MAKE_INSTALL: remove sxaceclient, no longer supported. + + + </li> + <li> w9/belvu.c: fix bug, testing feof on a pipe that's been free'd. + + + </li> + <li> w4/command.c: add dump type to smapdump call, needs more options + in the future. + + + </li> + <li> w7/fmap_.h: add defines, fields to support dumping assembly path. + + + </li> + <li> wh/smap.h: add types to support dumping only parts of smap and + dumping smap assembly. + + + </li> + <li> wh/smapconvert.h, w7/smapconvert.c: add code to support dumping + assembly path. + + + </li> + <li> w7/gff.c: add code to support dumping smap assembly, remove + redundant zmap code. + + + </li> + <li> w6/smap.c: add code to support dumping subparts of smap and smap + assembly. + + + </li> + <li> w9/belvu.c: fix bad bug using global ALN pointer badly. + + + </li> + <li> w7/smapconvert.c: fix method name filtering for assembly_path + + + </li> + <li> w7/gff.c: Improve assembly path dumping to give strand etc etc. + + + </li> + <li> waql/aqlparse.y: remove special linux code that altered file + handles for yyparser, causes a crash now. + + + </li> + <li> w7/fmapcontrol.c: fix bug in reference point for gff dump. + + + </li> + <li> w9/belvu.c: add in some minor changes by Erik and some by me, + including removing his arrayInsert work around. + + + </li> + <li> w9/belvu.c: [no log message] + + + </li> + <li> w7/gff.c: fix glitch in offset calculation, wrong when -coords + and -refseq options specified. + + + </li> + <li> w7/fmapfeatures.c: add code to export the match sequence strand + in 'extended' versions of exblx and seqbl files. + + + </li> + <li> wh/smap.h: improve comments + add param to sMapMapAlign() to + record key of homol. + + + </li> + <li> w6/smap_.h: improve commenting. + + + </li> + <li> w6/smap.c: Improve block verify code. add sort func for reverse + mapping, make sure ref/match strands returned from alignmap. + + + </li> + <li> w9/blxparser.c: Extend exblx and seqbl to parse match strand now + exported by acedb. + + + </li> + <li> wh/blxview.h: tidy up enum for file types. + + + </li> + <li> w9/blxview.c: Fix the gapCoord func to work with -ve match + strands. Fix bug in indel marker drawing. + + + </li> + <li> w7/smapconvert.c: make sure match strand properly reported and + properly set. Fix bug in misalign handling. + + <!-- --- End editing ACeDB changes here... --- --!> + </li> +</ul> +</fieldset> +<br /> + +<!--#include virtual="/perl/footer" --> + -- GitLab