Acedb Newsletters for Year2003

January

• New Features
• Set your DNA highlight colour
• More changes to the EMBL dumper
• Server download package now includes all server documentation.
• Articles
• MakeAceDB - A new script for setting up an acedb database from scratch
• Bugs Fixed
• Allowable names for -tsuser option
• GMap cursor movement bug
• Dotter and invalid sequence query bug
• Developers Corner
• Old array bug
• Main routine utilities
• Smapconvert routine uses new smap call to check orientation
• Smapconvert and the new use of the Allele subtag in the Sequence class
• Web/Aquila improvements

February

• New Features
• Message window changes in xace and the stand-alone blixem
• "Time_Stamps" command now prints out current time stamp status
• DAS dumping from acedb
• Status command now reports last database save date
• AceDB on the HP Itanium
• Bugs Fixed
• Temp Gene on reverse strand off by 2
• Huge block files
• Bug in sMapDNA
• Future Plans
• Client/server version of FMap
• Developers Corner
• Glib usage
• Change to GFF dumping code in acedb

March

• General News
• New Features
• New and improved giface commands
• FMap and display of reverse strand features.
• You saw it here first
• FMap keyboard shortcuts
• Controlling the frequency of timestamps in the server log file
• GFF output, unknown fields
• Articles
• New Gene Features program available
• Bugs Fixed
• Losing the active feature on scrolling in FMap
• Server exit message twice
• Developers Corner
• Incredible dotter bug
• Array and keyset bug
• New graph package call
• Some changes to the gex/graph package
• Some changes to the build system
• Some changes to smap to fix a pernicious bug

April

• General News
• AceDB powers the worm...or something like that...
• New Features
• DNA FMap keyboard shortcut
• AceDB now supports different genetic codes
• Improved text search in tree display
• A new "-list" option for the "gif seqfeatures" command.
• Articles
• Tightening up GFF output format from AceDB
• Running the AceDB server under the control of xinetd
• Bugs Fixed
• DNA dumping
• GFF dumping the "reverse" strand
• Developers Corner
• bIndexGetTag2Key() function
• Getting graph and gex to co-exist for key bindings
• sMapTreeCoords(): a more general sMapTreeRoot()
• Getting the object from which an FMap seg was derived

May

• New Features
• A rare addition to the new Genetic_code class
• A load of old pfetch-blixem-dotterness
• An extension to using Keysets in the ACEDB Query Language
• Articles
• An update to the tree display find facility
• Editting LongText
• Bugs Fixed
• Big sequence bug in blixem
• Developers Corner
• Bug in catText
• Graph PICK and modifiers
• Rationalisation of peptide routines
• New wdoc subdirectories for developer docs
• Small makefile change
• Fixing Database partition size in AceDB

June

• General News
• New Features
• Expanding Keysets in the ACEDB query language
• Getting the xace main window id for use with xremote
• Ace-C: a new C interface to acedb
• Named Keysets
• Articles
• Editting wspec/models.wrm
• Bugs Fixed
• Gene curation bug in FMap
• Blixem not displaying homologies that extend to end of sequence
• acediff bugs
• Printer list in print window
• makefile shenanigans
• Developers Corner
• Performance and acedb
• About catText catBinary
• Server speed up
• Optimisations
• Chrono

July

• New Features
• Blixem and selected homologies
• New "subset" command in tace/giface
• New "Toggle TagCount" menu option in tree display
• Articles
• Cut, Paste and Text windows
• Genetic_code class: one more time
• Case sensitivity and object names
• Bugs Fixed
• Database reindex messages
• Blixem not showing homologies correctly (part 25)
• Future Plans
• Configurable error messages
• ZMap, Son of FMap
• Developers Corner
• New "chrono" command in tace/giface
• Change to the way SMap constructs the DNA for a virtual sequence
• Adding new tests to aquila

August

• Articles
• Acedb and MS Windows
• SMap and FMap
• Bugs Fixed
• Tree display
• Blixem bug when showing gapped homologies
• Developers Corner
• Aquila documentation

September

• General News
• New Features
• Blixem/Dotter for Windows
• Troubles with "make"
• Articles
• The future of acedb
• Searching text in acedb
• Bugs Fixed
• DNA highlighting lost in FMap
• Reusing an FMap and reverse-complementing
• No_display tag in Method class
• Developers Corner
• New vtxt functions

October

• General News
• New Features
• Composite classes: the opposite of Subclasses
• Gene Finder changes: Making Temp Genes
• Articles
• GTK 2: moving on with the times
• FMap changes
• Bugs Fixed
• Small Dotter change
• Find bug in Tree display
• FMap bugs
• Server bug
• Developers Corner
• New Pick function for Composite classes
• Various sMapConvert() bits
• Aquila

November

• General News
• New Features
• GTK versions 1 and 2
• AceConn error message routine
• Articles
• Improved GFF dumping
• Bugs Fixed
• SMap bug with Align tag
• Developers Corner
• ZMap Work
• Build/Test

December

• New Features
• Confirmed Introns in FMap
• Articles
• EMBL dumping
• More FMap/SMap/GFF changes
• GFF changes
• Bugs Fixed
• Confirmed Intron bug
• SMap bug
• Blixem bug
• Developers Corner
• ZMap
• classModel2Class() function
• Aquila changes