Version information


Version 2.1.4 (May 05 2017)
---------------------------
- Updated the expired SSL certificates


Version 2.1.3 (Dec 30 2014)
---------------------------
- Select range of nucleotides/aminoacids in the sequence editor
- The source of the online documentation could be selected
- Temporary EMBOSS output files are saved in a temporary directory. On exit the complete temporary directory is deleted, thus remaining temporary output files are avoided
- kemboss requires Qt Version 5.2 or higher. Compiling with Qt 4.x is not possible any more
- kembossd-admin: Print userlist to a file
- kembossd-admin: Delete cached input files that were not accessed for x days
- kembossd-admin: Clean up input file cache (Delete files in the filecache that are not in the database and delete database entries where the files are not present in the filecache)
- Sourcecode improvements


Version 2.1.2 (Apr 21 2014)
---------------------------
- Bugfix: kembossd: Fixed the SQL statement for creating a new user that was not compatible with the latest MariaDB version


Version 2.1.1 (Mar 02 2014)
---------------------------
- kembossd: Use of SQLite database instead of MySQL database possible
- kembossd: Improved stability of the kemboss server due to changes in the multithreading concept
- Bugfix: The configure dialog does not complain about missing help files if the EMBOSS online documentation is used


Version 2.1 (Feb 09, 2014)
--------------------------
- Updated to version 6.6.0 of EMBOSS
- If You start kemboss with the parameter '-portable' the configuration parameters are stored in .ini files in the subdirectory 'config' of the applications executable directory. This is especially useful on windows to create a portable version of kemboss that dos not use the registry and can be run without admin privileges from a usb stick.
- A variable EMBOSS_TEST can be entered as the path to the EMBOSS test directory. The variable has to be declared in the configfile 'Configuration' or the registry (CURRENT_USER -> Software -> kemboss.org -> Configuration). When input / output files are defined in kemboss EMBOSS_TEST can be used as a placeholder.
- Fixed an error in checking the EMBOSS version number in the about dialog
- The check for EMBOSS updates is performed only if the EMBOSS version is >= 6.5.0
- kembossd: The client OS is stored in the server log for statistical evaluation
- kembossd-admin: Delete log entries older than x days
- Bugfix: On Windows kemboss crashed on startup if EMBOSS was not installed, making it impossible to use kemboss as a client
- Fixed several more bugs


Version 2.0 (Jun 24, 2013)
--------------------------
- Added possibility to use kemboss as a client and access an EMBOSS installation on a remote server
- Added 'Whats this' help text
- Code cleanup and additional code documentation
- Compilation with Qt5 is possible but no tests have been performed yet
- Bugfix: On Linux the check for updates of EMBOSS did not work correct


Version 1.3 (Oct 29, 2012)
--------------------------
- Updated for version 6.5.7 of EMBOSS
- Added user interfaces for programs:
   assemblyget
   infoassembly
   refseqget
   variationget
   featmerge
- Updated the associated qualifiers forms
- The about dialog checks for updates of EMBOSS or kemboss


Version 1.2 (Apr 05, 2012)
--------------------------
- Enhanced database dialog
- Possibility to use the online documentation of the EMBOSS programs instead of the local help files
- EMBOSS output PDF and SVG files are viewed using the systems viewers
- Bugfixes in the database dialog


Version 1.1 (Mar 09, 2012)
--------------------------
- Updated for version 6.4.0 of EMBOSS
- Added user interfaces for programs:
    cachedas
    cachedbfetch
    cacheebeyesearch
    cacheensembl
    drfinddata
    drfindformat
    drfindid
    drfindresource
    dbxcompress
    dbxedam
    dbxobo
    dbxreport
    dbxresource
    dbxstat
    dbxtax
    dbxuncompress
    edamdef
    edamhasinput
    edamhasoutput
    edamisformat
    edamisid
    edamname
    ontocount
    ontoget
    ontogetcommon
    ontogetdown
    ontogetobsolete
    ontogetroot
    ontogetsibs
    ontogetup
    ontoisobsolete
    ontotext
    seqcount
    taxget
    taxgetdown
    taxgetrank
    taxgetspecies
    taxgetup
    godef
    goname
    drget
    drtext
    textget
    urlget
    seqxref
    seqxrefget
    showserver
    servertell
    dbtell
    eprimer32
    nthseqset
    seqretseqall
    splitsource
    feattext

- Moved database indexing from the kemboss configuration dialog to a new database dialog


Version 1.0.1 (Oct 06, 2010)
----------------------------
- Fixed qualifier names in keprimer3 (were changed in version 6.1.0 of EMBOSS and missed in the kemboss update)
- Removed qtfindreplacedialog library and integrated the code into the main executable
- Added automatic detection of EMBOSS and kemboss directories on MacOS using fink


Version 1.0 (Jul 18, 2010)
---------------------------
- Updated for version 6.3.0 of EMBOSS
- Enhanced desktop integration for Linux and MacOS
- Find/Replace for the editors
- The colors for sequence highlighting can be selected in the configuration dialog
- Default settings files moved to /etc/kemboss
- Some small changes to find the directories for the configuration files


Version 0.11 (Apr 04, 2010)
---------------------------
- Updated for version 6.2.0 of EMBOSS
- Updated for version 3.69 of PHYLIPNEW
- Sequence highlighting for the editors (leaving room for improvement)
- The time, the emboss program was running, is displayed in the program progress window


Version 0.10 (Aug 02, 2009)
---------------------------
- Updated for version 6.1.0 of EMBOSS
- Added user interface for showpep (must have missed it until now)
- Bugfix: "minscore" in extractfeat was not used


Version 0.9 (May 23, 2009)
--------------------------
- Added printing of input and output files
- Added features associated qualifiers to featreport and featcopy
- Added scaling and rotating of output graphics


Version 0.8 (Sep 27, 2008)
--------------------------
- Added possibility to copy EMBOSS program command line to clipboard
- Added user interfaces for PHYLIP programs:
	fdnadist
	fprotdist
	fgendist
	fclique
	fconsense
	fcontml
	fcontrast
	fdnacomp
	fdnainvar
	fdnaml
	fdnamlk
	fdollop
	ffitch
	fkitsch
	fneighbor
	fmix
	fpars
	fdnapars
	fprotpars
	fdnapenny
	fdolpenny
	fpenny
	frestml
	fseqboot
	fseqbootall
	ffreqboot
	frestboot
	frestdist
	ftreedist
	ftreedistpair
	fdiscboot
	fdrawgram
	fdrawtree
	ffactor

- Programs not included:
	fdnamove
	fdolmove
	fmove
	fretree

- Added user interface for epestfind


Version 0.7 (Aug 25, 2008)
--------------------------
- Added option to hide the toolbars
- Source code optimizations
- Bugfix: A problem with the Oxygen style layout has been fixed


Version 0.6 (Aug 12, 2008)
--------------------------
- Added possibility to select GUI style (e.g. Windows, Motif, CDE, Plastique, etc.). The main reason for adding this function was, that under certain circumstances I experienced problems with fonts when the Oxygen style of KDE 4 is used. This function lets you chose the style independently of the window manager
- Added cut, copy, paste, undo, redo to the input / output text editors
- Implemented 'Open recent file' for kemboss main window
- Bugfix: When a set of open program windows was saved via the kemboss main window, the window name and not the EMBOSS program name was used, causing trouble with program windows for multiple EMBOSS programs


Version 0.5 (Aug 04, 2008)
--------------------------
- Simplified layout of the configuration dialog
- Settings of the 'index database' page in the configuration dialog are saved
- Added possibility to add database to 'emboss.default' or '.embossrc' file
- Line wrapping of the input and output text edits can be changed
- Bugfix: Indexing sequence databases failed due to wrong parameter declaration
- Bugfix: Selection of columns to show in Infoseq, Infoalign and Textsearch were not handed over correctly


Version 0.4 (July 28, 2008)
---------------------------
- Updated for version 6.0.1 of EMBOSS:
- Added user interfaces for EMBOSS programs:
	aligncopy
	aligncopypair
	featcopy
	featreport
	maskambignuc
	maskambigprot
	consambig
	sizeseq
	nohtml
	nospace
	notab
	trimspace
	skipredundant
	density
	jaspscan
	jaspextract
	infobase
	inforesidue
- Source code optimizations
- Bugfix: If a program window didn't contain an input tab, the output tab was not shown automatically after the emboss program was executed (e.g. redata)


Version 0.3 (June 22, 2008)
---------------------------
- If the output of an EMBOSS program is changed manually in the outputs text edit, the edited text file is saved instead of the original EMBOSS program output
- The font type and size of the input and output file text edits can be changed
- Some small bugfixes


Version 0.2 (May 23, 2008)
--------------------------
- Source code optimization, resulting in greatly reduced file size
- Some small bugfixes


Version 0.1 (May 13, 2008)
--------------------------
- Available user interfaces for EMBOSS programs:
	aaindexextract
	abiview
	antigenic
	backtranseq
	backtranambig
	banana
	biosed
	btwisted
	cai
	chaos
	charge
	checktrans
	chips
	cirdna
	codcmp
	codcopy
	coderet
	compseq
	cons
	cpgplot
	cpgreport
	cusp
	cutgextract
	cutseq
	dan
	dbiblast
	dbifasta
	dbiflat
	dbigcg
	dbxfasta
	dbxflat
	dbxgcg
	degapseq
	descseq
	diffseq
	digest
	distmat
	dotmatcher
	dotpath
	dottub
	dreg
	edialign
	einverted
	emma
	emowse
	entret
	eprimer3
	equicktandem
	est2genome
	etandem
	extractalign
	extractfeat
	extractseq
	findkm
	freak
	fuzznuc
	fuzzpro
	fuzztran
	geecee
	garnier
	geeceex
	getorf
	helixturnhelix
	hmoment
	iep
	infoalign
	infoseq
	isochore
	lindna
	listor
	makenucseq
	makeprotseq
	marscan
	maskseq
	matcher
	megamerger
	merger
	msbar
	mwfilter
	mwcontam
	needle
	newcpgreport
	newcpgseek
	newseq
	noreturn
	notseq
	nthseq
	octanol
	oddcomp
	palindrome
	pasteseq
	patmatdb
	patmatmotifs
	pepcoil
	pepinfo
	pepnet
	pepstats
	pepwheel
	pepwindow
	pepwindowall
	plotcon
	plotorf
	polydot
	preg
	prettyplot
	prettyseq
	profit
	prophecy
	prophet
	prosextract
	primersearch
	printsextract
	pscan
	psiphi
	rebaseextract
	recoder
	redata
	remap
	restover
	restrict
	revseq
	seqmatchall
	seqret
	seqretsplit
	showalign
	showdb
	showorf
	showseq
	shuffleseq
	sigcleave
	silent
	sirna
	sixpack
	skipseq
	splitter
	stretcher
	stssearch
	supermatcher
	syco
	tcode
	textsearch
	tfextract
	tfscan
	tmap
	tranalign
	transeq
	trimest
	trimseq
	twofeat
	union
	vectorstrip
	water
	whichdb
	wobble
	wordcount
	wordfinder
	wordmatch
	wossname

- Programs not included:
	acdc
	acdpretty
	acdtable
	acdtrace
	acdvalid
	tfm
	seealso
	yank: parameters "start", "end" and "reverse strand" are only accessible via command line