Version information
Version 2.1.5 (Jul 18 2020)
---------------------------
- For EMBOSS programs with two input files (e.g. needle): Ability to paste both 'files' (e.g. sequences) into two sequence editor windows without the need to specify input files
- Removed setting the color palette on startup if GUI style is set to 'default', allowing the definition of an individual color palette, e.g. on linux by using qt5ct
- Removed Qt4 support from kembossd. kembossd requires at least Qt 5.2
- Added version information to kembossd
- Sourcecode improvements
Version 2.1.4 (May 05 2017)
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- Updated the expired SSL certificates
Version 2.1.3 (Dec 30 2014)
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- 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)
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- 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)
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- 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