How to get version and history from the jPREdictor
To get information on which version of the jPREdictor is currently running on
your system either start the jPREdictor in command line mode by typing
java -jar jPREdictor.jar --version or start it in GUI
mode by typing java -jar jPREdictor.jar (without any
parameters) and select Help->About from the menu.
The command line parameter --version was implemented in verion 1.01 of the
jPREdictor. If it does not function you have the first release version with version
number 1.0 on your system. A menu was not added to the jPREdictor until version
number 1.07, so to get version informations before release candidate 1.07 the only
choice is using the command line parameter --version.
The development history for the jPREdictor can be gotten by typing
java -jar jPREdictor.jar --history . This parameter was
implemented in verion 1.01 of the jPREdictor. If it does not function you have the
final release version 1.0 on your system. Another way is to choose Help->History in
the graphical user interface. The menu was not added before version 1.07 of the
jPREdictor so this choice might not be available.
Version 1.23 (release 2008/04/24)
- added the new parameter 'searchDirection' for MultiMotifs defined via
option files
- fixed an error with flat triple- and higher-order motifs reporting to few
hits; this error occured rarely but regulary and did not occur for DoubleMotifs
or non-flat composite-motifs consising of Double- motifs, such as
(Pho-DSP1)-(Pho-DSP1)
Version 1.22 (release 2008/04/22)
- added the motif evolution (in fact, evolution was already implemented and
usable in version 1.21)
- added the motif clustering (in fact this was also already
implemented)
- added parameter '-C' to fine-tune evolution and clustering
- changed parameter '-p' to accept arbitrary distances
- changed behavior of motif evolution: N-characters are now possible to
occur in sequence motifs in the process of mutation
- changed behavior of motif evolution: recombination is changed to be a
crossover between arbitrary MultiMotifs (limitation to DoubleMotifs is
removed)
- changed output for searching motifs (parameter '-t') to contain more
information (especially useful for the search of motif patterns)
Version 1.21 (release 2008/01/09)
- added the argument 'uniform' for option file parameter
'background'
- added parameter '-G' to switch off the use of predefined motifs in any
case, this might be useful to start the motif evolution with an empty (randomly
generated) motif set
- added the version and a timestamp to be printed in the first line when
option '-v' is given
- added warnings for inconsistencies during creation of the final motif
list, which may occur when parameter '-p' is used together with the usable flag
in the option file
- added the final list of motifs used by the program to be printed after it
was created (verbose mode only, parameter '-v')
- changed the GUIs 'Load ...' routine the way, that the usable flag set in
the option file decides whether loaded motifs are checked or not
- changed the GUIs 'Save ...' routine the way, that the motifs checking is
reflected by the 'usable' flag in the option file
- changed for [MultiMotifList]s in option files that built double motifs get
the distance informations stored in the name
- fixed an error in the MotifMaker responsible for an empty PSSM matrix
after 'Pasting...' sequences and after switching the tabs
- fixed the rare out-of-memory error while scoring
- fixed the error in the MotifMaker that motifs with equal sequence were
rejected in the 'Build Double Motifs' process
- fixed the error in the GUI that checking or unchecking the FASTA box after
pasting or browsing did not change the type of that sequence
- fixed the error that scoring of sequences in RAW format does not yield the
same result whether they are provided as file (here, new-lines are discarded
correctly) or pastet via GUI
- fixed an error with the vertical bar in the ScorePlotBrowser which did not
follow under the mouse pointer but slightly shifted to the right
- fixed the error that multiple files given to option '-b' and '-m' were
treated as table files if a format string was omitted; now if multiple files are
given they are treated as sequence files to be concatenated, per default in
FASTA format
Version 1.2 (release 2007/06/12)
- WARNING: changed default for sequence length normalization to 'true' and
therefore added option '-A' to switch it off
- WARNING: changed default for window shift value from 100 to 10
- added multi file support for GUI browse options
- added option '--seed' to set the seed of the random number
generator
- added options to force the jPREdictor into performing certain tasks:
'--forceSearchMotifs', '--forceWeightMotifs', '--forceScoreSequence', help for
this options can be found using parameter '-hs'
- added option '--forceGUI' to start the GUI after parameter evaluation was
done
- added option 'cutoff' to [Sequence] section in option file
- changed verbose option '-v' to output the seed as well, even if the random
number generator is never used
- changed the insert-Motifs-into-MultiMotif policy in the MotifMaker to
insert all selected motifs and not only the first-level ones
- changed 'Clear Tab' behaviour in MotifMaker to not clear both PSPMs as
well as PSSMs table when clicked once
- changed GUI to make it more resizable
- changed GUI to make the motifs selectable
- changed option '--compriseToBands' to not perform a cutoff calculation in
case a cutoff is given through option '-c' but to output all bands above that
cutoff
- changed option '-c' and '-u' to not longer work mutially exclusive but in
case both are given to print first the bands followed by the best
- changed the output text field in the GUI to become faster
- fixed an error in the score plot browser, which caused a broken plot when
only low scores appeared, and which was also responsible for an incorrect
behavior of the slider bar
- fixed parameter '--compriseToBands' to work correctly with stdin
now
- fixed a NullPointerException occuring arbitrarily
Version 1.14 (release 2006/11/23)
- added option-file help and jPREdictor-development history to
GUI
- added parameter '-?' to get help
- added Alt+x (exit without change) functionality to every window
- added 'Overwrite', 'Replace', 'Clear selection' button to
MotifMaker
- revised the usage informations (parameter '-h')
- changed register and insertion policies of MotifMaker and option file the
way, that duplicate names are prohibited
- changed functionality of MotifMaker button 'Edit' to edit the motif
nearest the first selection but less or equal in depth
- changed name of MotifMaker button 'Clear fields' to 'Clear tab' and of
'Clear all' to 'Clear all tabs'
- changed functionality of MotifMaker buttons 'Clear tab' and 'Clear all
tabs' to set the search direction to both
- changed functionality of MotifMaker button 'Register' to include the
function of button 'Build multi motif' which in turn was removed
- fixed an error with the GUI on Mac platforms, where the windows were
neither removable nor resizeable due to missing window decorations
- fixed an error occuring in the GUI when the threshold was zero
Version 1.13 (release 2006/10/24)
- renamed normal/revcomp search direction to plus/minus
- fixed the error, that '-' was treated as filename when it was the only
argument for parameter '-f' (first occurrence in v1.05)
- changed the command line parameter '--cutoffCalc' to print some status
(progress) informations, which are sent to stderr
- fixed an error with the name generation in MotifMakers 'Build double
motifs' action for multi motifs
Version 1.12 (release 2006/09/14)
- added score-cutoff calculator for command line; parameter
--cutoffCalc
Version 1.101 (release 2006/08/17)
- added multi file support for loading option files in GUI
- changed ScorePlotBrowser to show whole score plot in the beginning and
after the user resets the x- or the y-zoom, respectively
- added scroll bar for y-axis in ScorePlotBrowser
- fixed issues with a wrongly printed error message after exporting the
screen in the ScorePlotBrowser
Version 1.1 (release 2006/07/03)
- changed the tree field on the MultiMotif panel (MotifMaker window) to
store individual distances between motifs as well; MultiMotif creation uses such
information
- error messages are now completely sent to stderr rather then
stdout
- changed the behavior of motif insertion to have motifs added to a tree
always before the first selected one
- fixed an error with removing motifs in the MotifMaker window
- changed the parameter '--PSSMprobs' to use the globally set background
character distribution instead of a uniform one, changed the algorithm behind to
become faster
- added the new attribute 'global_background' for option files
Version 1.07 (release 2006/06/01)
- added menu to the jPREdictor main screen
- fixed option '-u' to output correct values rather than 'true'
- changed the handling of FASTA file head lines: up to 32,000 characters are
saved and output together with the results
- changed the main window's behavior in case of error: most error output is
now shown in the lower text area, which was meant for that purpose
- changed the CutoffCalculator-button to be disabled together with the other
action buttons
- changed Load/Save buttons to read not only the motifs from a file but the
settings too
- moved Load/Save buttons from MotifMaker window to main window
surface
Version 1.05 (release 2006/05/11)
- added multi file support for parameter '-b' and '-m'
- fixed an error for option '-f', where the argument '-,fasta' was not
recognized properly
- fixed an error for '--compriseToBands', where the comprising sometimes
reported to much bands especially for high scores
- fixed an error for option '--compriseToBands', where the file given by
option '-f' could not be opened due to the multi file support for '-f'
introduced in version 1.01
- changed option '--compriseToBands' the way, that the sequence window width
is no longer taken from the processed file but from option '-w'; changed help to
reflect it
- changed output of time to show seconds, minutes, hours and days
- the Cutoff-Calculator will show the time needed for calculation
Version 1.04 (release 2006/04/03)
- fixed an error in option '-d', where the number of allowed errors was not
recognized properly
- added parameter -ho
- changed output for occurrences of motifs slightly: each occurrence of
subsequent ones for the same motif is now ouput to a new line rather than in the
same line
Version 1.03 (release 2006/03/29)
- added score cutoff calculator
Version 1.02 (release 2006/03/28)
- added menu in score plot browser
- removed buttons from surface in score plot browser
- added export for sequence in score plot browser
- added weight changing possibility in MotifMaker
Version 1.01 (release 2006/02/28)
- added multi file support for parameter '-f'
- added parameter --version
- added parameter --history
- changed help text and description slightly
- changed sequence colors in ScorePlotBrowser
Version 1.0 (release 2006/02/23)
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