BiBiServ2 - jPREdictor

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