June 3rd, 2013· NEW FEATURE: The species can now be set in the PeptideShakerSettingsDialog.
· NEW FEATURE: Added a check for duplicate spectrum titles when selecting mgf files.
· LIBRARY UPDATE: Updated utilities to version 3.13.30.
May 14th, 2013· BUG FIX: Fixed a bug where white space was not allowed in the installation path.
· LIBRARY UPDATE: Updated utilities to version 3.13.18.
May 13th, 2013· BUG FIX: Fixed a bug related to setting the OMSSA modification indexes when running SearchGUI from the command line.
· LIBRARY UPDATE: Updated utilities to version 3.13.17.
May 12th, 2013· NEW FEATURE: Added MGF splitting options to the command line.
· NEW FEATURE: The size of the MGF files is now also checked when using the PeptideShaker PRIDE Reshake feature.
· FEATURE IMPROVEMENT: Tried to improve the error message displayed if the SearchGUI to PeptideShaker link fails.
· FEATURE IMPROVEMENT: Added an extra test to check that the provided PeptideShaker path actually exists before starting the PeptideShaker processing.
· FEATURE IMPROVEMENT: Only mgf files are now supported as spectrum file input, as this is the only format currently supported in PeptideShaker.
· BUG FIX: Fixed a problem with starting the tool on the latest Java release.
· BUG FIX: Fixed a bug in the SearchGUI command line where fixed modification was used instead of variable modification, making all PTMs fixed. (Only affected command lines where the PTMs were provided directly.)
· BUG FIX: Fixed a bug that resulted in the PTMs not actually being used even when provided directly on the command line.
· BUG FIX: Renamed the X!Tandem Linux binaries so that they can be auto detected.
· BUG FIX: OMSSA PTM indexes are now set for all search parameters.
· LIBRARY UPDATE: Updated utilities to version 3.13.16.
April 3rd, 2013· BUG FIX: Fixed a problem with the renaming of X!Tandem files.
· LIBRARY UPDATE: Updated utilities to version 3.11.29.
March 26th, 2013· FEATURE IMPROVEMENT: The search report now includes the search parameters, and is also created when ran from the command line (but then with just the search parameters).
· BUG FIX: Fixed a bug that made it impossible to change the memory settings.
· LIBRARY UPDATE: Updated utilities to version 3.11.27.
March 25th, 2013· NEW FEATURE: Added command line options for setting the search engine locations.
· FEATURE IMPROVEMENT: Updated X!Tandem to version CYCLONE (2013.2.01) for all platforms.
· FEATURE IMPROVEMENT: The SettingsDialog now tries to check if the search parameters have changed when the user clicks the OK button, and if any changes are detected ask the user if he/she wants to save the changes.
· FEATURE IMPROVEMENT: Added a check for if the PeptideShaker jar file actually exists in the PeptideShakerSettingsDialog.
· BUG FIX: Fixed a bug in the on/off settings for the search engines when run from the command line.
· BUG FIX: Fixed some issues that occurred when opening SearchGUI with search parameters and/or mgf files.
· BUG FIX: Fixed a bug in the check for new versions for SearchGUI that assumed that new versions for all operating systems were always released at the same time.
· BUG FIX: Tried to fix a problem occurring with X!Tandem file names with regular expressions in them.
· BUG FIX: Fixed minor code issues detected by FindBugs.
· LIBRARY UPDATE: Excluded unused transitive dependency ssj.
· LIBRARY UPDATE: Updated utilities to version 3.11.25.
February 7th, 2013· NEW FEATURE: Brand new more userfriendly frontend!
· NEW FEATURE: Search results can now be automatically processed in PeptideShaker.
· NEW FEATURE: Reimplemented the SearchGUI command line support from scratch. (http://code.google.com/p/searchgui/wiki/SearchCLI)
· NEW FEATURE: Modifications can now be defined using sequence patterns. (Note that the patterns are ignored until the data is loaded in PeptideShaker, as the search engines do not support the patterns directly.)
· NEW FEATURE: Added an option to the Advanced Settings (and the command line) to export the OMSSA results in the OMSSA csv format.
· NEW FEATURE: Made it possible to set the Java options from the Edit menu. (Not really needed for SearchGUI, but comes in handy when starting PeptideShaker from SearchGUI.)
· NEW FEATURE: Made it possible to select which PTMs to label as default and thus show up in the "most used modifications" table.
· NEW FEATURE: Improved the X!Tandem input format to support more advanced modification setups.
· FEATURE IMPROVEMENT: Changed the X!Tandem parameter "use noise suppression" from "yes" to "no", such that all spectra are searched and that the user's maximum precursor charge value is now respected. (Previously spectra with a charge higher than 3+ were ignored by X!Tandem...)
· FEATURE IMPROVEMENT: An exception is now thrown if multiple fixed modifications have the same target, as this is not really supported by X!Tandem.
· FEATURE IMPROVEMENT: The main progress bar in the waiting dialog is longer stuck at 0% until the first search is completed, but instead shows that some progress has been made.
· FEATURE IMPROVEMENT: SearchGUI can be run from paths containing special characters.
· FEATURE IMPROVEMENT: The spectrum files used in the OMSSA search can now have both lower and upper case file name types, e.g., mgf and MGF. (And not only mgf as before.)
· FEATURE IMPROVEMENT: Replaced the modification lists with tables so that more information can be shown, plus allows the users to set the ptm colors.
· FEATURE IMPROVEMENT: The OMSSA and X!Tandem processes are now actually canceled if the user cancels the search.
· FEATURE IMPROVEMENT: Added a check for duplicate entries when loading FASTA files.
· BUG FIX: Fixed a bug with the masses of user defined PTMs in the PRIDE export being set to null if a CV mapping was set.
· BUG FIX: Fixed a shortcoming in the TandemProcessBuilder where multiple variable modifications with the same target were not handled correctly.
· BUG FIX: Removed the indexing of the mgf files, as there seemed to be a bug in the indexing when splitting mgfs. Indexing is now done in PeptideShaker instead.
· BUG FIX: Made a minor change to the pom file to handle a recursive issue that occured when opening the project in NetBeans 7.2.
· LIBRARY UPDATE: Updated the X!Tandem windows versions to version 2011.12.01.1.
· LIBRARY UPDATE: Updated utilities to version 3.11.2.
September 17th, 2012· LIBRARY UPDATE: Updated utilities to version 3.8.9, to be compatible with PeptideShaker 0.18.3.
September 14th, 2012· BUG FIX: SearchGUI no longer resets the PeptideShaker memory settings.
· FEATURE IMPROVEMENT: The code now supports Maven 7.
· LIBRARY UPDATE: Updated ols-dialog to version 3.4.0
· LIBRARY UPDATE: Updated jsparklines to version 0.5.40.
· LIBRARY UPDATE: Updated jmzml to version 1.6.8.
· LIBRARY UPDATE: Updated utilities to version 3.8.9.
September 8th, 2012· FEATURE IMPROVEMENT: Minor fixes to make SearchGUI better compatible with PeptideShaker v0.18.0
· BUG FIX: Fixed a path bug that occurred when running SearchGUI from PeptideShaker.
· LIBRARY UPDATE: Updated utilities to version 3.8.6.
August 27th, 2012· NEW FEATURE: The selected output folder can now be created if it does not already exist.
· FEATURE IMPROVEMENT: Added right click Edit popup menus for the tables in the modification tab.
· BUG FIX: Fixed an issue with the indexing of the FASTA file when appending decoys.
· BUG FIX: The mgf files are now re-indexed if needed.
· LIBRARY UPDATE: Updated utilities to version 3.8.2.
August 23rd, 2012· FEATURE IMPROVEMENT: Dramatically reduced the time required to index and split files, and add decoys.
· FEATURE IMPROVEMENT: Improved the canceling of searches, such that the actual search processes are now canceled if the user clicks the cancel button.
· FEATURE IMPROVEMENT: Set the default splitting limit to 1000 MB, and 25000 spectra per MGF file.
· FEATURE IMPROVEMENT: Replaced uses of "\n" with System.getProperty("line.separator").
· LIBRARY UPDATE: dated utilities to version 3.7.6.
July 20th, 2012· FEATURE IMPROVEMENT: Double clicking in the defaults PTM table now brings up the PTM details.
· FEATURE IMPROVEMENT: Added a test so that the user does not load different mgf files with the same name.
· FEATURE IMPROVEMENT: Re-indexes the mgf files if the indexes do not contain precursor intensities.
· FEATURE IMPROVEMENT: Re-added the database selection to the Settings tab.
· FEATURE IMPROVEMENT: Improved the handling of errors in the user input.
· FEATURE IMPROVEMENT: Improved the look and feel of the titled borders when using Java 7.
· BUG FIX: Corrected a bug in the PTM jump to table feature.
· BUG FIX: Fixed an issue in the ProgressDialogX that resulted in threading issues and deadlock on Java 7.
· LIBRARY UPDATE: Updated utilities to version 3.6.10.
June 26th, 2012· FEATURE IMPROVEMENT: The tool will now detect if the user tries to start it from within a zip file.
· FEATURE IMPROVEMENT: Fixed the font color of the titled borders to look better when using Java 7.
· BUG FIX: Made it possible to edit the user defined PTMs.
· BUG FIX: The progress bars shown when adding decoy sequences and splitting mgf files are now working again.
· LIBRARY UPDATE: Updated utilities to version 3.5.6.
June 19th, 2012· FEATURE IMPROVEMENT: File shortcuts (lnk files) are now shown in the file selection dialogs.
· BUG FIX: Corrected a bug in the handling of neutral losses.
June 8th, 2012· BUG FIX: Fixed a thread issue that could cause the GUI to hang.
· FEATURE IMPROVEMENT: Increased the default size before the user is asked if he/she wants to split mgf files (> 2 0000 MB, > 25 000 000 spectra).
December 16th, 2010· New: Added tooltips to the modification lists showing modification mass, residues affected etc.
· Bug fix: Fixed a bug that occurred when switching between "Most Used Modifications" and "All Modifications" in the drop down menu.
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