ReleaseNotes

Changes in DeNovoGUI 1.16.8 (July 5. 2022):

  • FEATURE IMPROVEMENT: Updated BareBonesBrowserLaunch to version 3.1.

Changes in DeNovoGUI 1.16.7 (June 8. 2022):

  • BUG FIX: Updated the link in the check for new versions.

Changes in DeNovoGUI 1.16.6 (January 26. 2020):

  • FEATURE IMPROVEMENT: Moved the code to Java 8.
  • FEATURE IMPROVEMENT: Made the JavaDoc compiler work on Java 9 and newer.

Changes in DeNovoGUI 1.16.5 (August 23. 2019):

  • BUG FIX: Fixed a bug in the use of the PathSettingsCLI.

Changes in DeNovoGUI 1.16.4 (May 15. 2019):

  • BUG FIX: Fixed a bug in the use of user-defined terminal PTMs.

  • LIBRARY UPDATE: Updated utilities to version 4.12.14

Changes in DeNovoGUI 1.16.3 (May 8. 2019):

  • BUG FIX: The paths are now updated before the IdentificationParametersCLI is executed.

Changes in DeNovoGUI 1.16.2 (June 14. 2018):

  • FEATURE IMPROVEMENT: Ensured that Novor results can be loaded across operating systems, e.g. run on Windows and open on Linux.

  • LIBRARY UPDATE: Updated utilities to version 4.12.7.

Changes in DeNovoGUI 1.16.1 (June 12. 2018):

  • LIBRARY UPDATE: Updated utilities to version 4.12.6.

Changes in DeNovoGUI 1.16.0 (April 25. 2018):

  • FEATURE IMPROVEMENT: Updated pNovo to version 3.1.1.

  • BUG FIX: Fixed a bug that resulted in changes to the paths to the algorithms being ignored.

Changes in DeNovoGUI 1.15.12 (September 6. 2017):

  • BUG FIX: Fixed a bug where the PTM mappings for PepNovo+ were not reset when changing the parameter file, which could result in unmapped PTMs unless the tool was restarted between runs.
  • BUG FIX: Fixed a bug where the Novor scores had gone missing from the Peptide Matches export.

Changes in DeNovoGUI 1.15.11 (June 23. 2017):

  • LIBRARY UPDATE: Updated utilities to version 4.11.17.

Changes in DeNovoGUI 1.15.10 (June 9. 2017):

  • LIBRARY UPDATE: Updated utilities to version 4.11.15.

Changes in DeNovoGUI 1.15.9 (May 16. 2017):

  • FEATURE IMPROVEMENT: Added a check for quotation marks in accession numbers when parsing FASTA files.

  • BUG FIX: Corrected the links to the compomics.github.io wiki pages.

  • LIBRARY UPDATE: Updated utilities to version 4.11.12.

Changes in DeNovoGUI 1.15.8 (May 8. 2017):

  • BUG FIX: Fixed a typo in the “Dimethylation of K 2H4” PTM.

  • LIBRARY UPDATE: Updated utilities to version 4.11.9.

Changes in DeNovoGUI 1.15.7 (May 8. 2017):

  • FEATURE IMPROVEMENT: Added “Dimethylation of K 2H4” to the standard list of PTMs.

  • LIBRARY UPDATE: Updated utilities to version 4.11.8.

Changes in DeNovoGUI 1.15.6 (April 1. 2017):

  • LIBRARY UPDATE: Updated utilities to version 4.11.5.

Changes in DeNovoGUI 1.15.5 (March 17. 2017):

  • BUG FIX: Fixed bugs in the set up of the identification parameters from the command line.

  • LIBRARY UPDATE: Updated utilities to version 4.11.4.

Changes in DeNovoGUI 1.15.4 (March 2. 2017):

  • FEATURE IMPROVEMENT: Changed the default number of solutions for DirecTag from 20 to 10.

  • LIBRARY UPDATE: Updated utilities to version 4.11.3.

Changes in DeNovoGUI 1.15.3 (February 17. 2017):

  • FEATURE IMPROVEMENT: pNovo+ should now finally work again.

Changes in DeNovoGUI 1.15.2 (February 15. 2017):

  • LIBRARY UPDATE: Updated utilities to version 4.11.2.

Changes in DeNovoGUI 1.15.1 (February 8. 2017):

  • LIBRARY UPDATE: Updated utilities to version 4.11.0.

Changes in DeNovoGUI 1.15.0 (January 31. 2017):

  • BUG FIX: The path to the jar file is now set even if the GUI has not been run first.
  • BUG FIX: The taxonomy files have been added, as these were needed when setting up the identification parameters on the command line.
  • LIBRARY UPDATE: Updated utilities to version 4.10.0.

Changes in DeNovoGUI 1.14.5 (December 21. 2016):

  • LIBRARY UPDATE: Updated utilities to version 4.8.9.

Changes in DeNovoGUI 1.14.4 (December 21. 2016):

  • BUG FIX: Fixed bugs in the IdentificationParametersInputBean for checking the isotope range where negative values were not allowed.

  • LIBRARY UPDATE: Updated utilities to version 4.8.8.

Changes in DeNovoGUI 1.14.3 (December 11. 2016):

  • LIBRARY UPDATE: Updated utilities to version 4.8.7.

Changes in DeNovoGUI 1.14.2 (December 7. 2016):

  • BUG FIX: Fixed an issue in the Find feature where the focus was lost in the text input field.

  • LIBRARY UPDATE: Updated utilities to version 4.8.6.

Changes in DeNovoGUI 1.14.1 (December 5. 2016):

  • BUG FIX: Fixed the backwards compatibility.

  • LIBRARY UPDATE: Updated utilities to version 4.8.5.

Changes in DeNovoGUI 1.14.0 (December 4. 2016):

  • FEATURE IMPROVEMENT: Improvements to the identification parameters.

  • FEATURE IMPROVEMENT: Improved the use of the cache.

  • BUG FIX: Corrected bugs in the DirectTag settings dialog.

  • LIBRARY UPDATE: Updated utilities to version 4.8.4.

Changes in DeNovoGUI 1.13.1 (October 10. 2016):

  • LIBRARY UPDATE: Updated utilities to version 4.7.5.

Changes in DeNovoGUI 1.13.0 (October 6. 2016):

  • FEATURE IMPROVEMENT: pNovo+ should now finally work again.

  • LIBRARY UPDATE: Updated utilities to version 4.7.4.

Changes in DeNovoGUI 1.12.5 (September 27. 2016):

  • BUG FIX: Made sure that the log parameter is recognized when using the command line.

  • LIBRARY UPDATE: Updated utilities to version 4.7.3.

Changes in DeNovoGUI 1.12.4 (September 12. 2016):

  • FEATURE IMPROVEMENT: Added the retention time to the export.

  • LIBRARY UPDATE: Updated utilities to version 4.7.2.

Changes in DeNovoGUI 1.12.3 (August 19. 2016):

  • LIBRARY UPDATE: Updated utilities to version 4.7.1.

Changes in DeNovoGUI 1.12.2 (August 13. 2016):

  • FEATURE IMPROVEMENT: Proteins are now sorted when mapping to a FASTA file.

  • FEATURE IMPROVEMENT: Attempt at making the command line exit codes follow the Unix convention.

  • LIBRARY UPDATE: Updated utilities to version 4.7.0.

Changes in DeNovoGUI 1.12.1 (July 7. 2016):

  • FEATURE IMPROVEMENT: Fixed an issue in the mgf reader where lines ending with \r could cause problems.

  • LIBRARY UPDATE: Updated utilities to version 4.6.3.

Changes in DeNovoGUI 1.12.0 (June 24. 2016):

  • FEATURE IMPROVEMENT: Cleaned up the DirecTag and Novor settings dialogs, and added a new PepNovo settings dialog.

  • LIBRARY UPDATE: Updated utilities to version 4.6.1.

Changes in DeNovoGUI 1.11.0 (June 7. 2016):

  • FEATURE IMPROVEMENT: Significantly sped up the peptide/tag to protein mapping.

  • LIBRARY UPDATE: Updated utilities to version 4.5.20.

Changes in DeNovoGUI 1.10.4 (April 19. 2016):

  • BUG FIX: Minor correction in the command line documentation for the import_precurosor_mz and import_precurosor_mz_ppm parameters.
  • BUG FIX: Tried to fix issues with the use of PepNovo on Linux/Mac (where the line file endings where not supported).

  • BUG FIX: Fixed an error on Linux/Mac where the enzyme file could not be found.

  • LIBRARY UPDATE: Updated utilities to version 4.5.12.

Changes in DeNovoGUI 1.10.3 (April 7. 2016):

  • LIBRARY UPDATE: Updated utilities to version 4.5.11.

Changes in DeNovoGUI 1.10.2 (April 1. 2016):

  • BUG FIX: Fixed bugs in the modification type for “Dimethylation of peptide N-term 2H(4)” and “Dimethylation of peptide N-term”.

  • LIBRARY UPDATE: Updated utilities to version 4.5.8.

Changes in DeNovoGUI 1.10.1 (March 16. 2016):

  • FEATURE IMPROVEMENT: Added new PTM: Dimethylation of K 2H(6) 13C(2).

  • BUG FIX: Fixed bugs in the validation of the following parameters when given as input on the command line: IMPORT_PRECURSOR_MZ_PPM, PREC_PPM, FRAG_PPM. Note that that the input is now binary (0 for Da and 1 for ppm, instead of 2 for Da and 1 for ppm as before).

  • LIBRARY UPDATE: jsparklines to version 1.0.8.
  • LIBRARY UPDATE: Updated utilities to version 4.5.7.

Changes in DeNovoGUI 1.10.0 (March 4. 2016):

  • BUG FIX: Fixed bugs in the loading of Novor result files.

  • BUG FIX: Fixed bugs in the display of fixed and variable modifications.

  • LIBRARY UPDATE: Updated utilities to version 4.5.3.

Changes in DeNovoGUI 1.9.10 (February 29. 2016):

  • BUG FIX: The Peptide Matches export now also works for Novor results.

  • BUG FIX: Improved the test for checking if a user selected Java home folder contains a valid Java installation or not.

  • LIBRARY UPDATE: Updated utilities to version 4.5.1.

Changes in DeNovoGUI 1.9.9 (February 12. 2016):

  • LIBRARY UPDATE: Updated utilities to version 4.3.22.

Changes in DeNovoGUI 1.9.8 (February 6. 2016):

  • LIBRARY UPDATE: Updated utilities to version 4.3.21.

Changes in DeNovoGUI 1.9.7 (February 5. 2016):

  • BUG FIX: Fixed bugs in the loading of custom PTMs.

  • LIBRARY UPDATE: Updated jsparklines to version 1.0.7.
  • LIBRARY UPDATE: Updated utilities to version 4.3.20.

Changes in DeNovoGUI 1.9.6 (January 28. 2016):

  • BUG FIX: Solved a potential threading issue in the peptide mass estimation.

  • LIBRARY UPDATE: Updated utilities to version 4.3.18.

Changes in DeNovoGUI 1.9.5 (January 22. 2016):

  • BUG FIX: Fixed an issue that resulted in the tool not starting if a custom Java home was set and it could not be found.

  • LIBRARY UPDATE: Updated utilities to version 4.3.16.

Changes in DeNovoGUI 1.9.4 (January 5. 2016):

  • FEATURE IMPROVEMENT: Made sure that the 24 hour format is used in all time stamps.

  • FEATURE IMPROVEMENT: Corrected minor issues with the command line documentation and made it more readable.

  • LIBRARY UPDATE: Updated utilities to version 4.3.6.

Changes in DeNovoGUI 1.9.3 (December 23. 2015):

  • FEATURE IMPROVEMENT: A log folder can now be selected when operating in command line.

  • LIBRARY UPDATE: Updated utilities to version 4.3.3.

Changes in DeNovoGUI 1.9.2 (December 7. 2015):

  • LIBRARY UPDATE: Updated utilities to version 4.1.15.

Changes in DeNovoGUI 1.9.1 (December 3. 2015):

  • FEATURE IMPROVEMENT: The de novo algorithm command lines used are now written to the log file.

Changes in DeNovoGUI 1.9.0 (December 2. 2015):

  • FEATURE IMPROVEMENT: Updated Novor to v1.05.0573.

  • FEATURE IMPROVEMENT: Updated the parameters related classes to work with json files.

  • BUG FIX: Re-added the amino acid scores for Novor.

  • LIBRARY UPDATE: Updated utilities to version 4.1.13.

Changes in DeNovoGUI 1.8.2 (November 3. 2015):

  • BUG FIX: Fixed a bug in the displayed peptide mass for Novor results.

Changes in DeNovoGUI 1.8.1 (October 22. 2015):

  • BUG FIX: Made the tool work on Java 1.6 again.

  • LIBRARY UPDATE: Updated utilities to version 4.1.8.

Changes in DeNovoGUI 1.8.0 (October 19. 2015):

  • FEATURE IMPROVEMENT: Reordered the de novo algorithms.
  • FEATURE IMPROVEMENT: Improved the progress display.

Changes in DeNovoGUI 1.7.13 (October 17. 2015):

  • BUG FIX: The tag matches and BLAST exports now works again for Novor.

  • LIBRARY UPDATE: Updated utilities to version 4.1.2.

Changes in DeNovoGUI 1.7.12 (October 15. 2015):

  • BUG FIX: The peptide matches export now works again for Novor.
  • BUG FIX: Fixed a bug where the PTM mappings for the de novo algorithms where not saved correctly in the search parameters.

Changes in DeNovoGUI 1.7.11 (October 14. 2015):

  • FEATURE IMPROVEMENT: Extended the user selected file methods to support suggested/default file names.

  • LIBRARY UPDATE: Updated utilities to version 4.0.15.

Changes in DeNovoGUI 1.7.10 (October 12. 2015):

  • FEATURE IMPROVEMENT: Tags that are too short are now ignored in the peptide to protein mapping export.

  • LIBRARY UPDATE: Updated utilities to version 4.0.14.

Changes in DeNovoGUI 1.7.9 (October 8. 2015):

  • FEATURE IMPROVEMENT: Updated Novor to version v1.03.0489, fixing potential issues related to high resolution data with very low fragment ion tolerance.

Changes in DeNovoGUI 1.7.8 (October 3. 2015):

  • BUG FIX: Fixed a bug related to PTMs not targeting specific amino acids when setting up pNovo jobs.

  • LIBRARY UPDATE: Updated utilities to version 4.0.13.

Changes in DeNovoGUI 1.7.7 (October 1. 2015):

  • FEATURE IMPROVEMENT: Improved how some of the dialogs resize in low screen resolution conditions.

  • LIBRARY UPDATE: Updated utilities to version 4.0.11.

Changes in DeNovoGUI 1.7.6 (October 1. 2015):

  • BUG FIX: Corrected a typo on the sequencing handler resulting in a null pointer.

  • LIBRARY UPDATE: Updated utilities to version 4.0.10.

Changes in DeNovoGUI 1.7.5 (September 26. 2015):

  • FEATURE IMPROVEMENT: One algorithm is now run at a time and the duration of each is reported.

Changes in DeNovoGUI 1.7.4 (September 23. 2015):

  • FEATURE IMPROVEMENT: Updated Novor to version 1.03.0479, adding support for setting the fragmentation type and mass analyzer.

  • BUG FIX: The peptide matches export now works again.

  • LIBRARY UPDATE: Updated utilities to version 4.0.8.

Changes in DeNovoGUI 1.7.3 (September 21. 2015):

  • NEW FEATURE: Added support for residue specific alpha values in the spectrum annotations, and used this to indicate the amino acid scores for Novor.

  • BUG FIX: Fixed a bug in the search feature which only searched the PepNovo results.

  • LIBRARY UPDATE: Updated utilities to version 4.0.6.

Changes in DeNovoGUI 1.7.2 (September 14. 2015):

  • FEATURE IMPROVEMENT: Updated Novor to version 1.01.0446, fixing an issue with reading some non-standard mgf files.

  • BUG FIX: Fixed a bug in the show all peaks option in the spectrum menu.
  • BUG FIX: Made sure that the Results Dialog is only opened if the sequencing actually generated any result files.

Changes in DeNovoGUI 1.7.1 (September 12. 2015):

  • BUG FIX: Novor fragment ion tolerances in ppm are now converted to Dalton in the backend (as ppm is not yet supported).

  • LIBRARY UPDATE: Updated jsparklines to version 1.0.6.
  • LIBRARY UPDATE: Updated utilities to version 4.0.5.

Changes in DeNovoGUI 1.7.0 (September 3. 2015):

  • NEW FEATURE: Added support for Novor.

  • FEATURE IMPROVEMENT: Added path settings option to the GUI.

  • BUG FIX: Fixed an issue with the wrapper in handling memory warnings for 32 bit Java 8.

  • LIBRARY UPDATE: Updated utilities to version 4.0.4.

Changes in DeNovoGUI 1.6.0 (August 27. 2015):

  • NEW FEATURE: PTM masses are now set via the atomic composition.

  • NEW FEATURE: The settings files are now called .par instead of .parameter.

  • FEATURE IMPROVEMENT: Improved the parsing of modifications from DirecTag output, such that PTMs targeting more than one residue can be parsed.

  • BUG FIX: Fixed a bug that made is impossible to swap between spectrum files in the Results frame.
  • BUG FIX: Fixed bugs in PathSettingsCLI where the paths could not be set.
  • BUG FIX: Corrected the handling of terminal PTMs for DirecTag.
  • BUG FIX: Corrected a bug in the peptide mapping.
  • BUG FIX: Fixed bugs in the exports where pNovo+ was not added correctly.

  • BUG FIX: Fixed an issue in the “More than one amino acid can be targeted by the modification X” warning where the name of the PTM was not shown.

  • LIBRARY UPDATE: Updated utilities to version 4.0.0.

Changes in DeNovoGUI 1.5.2 (July 14. 2015):

  • FEATURE IMPROVEMENT: Made it possible to open pNovo+ files via the Open menu item.

  • FEATURE IMPROVEMENT: Added a message that PepNovo+ does not have any advanced settings.

  • BUG FIX: Fixed bugs in the Tag Matches and BLAST exports.
  • BUG FIX: Fixed a bug in the loading of the results which slowed down the loading process.

  • BUG FIX: Fixed a bug in the sorting of the columns.

  • LIBRARY UPDATE: Updated utilities to version 3.49.23.

Changes in DeNovoGUI 1.5.1 (July 6. 2015):

  • FEATURE IMPROVEMENT: Redesigned the settings dialog to work better on smaller screens.

  • FEATURE IMPROVEMENT: Improved the way the advanced de novo parameters are set.

  • LIBRARY UPDATE: Updated utilities to version 3.49.22.

Changes in DeNovoGUI 1.5.0 (June 19. 2015):

  • NEW FEATURE: Added support for pNovo+ (beta).

  • NEW FEATURE: Added support for mirrored spectra in the results frame.

  • FEATURE IMPROVEMENT: Mass tolerances can now be provided in ppm.
  • FEATURE IMPROVEMENT: Improved the color coding for the ID column in the Results frame.
  • FEATURE IMPROVEMENT: Updated the “please cite us” link in the tip of the day to include the real link to the paper.
  • FEATURE IMPROVEMENT: Added a check for if DeNovoGUI is started from within a zip file.
  • FEATURE IMPROVEMENT: Increased the size of the spectrum panel.
  • FEATURE IMPROVEMENT: Made it possible to set the Java Home from the GUI.
  • FEATURE IMPROVEMENT: Improvements to the handling of errors on the command line.

  • FEATURE IMPROVEMENT: Added a new simpler way of resetting the spectrum annotation.

  • BUG FIX: Fixed a bug in the progress counter for PepNovo+.
  • BUG FIX: Fixed JavaDoc errors so that it builds again in Java 8.

  • BUG FIX: Fixed an issue in the annotation preferences that occurred if no identifications were found.

  • LIBRARY UPDATE: Updated utilities to version 3.49.11.

Changes in DeNovoGUI 1.4.12 (October 23. 2014):

  • FEATURE IMPROVEMENT: PTM tooltips now include “confident” or “not confident” in addition to the color coding.

  • FEATURE IMPROVEMENT: Renamed “no enzyme” to the more understandable “unspecific”.

  • BUG FIX: Fixed issues with using search parameter settings files from SearchGUI.

  • LIBRARY UPDATE: Updated utilities to version 3.40.0.

Changes in DeNovoGUI 1.4.11 (September 17. 2014):

  • FEATURE IMPROVEMENT: Fixed an issue with indexing mgf files with empty charge tags.

  • LIBRARY UPDATE: Updated utilities to version 3.37.3.

Changes in DeNovoGUI 1.4.10 (September 12. 2014):

  • BUG FIX: Fixed more bugs where the export of peptide matches was broken.

Changes in DeNovoGUI 1.4.9 (September 11. 2014):

  • BUG FIX: Fixed a bug where the export of peptide matches was broken.

  • LIBRARY UPDATE: Updated jsparklines to version 1.0.4.
  • LIBRARY UPDATE: Updated utilities to version 3.37.1.

Changes in DeNovoGUI 1.4.8 (August 29. 2014):

  • NEW FEATURE: Added “type to find” in the PTM table in the Search Settings dialog.

  • NEW FEATURE: Added PTM tooltips in the Search Settings dialog.

  • BUG FIX: Fixed a bug in the use of custom PTM patterns.

  • LIBRARY UPDATE: Updated utilities to version 3.35.5.

Changes in DeNovoGUI 1.4.7 (August 27. 2014):

  • BUG FIX: Fixed a bug that stopped DeNovoGUI if only DirecTag was used.

Changes in DeNovoGUI 1.4.6 (August 21. 2014):

  • BUG FIX: Fixed an issue in the auto update feature that could occur on specific client machine setups.

  • LIBRARY UPDATE: Updated utilities to version 3.35.3.

Changes in DeNovoGUI 1.4.5 (August 8. 2014):

  • BUG FIX: Fixed a bug in the spectrum annotation of tags.

  • LIBRARY UPDATE: Updated utilities to version 3.31.2.

Changes in DeNovoGUI 1.4.4 (July 31. 2014):

  • FEATURE IMPROVEMENT: Improved the tag to protein mapping.

  • LIBRARY UPDATE: Updated utilities to version 3.30.1.

Changes in DeNovoGUI 1.4.3 (July 29. 2014):

  • NEW FEATURE: Added indicators of the supported platforms for each search engine.

  • FEATURE IMPROVEMENT: Added the TIC cut-off in the DirecTag command line.

  • FEATURE IMPROVEMENT: Made sure that closing a dialog is always considered the same as using the cancel button.

  • LIBRARY UPDATE: Updated jsparklines to version 0.8.0.
  • LIBRARY UPDATE: Updated utilities to version 3.29.7.

Changes in DeNovoGUI 1.4.2 (June 25. 2014):

  • FEATURE IMPROVEMENT: If there is no internet connection the check for new version no longer prints an error log to the log file.
  • FEATURE IMPROVEMENT: Improved the speed of the Waiting Dialog.

  • FEATURE IMPROVEMENT: Cleaned up the closing of internal database connection.

  • LIBRARY UPDATE: Updated utilities to version 3.28.30.

Changes in DeNovoGUI 1.4.1 (May 19. 2014):

  • FEATURE IMPROVEMENT: Updated the Java Settings dialogs.

  • BUG FIX: Fixed a bug in the Peptide Matches export where the database connection was dropped.

  • LIBRARY UPDATE: Updated utilities to version 3.26.38.

Changes in DeNovoGUI 1.4.0 (April 30. 2014):

  • NEW FEATURE: Added Linux support for DirecTag (32 and 64 bit).
  • NEW FEATURE: Added 32 bit and 64 bit versions of DirecTag for Windows.
  • NEW FEATURE: DirecTag is now disabled on Mac (as a Mac build is not yet available).
  • NEW FEATURE: PepNovo is now disabled on Linux 32 bit (as a 32 bit build is not available).

  • NEW FEATURE: Added new command line options for path configuration.

  • FEATURE IMPROVEMENT: Added the possibility for the user to turn the auto update on and off.

  • FEATURE IMPROVEMENT: The Bug Report dialog now refers to the DeNovoGUI Google Group.

  • BUG FIX: Fixed a typo in the reference to the CLI wiki page.
  • BUG FIX: Fixed a bug in the Job class where the process was always referred to as PepNovo.
  • BUG FIX: Fixed a bug in the algorithm location dialog where the browse button for DirecTag referred incorrectly to PepNovo.

  • BUG FIX: If either the PepNovo or DirecTag commands fails the whole process is now canceled. (Instead of opening empty results as before.)

  • LIBRARY UPDATE: Updated utilities to version 3.26.28.

Changes in DeNovoGUI 1.3.7 (April 10. 2014):

  • NEW FEATURE: The DeNovoGUI report is now saved in the output folder.

  • BUG FIX: Fixed a bug in the peptide matches export filters.

Changes in DeNovoGUI 1.3.6 (April 8. 2014):

  • FEATURE IMPROVEMENT: Added score and number of matches filter for all export options.

Changes in DeNovoGUI 1.3.5 (April 3. 2014):

  • BUG FIX: Enabled the export for DirecTag results.

  • BUG FIX: Fixed an issue with the creation of terminal PTMs without specific targets.

  • LIBRARY UPDATE: Updated utilities to version 3.26.9.

Changes in DeNovoGUI 1.3.4 (April 1. 2014):

  • FEATURE IMPROVEMENT: Implemented memory setting and restart by the user.

  • FEATURE IMPROVEMENT: Added catching of the out of memory error when mapping to FASTA file.

  • BUG FIX: Fixed a bug in the protein iterator where the last protein was not included.

  • LIBRARY UPDATE: Updated utilities to version 3.26.4.

Changes in DeNovoGUI 1.3.3 (March 30. 2014):

  • BUG FIX: Fixed a bug that made it impossible to load DirecTag results without at least one fixed modification in the settings.

  • LIBRARY UPDATE: Updated utilities to version 3.26.3.

Changes in DeNovoGUI 1.3.2 (March 27. 2014):

  • BUG FIX: Fixed a bug where results from both algorithms was tried loaded at the end of the processing even if only one algorithm was used.

Changes in DeNovoGUI 1.3.1 (March 27. 2014):

  • BUG FIX: Fixed a bug in the method for getting all non fixed modifications, used in the export peptides feature.

  • LIBRARY UPDATE: Updated utilities to version 3.25.14.

Changes in DeNovoGUI 1.3.0 (March 26. 2014):

  • NEW FEATURE: Added support for DirecTag.
  • NEW FEATURE: Added tags to FASTA file mapping. (beta)
  • NEW FEATURE: Added the possibility to create identification parameters files from the command line.

  • NEW FEATURE: Added the option of setting the maximum number of hits to export per spectrum for the BLAST export.

  • FEATURE IMPROVEMENT: Improved the memory handling of the object cache.
  • FEATURE IMPROVEMENT: Updated the TMT modifications to support 10-plex.
  • FEATURE IMPROVEMENT: Extended the export.

  • FEATURE IMPROVEMENT: Added the high resolution annotation option to the spectrum menu.

  • BUG FIX: Fixed a bug in the settings dialog that closed the settings dialog if the user canceled the save as dialog.

  • LIBRARY UPDATE: Updated utilities to version 3.25.12.

Changes in DeNovoGUI 1.2.3 (November 27. 2013):

  • FEATURE IMPROVEMENT: Improved the information printed to the waiting dialog during the sequencing.
  • FEATURE IMPROVEMENT: The possible mass deltas for the manual de novo sequencing are now set in correspondence with the PTMs used for the sequencing.
  • FEATURE IMPROVEMENT: Added tooltips with the maximum fragment ion and precursor mass tolerances to the Settings Dialog.
  • FEATURE IMPROVEMENT: The default PTMs selection in the Search Settings Dialog is now only shown if All Modifications is selected.

  • FEATURE IMPROVEMENT: Removed the Search Settings saving from the Settings Dialog.

  • BUG FIX: The PepNovo PTM mapping is now stored in the search parameters.
  • BUG FIX: Made sure that only valid search parameter files can be selected.
  • BUG FIX: Fixed GUI bugs in the progress dialogs when exporting to file.

  • BUG FIX: The exception handler now refers to DeNovoGUI web pages (and not PeptideShaker as before).

  • LIBRARY UPDATE: Updated utilities to version 3.18.10.

Changes in DeNovoGUI 1.2.2 (October 8. 2013):

  • BUG FIX: Fixed a bug where the startup log was always empty.

  • BUG FIX: Fixed a bug in the wrapper used to start the tool.

  • LIBRARY UPDATE: Updated utilities to version 3.15.23.

Changes in DeNovoGUI 1.2.1 (October 5. 2013):

  • BUG FIX: Fixed a bug in the reporter ion masses shown in the Modification Details dialog.

  • LIBRARY UPDATE: Updated utilities to version 3.15.20.

Changes in DeNovoGUI 1.2.0 (September 27. 2013):

  • NEW FEATURE: Added a “one-click BLAST” option to the De Novo Peptides table.
  • NEW FEATURE: Added BLAST compatible matches export.
  • NEW FEATURE: Added a spectrum annotation dialog to the results dialog where the user can select the annotation accuracy and level.

  • NEW FEATURE: Added an edit modifications edit option to the settings dialog.

  • FEATURE IMPROVEMENT: Added the spectrum details in front of every PSM in the default export.
  • FEATURE IMPROVEMENT: Updated the help text regarding the terminal mass gaps and how they affect the peak annotation.
  • FEATURE IMPROVEMENT: Hid the enzyme and model settings from the settings dialog.
  • FEATURE IMPROVEMENT: Added a new default precursor tolerance of 0.5 Dalton.

  • FEATURE IMPROVEMENT: Fixed terminal PTMs are now treated as variable PTMs.

  • BUG FIX: Reporter ions are now displayed in the spectrum annotation.
  • BUG FIX: The same fragment ion accuracy is now used in the manual and automatic de novo sequencing and peak annotation.

  • BUG FIX: Removed the spectrum help details referring to the plots that are not used.

  • LIBRARY UPDATE: Updated utilities to version 3.15.6.

Changes in DeNovoGUI 1.1.0 (August 11. 2013):

  • NEW FEATURE: Added a first version of a peptide sequence search feature in the results frame. (beta)

  • FEATURE IMPROVEMENT: Improved the way the N and C terminal gaps are shown in sequence column in the de novo matches table.
  • FEATURE IMPROVEMENT: Added the version number to the results frame title bar.
  • FEATURE IMPROVEMENT: Made sure that the results frame is shown in the middle of the screen if minimized.
  • FEATURE IMPROVEMENT: Added better error handling when re-loading de novo results and the wrong mgf file is selected.
  • FEATURE IMPROVEMENT: Fixed some issues with the size of the help dialogs.
  • FEATURE IMPROVEMENT: Added a progress dialog if the reference dataset has to be re-indexed.

  • FEATURE IMPROVEMENT: Fixed PTMs can now be shown in the GUI (both for the table and the spectrum).

  • BUG FIX: Terminal PTMs are now handled correctly.
  • BUG FIX: Fixed PTMs are now handled correctly.
  • BUG FIX: Added support for the N and C terminal gaps in the spectrum annotation.
  • BUG FIX: Set the correct max values for the spinners in the Settings dialog.
  • BUG FIX: The Settings dialog now resizes correctly.

  • BUG FIX: Fixed bugs in the peptide m/z values in the peptide table.

  • LIBRARY UPDATE: Updated utilities to version 3.14.21.

Changes in DeNovoGUI 1.0.0 (July 16. 2013):

  • The first public release of DeNovoGUI.
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DeepLC ThermoRawFileParser ThermoRawFileParserGUI colims compomics-utilities dbtoolkit denovogui fragmentation-analyzer iceLogo jsparklines jtraml mappi-dat mascotdatfile meta-proteome-analyzer moff ms-lims ms2pip_c ms2rescore omssa-parser pepshell peptide-shaker pladipus pride-asa-pipeline reporter search-all-assess-subset searchgui spectrum_similarity thermo-msf-parser xilmass xtandem-parser