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DeNovoGUI Changelog

What's new in DeNovoGUI 1.16.7

Jun 11, 2022
  • BUG FIX: Updated the link in the check for new versions.

New in DeNovoGUI 1.16.6 (Jun 11, 2022)

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

New in DeNovoGUI 1.16.5 (Jun 11, 2022)

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

New in DeNovoGUI 1.16.4 (Jun 11, 2022)

  • BUG FIX: Fixed a bug in the use of user-defined terminal PTMs.
  • LIBRARY UPDATE: Updated utilities to version 4.12.14

New in DeNovoGUI 1.16.3 (Jun 11, 2022)

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

New in DeNovoGUI 1.16.2 (Jun 11, 2022)

  • 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.

New in DeNovoGUI 1.16.1 (Jun 11, 2022)

  • LIBRARY UPDATE: Updated utilities to version 4.12.6.

New in DeNovoGUI 1.16.0 (Jun 11, 2022)

  • 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.

New in DeNovoGUI 1.15.12 (Jun 11, 2022)

  • 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.

New in DeNovoGUI 1.15.11 (Jun 11, 2022)

  • LIBRARY UPDATE: Updated utilities to version 4.11.17.

New in DeNovoGUI 1.15.10 (Jun 11, 2022)

  • LIBRARY UPDATE: Updated utilities to version 4.11.15.

New in DeNovoGUI 1.15.9 (Jun 11, 2022)

  • 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.

New in DeNovoGUI 1.15.8 (May 10, 2017)

  • BUG FIX: Fixed a typo in the “Dimethylation of K 2H4” PTM.
  • LIBRARY UPDATE: Updated utilities to version 4.11.9.

New in DeNovoGUI 1.15.6 (Apr 1, 2017)

  • LIBRARY UPDATE: Updated utilities to version 4.11.5.

New in DeNovoGUI 1.15.5 (Mar 20, 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.

New in DeNovoGUI 1.15.4 (Mar 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.

New in DeNovoGUI 1.15.3 (Feb 17, 2017)

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

New in DeNovoGUI 1.15.2 (Feb 16, 2017)

  • LIBRARY UPDATE: Updated utilities to version 4.11.2.

New in DeNovoGUI 1.15.1 (Feb 8, 2017)

  • LIBRARY UPDATE: Updated utilities to version 4.11.0.

New in DeNovoGUI 1.15.0 (Jan 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.

New in DeNovoGUI 1.14.5 (Dec 27, 2016)

  • LIBRARY UPDATE: Updated utilities to version 4.8.9.

New in DeNovoGUI 1.14.3 (Dec 12, 2016)

  • LIBRARY UPDATE: Updated utilities to version 4.8.7.

New in DeNovoGUI 1.14.2 (Dec 8, 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.

New in DeNovoGUI 1.13.1 (Oct 11, 2016)

  • LIBRARY UPDATE: Updated utilities to version 4.7.5.

New in DeNovoGUI 1.12.5 (Sep 28, 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.

New in DeNovoGUI 1.12.4 (Sep 12, 2016)

  • FEATURE IMPROVEMENT: Added the retention time to the export.
  • LIBRARY UPDATE: Updated utilities to version 4.7.2.

New in DeNovoGUI 1.12.3 (Sep 5, 2016)

  • LIBRARY UPDATE: Updated utilities to version 4.7.1.

New in DeNovoGUI 1.12.2 (Aug 15, 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.

New in DeNovoGUI 1.12.1 (Jul 8, 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.

New in DeNovoGUI 1.12.0 (Jun 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.

New in DeNovoGUI 1.11.0 (Jun 9, 2016)

  • FEATURE IMPROVEMENT: Significantly sped up the peptide/tag to protein mapping.
  • LIBRARY UPDATE: Updated utilities to version 4.5.20.

New in DeNovoGUI 1.10.4 (Apr 21, 2016)

  • BUG FIX: Minor correction in the command line documentation for the import_precurosor_mz and import_precurosor_mz_ppm parameters.
  • LIBRARY UPDATE: Updated utilities to version 4.5.12.

New in DeNovoGUI 1.10.3 (Apr 7, 2016)

  • LIBRARY UPDATE: Updated utilities to version 4.5.11.

New in DeNovoGUI 1.10.1 (Mar 17, 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.

New in DeNovoGUI 1.10.0 (Mar 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.

New in DeNovoGUI 1.9.10 (Feb 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.

New in DeNovoGUI 1.9.9 (Feb 12, 2016)

  • LIBRARY UPDATE: Updated utilities to version 4.3.22.

New in DeNovoGUI 1.9.8 (Feb 8, 2016)

  • LIBRARY UPDATE: Updated utilities to version 4.3.21.

New in DeNovoGUI 1.9.7 (Feb 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.

New in DeNovoGUI 1.9.6 (Jan 29, 2016)

  • BUG FIX: Solved a potential threading issue in the peptide mass estimation.
  • LIBRARY UPDATE: Updated utilities to version 4.3.18.

New in DeNovoGUI 1.9.5 (Jan 23, 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.

New in DeNovoGUI 1.9.4 (Jan 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.

New in DeNovoGUI 1.9.3 (Dec 29, 2015)

  • FEATURE IMPROVEMENT: A log folder can now be selected when operating in command line.
  • LIBRARY UPDATE: Updated utilities to version 4.3.3.

New in DeNovoGUI 1.8.1 (Nov 2, 2015)

  • BUG FIX: Made the tool work on Java 1.6 again.
  • LIBRARY UPDATE: Updated utilities to version 4.1.8.

New in DeNovoGUI 1.8.0 (Nov 2, 2015)

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

New in DeNovoGUI 1.6.0 (Aug 28, 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.

New in DeNovoGUI 1.5.2 (Jul 15, 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.

New in DeNovoGUI 1.5.1 (Jul 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.

New in DeNovoGUI 1.5.0 (Jun 22, 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.

New in DeNovoGUI 1.4.12 (Dec 15, 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.

New in DeNovoGUI 1.4.11 (Sep 18, 2014)

  • FEATURE IMPROVEMENT: Fixed an issue with indexing mgf files with empty charge tags.
  • LIBRARY UPDATE: Updated utilities to version 3.37.3.

New in DeNovoGUI 1.4.10 (Sep 12, 2014)

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

New in DeNovoGUI 1.4.9 (Sep 12, 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.

New in DeNovoGUI 1.4.8 (Sep 3, 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.

New in DeNovoGUI 1.4.5 (Aug 9, 2014)

  • BUG FIX: Fixed a bug in the spectrum annotation of tags.
  • LIBRARY UPDATE: Updated utilities to version 3.31.2.

New in DeNovoGUI 1.4.4 (Aug 9, 2014)

  • FEATURE IMPROVEMENT: Improved the tag to protein mapping.
  • LIBRARY UPDATE: Updated utilities to version 3.30.1.

New in DeNovoGUI 1.4.3 (Jul 30, 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.

New in DeNovoGUI 1.4.2 (Jul 9, 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.

New in DeNovoGUI 1.4.1 (Jul 9, 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.

New in DeNovoGUI 1.4.0 (May 19, 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.

New in DeNovoGUI 1.3.7 (May 19, 2014)

  • NEW FEATURE: The DeNovoGUI report is now saved in the output folder.
  • BUG FIX: Fixed a bug in the peptide matches export filters.

New in DeNovoGUI 1.3.6 (Apr 8, 2014)

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

New in DeNovoGUI 1.3.5 (Apr 7, 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.

New in DeNovoGUI 1.3.4 (Apr 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.

New in DeNovoGUI 1.3.3 (Apr 1, 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.

New in DeNovoGUI 1.3.2 (Mar 29, 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.

New in DeNovoGUI 1.3.1 (Mar 29, 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.

New in DeNovoGUI 1.3.0 (Mar 27, 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.

New in DeNovoGUI 1.2.3 (Jan 24, 2014)

  • 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.

New in DeNovoGUI 1.2.2 (Oct 10, 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.

New in DeNovoGUI 1.2.0 (Oct 1, 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.