What's new in DeNovoGUI 1.16.7
Jul 5, 2022
- BUG FIX: Updated the link in the check for new versions.
New 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
New in DeNovoGUI 1.16.3 (May 15, 2019)
- BUG FIX: The paths are now updated before the IdentificationParametersCLI is executed.
New in DeNovoGUI 1.16.2 (May 8, 2019)
- FEATURE IMPROVEMENT: Ensured that Novor results can be loaded across operating systems.
- LIBRARY UPDATE: Updated utilities to version 4.12.7.
New in DeNovoGUI 1.16.1 (Jun 13, 2018)
- LIBRARY UPDATE: Updated utilities to version 4.12.6.
New in DeNovoGUI 1.15.12 (Sep 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.
New in DeNovoGUI 1.15.11 (Jun 23, 2017)
- LIBRARY UPDATE: Updated utilities to version 4.11.17.
New in DeNovoGUI 1.15.10 (Jun 9, 2017)
- LIBRARY UPDATE: Updated utilities to version 4.11.15.
New 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.
New in DeNovoGUI 1.15.8 (May 9, 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 1.15.7 (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.
New in DeNovoGUI 1.15.6 (Apr 3, 2017)
- Released on April 1, 2017
- LIBRARY UPDATE: Updated utilities to version 4.11.5.
New in DeNovoGUI 1.15.5 (Mar 21, 2017)
- Released on 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.
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 (Aug 23, 2016)
- LIBRARY UPDATE: Updated utilities to version 4.7.1.
New in DeNovoGUI 1.12.2 (Aug 23, 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 (Aug 23, 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 27, 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 10, 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 9, 2016)
- LIBRARY UPDATE:
- Updated utilities to version 4.5.11.
New in DeNovoGUI 1.10.2 (Apr 9, 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.
New in DeNovoGUI 1.10.1 (Apr 9, 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.
- Updated utilities to version 4.5.7.
New in DeNovoGUI 1.10.0 (Mar 5, 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 (Mar 5, 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 9, 2016)
- LIBRARY UPDATE: Updated utilities to version 4.3.21.
New in DeNovoGUI 1.9.7 (Feb 6, 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 30, 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 26, 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 12, 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 1.9.2 (Dec 11, 2015)
- LIBRARY UPDATE: Updated utilities to version 4.1.15.
New in DeNovoGUI 1.9.1 (Dec 3, 2015)
- FEATURE IMPROVEMENT: The de novo algorithm command lines used are now written to the log file.
New in DeNovoGUI 1.9.0 (Dec 3, 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.
New in DeNovoGUI 1.8.2 (Nov 7, 2015)
- BUG FIX: Fixed a bug in the displayed peptide mass for Novor results.
New in DeNovoGUI 1.8.1 (Nov 7, 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 7, 2015)
- FEATURE IMPROVEMENT: Reordered the de novo algorithms
- FEATURE IMPROVEMENT: Improved the progress display
New in DeNovoGUI 1.7.13 (Nov 7, 2015)
- BUG FIX: The tag matches and BLAST exports now works again for Novor.
- LIBRARY UPDATE: Updated utilities to version 4.1.2.
New in DeNovoGUI 1.7.12 (Nov 7, 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.
New in DeNovoGUI 1.7.11 (Nov 7, 2015)
- FEATURE IMPROVEMENT: Extended the user selected file methods to support suggested/default file names.
- LIBRARY UPDATE: Updated utilities to version 4.0.15.
New in DeNovoGUI 1.7.10 (Nov 7, 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.
New in DeNovoGUI 1.7.9 (Nov 7, 2015)
- FEATURE IMPROVEMENT: Updated Novor to version v1.03.0489, fixing potential issues related to high resolution data with very low fragment ion tolerance.
New in DeNovoGUI 1.7.8 (Nov 7, 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
New in DeNovoGUI 1.7.7 (Nov 7, 2015)
- FEATURE IMPROVEMENT: Improved how some of the dialogs resize in low screen resolution conditions.
- LIBRARY UPDATE: Updated utilities to version 4.0.11.
New in DeNovoGUI 1.7.6 (Nov 7, 2015)
- BUG FIX: Corrected a typo on the sequencing handler resulting in a null pointer.
- LIBRARY UPDATE: Updated utilities to version 4.0.10.
New in DeNovoGUI 1.7.5 (Nov 7, 2015)
- FEATURE IMPROVEMENT: One algorithm is now run at a time and the duration of each is reported.
New in DeNovoGUI 1.7.4 (Nov 7, 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
New in DeNovoGUI 1.7.3 (Nov 7, 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.
New in DeNovoGUI 1.7.2 (Nov 7, 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.
New in DeNovoGUI 1.7.1 (Nov 7, 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
New in DeNovoGUI 1.7.0 (Nov 7, 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
New in DeNovoGUI 1.6.0 (Nov 7, 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 15, 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 24, 2015)
- NEW FEATURE:
- Added support for pNovo+ (beta)
- Added support for mirrored spectra in the results frame
- FEATURE IMPROVEMENT:
- Mass tolerances can now be provided in ppm
- Improved the color coding for the ID column in the Results frame
- Updated the "please cite us" link in the tip of the day to include the real link to the paper
- Added a check for if DeNovoGUI is started from within a zip file
- Increased the size of the spectrum panel
- Made it possible to set the Java Home from the GUI
- Improvements to the handling of errors on the command line
- Added a new simpler way of resetting the spectrum annotation
- BUG FIX:
- Fixed a bug in the progress counter for PepNovo+
- Fixed JavaDoc errors so that it builds again in Java 8
- 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 (Dec 15, 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 (Dec 15, 2014)
- BUG FIX: Fixed more bugs where the export of peptide matches was broken.
New in DeNovoGUI 1.4.9 (Dec 15, 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 (Dec 15, 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 1.4.7 (Dec 15, 2014)
- BUG FIX: Fixed a bug that stopped DeNovoGUI if only DirecTag was used.
New in DeNovoGUI 1.4.6 (Dec 15, 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.
New in DeNovoGUI 1.4.5 (Dec 15, 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 (Dec 15, 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 (Jul 9, 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 (Jul 9, 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 (Jul 9, 2014)
- FEATURE IMPROVEMENT: Added score and number of matches filter for all export options.
New in DeNovoGUI 1.3.5 (Jul 9, 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 (Jul 9, 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 (Jul 9, 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 (Jul 9, 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 (Jul 9, 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 1.2.3 (Nov 28, 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.
New in DeNovoGUI 1.2.2 (Oct 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.
New in DeNovoGUI 1.2.1 (Oct 8, 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.
New in DeNovoGUI 1.2.0 (Oct 8, 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.
New in DeNovoGUI 1.1.0 (Aug 14, 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.