ReleaseNotes


Changes in Reporter 0.7.7 (May 16. 2017):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.16.9.
  • LIBRARY UPDATE: Updated utilities to version 4.11.12.

Changes in Reporter 0.7.6 (May 8. 2017):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.16.7.
  • LIBRARY UPDATE: Updated utilities to version 4.11.9.

Changes in Reporter 0.7.5 (May 8. 2017):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.16.6.
  • LIBRARY UPDATE: Updated utilities to version 4.11.8.

Changes in Reporter 0.7.4 (April 25. 2017):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.16.5.
  • LIBRARY UPDATE: Updated utilities to version 4.11.7.

Changes in Reporter 0.7.3 (April 1. 2017):

  • LIBRARY UPDATE: Updated JSparklines to version 1.0.9.
  • LIBRARY UPDATE: Updated PeptideShaker to version 1.16.4.
  • LIBRARY UPDATE: Updated utilities to version 4.11.5.

Changes in Reporter 0.7.2 (March 17. 2017):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.16.3.
  • LIBRARY UPDATE: Updated utilities to version 4.11.4.

Changes in Reporter 0.7.1 (March 2. 2017):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.16.1.
  • LIBRARY UPDATE: Updated utilities to version 4.11.3.

Changes in Reporter 0.7.0 (February 15. 2017):

  • NEW FEATURE: Made it possible for the user to reorder the samples to change the order in the cluster displays.
  • NEW FEATURE: The sample names are now shown in the maximized versions of the cluster plots.

  • BUG FIX: Added checks in the clustering when no elements are selected to avoid null pointers.
  • BUG FIX: Avoided a null pointer that occurred if a dataset was loaded that did not contain any reporters.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.16.0.
  • LIBRARY UPDATE: Updated utilities to version 4.11.2.

Changes in Reporter 0.6.6 (January 31. 2017):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.15.0.
  • LIBRARY UPDATE: Updated utilities to version 4.10.0.

Changes in Reporter 0.6.5 (December 21. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.14.6.
  • LIBRARY UPDATE: Updated utilities to version 4.8.9.

Changes in Reporter 0.6.4 (December 21. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.14.5.
  • LIBRARY UPDATE: Updated utilities to version 4.8.8.

Changes in Reporter 0.6.3 (December 11. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.14.3.
  • LIBRARY UPDATE: Updated utilities to version 4.8.7.

Changes in Reporter 0.6.2 (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 PeptideShaker to version 1.14.2.
  • LIBRARY UPDATE: Updated utilities to version 4.8.6.

Changes in Reporter 0.6.1 (December 5. 2016):

  • BUG FIX: Fixed the backwards compatibility.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.14.1.
  • LIBRARY UPDATE: Updated utilities to version 4.8.5.

Changes in Reporter 0.6.0 (December 4. 2016):

  • NEW FEATURE: Added command line support.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.14.0.
  • LIBRARY UPDATE: Updated utilities to version 4.8.4.

Changes in Reporter 0.5.7 (October 10. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.13.6.
  • LIBRARY UPDATE: Updated utilities to version 4.7.5.

Changes in Reporter 0.5.6 (October 6. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.13.5.
  • LIBRARY UPDATE: Updated utilities to version 4.7.4.

Changes in Reporter 0.5.5 (September 27. 2016):

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

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.13.4.
  • LIBRARY UPDATE: Updated utilities to version 4.7.3.

Changes in Reporter 0.5.4 (September 10. 2016):

  • BUG FIX: Made sure that the number of clusters cannot be larger than the number of elements to cluster.
  • BUG FIX: Fixed a bug in the ratio loading that could occur if there were fewer ratios than ratio categories.
  • BUG FIX: Corrected a bug in the location of mgf files located in the same folder as the cpsx file or in the data folder.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.13.3.
  • LIBRARY UPDATE: Updated utilities to version 4.7.2.

Changes in Reporter 0.5.3 (August 19. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.13.1.
  • LIBRARY UPDATE: Updated utilities to version 4.7.1.

Changes in Reporter 0.5.2 (August 13. 2016):

  • FEATURE IMPROVEMENT: The cache size is now set according to the memory available.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.13.0.
  • LIBRARY UPDATE: Updated utilities to version 4.7.0.

Changes in Reporter 0.5.1 (July 7. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.12.2.
  • LIBRARY UPDATE: Updated utilities to version 4.6.3.

Changes in Reporter 0.5.0 (June 24. 2016):

  • NEW FEATURE: Started populating the peptide and PSM tables.
  • NEW FEATURE: Added a dialog for cluster selection and color coding.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.12.0.
  • LIBRARY UPDATE: Updated utilities to version 4.6.1.

Changes in Reporter 0.4.0 (June 7. 2016):

  • FEATURE IMPROVEMENT: Added the option to maximize the individual cluster charts.
  • FEATURE IMPROVEMENT: Added shared and unique ratios to the default export.
  • FEATURE IMPROVEMENT: Added the possibility to set a minimal number of unique peptides for a protein ratio.
  • FEATURE IMPROVEMENT: Allowed the estimation of protein ratios using all peptides.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.11.0.
  • LIBRARY UPDATE: Updated utilities to version 4.5.20.

Changes in Reporter 0.3.4 (May 2. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.10.2.
  • LIBRARY UPDATE: Updated utilities to version 4.5.16.

Changes in Reporter 0.3.3 (April 19. 2016):

  • BUG FIX: Minor correction in the command line documentation for the import_precurosor_mz and import_precurosor_mz_ppm parameters.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.10.0.
  • LIBRARY UPDATE: Updated utilities to version 4.5.12.

Changes in Reporter 0.3.2 (April 7. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.9.3.
  • LIBRARY UPDATE: Updated utilities to version 4.5.11.

Changes in Reporter 0.3.1 (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 PeptideShaker to version 1.9.1.
  • LIBRARY UPDATE: Updated utilities to version 4.5.8.

Changes in Reporter 0.3.0 (March 16. 2016):

  • FEATURE IMPROVEMENT: Improved the display of the quantification values in the protein table.
  • FEATURE IMPROVEMENT: Made it possible to select the most intense peak and set it as default for iTRAQ.

  • LIBRARY UPDATE: Updated jsparklines to version 1.0.8.
  • LIBRARY UPDATE: Updated PeptideShaker to version 1.9.0.
  • LIBRARY UPDATE: Updated utilities to version 4.5.7.

Changes in Reporter 0.2.16 (March 4. 2016):

  • BUG FIX: Correction in the iTRAQ 4-plex 115 mass.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.8.1.
  • LIBRARY UPDATE: Updated utilities to version 4.5.3.

Changes in Reporter 0.2.15 (February 29. 2016):

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

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.8.0.
  • LIBRARY UPDATE: Updated utilities to version 4.5.1.

Changes in Reporter 0.2.14 (February 12. 2016):

  • BUG FIX: Corrected an error in the definition of the iTRAQ 8plex 115 ion.
  • BUG FIX: Added different default reporter ion tolerances for TMT (0.0016 Da) and iTRAQ (0.05 Da).
  • BUG FIX: Fixed GUI alignment issues in the Welcome dialog.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.7.5.
  • LIBRARY UPDATE: Updated utilities to version 4.3.22.

Changes in Reporter 0.2.13 (February 6. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.7.3.
  • LIBRARY UPDATE: Updated utilities to version 4.3.21.

Changes in Reporter 0.2.12 (February 5. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.7.2.
  • LIBRARY UPDATE: Updated jsparklines to version 1.0.7.
  • LIBRARY UPDATE: Updated utilities to version 4.3.20.

Changes in Reporter 0.2.11 (January 28. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.7.0.
  • LIBRARY UPDATE: Updated utilities to version 4.3.18.

Changes in Reporter 0.2.10 (January 26. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.6.0.
  • LIBRARY UPDATE: Updated utilities to version 4.3.17.

Changes in Reporter 0.2.9 (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 PeptideShaker to version 1.5.0.
  • LIBRARY UPDATE: Updated utilities to version 4.3.16.

Changes in Reporter 0.2.8 (January 15. 2016):

  • FEATURE IMPROVEMENT: Improved the handling of low memory.
  • FEATURE IMPROVEMENT: Made the cache update synchronized.
  • FEATURE IMPROVEMENT: Made the usage of the cache more robust towards usage by multiple threads.
  • FEATURE IMPROVEMENT: Attempt at improving the batch size during matches iteration.
  • FEATURE IMPROVEMENT: Improved the handling of backed-up PTMs.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.4.0.
  • LIBRARY UPDATE: Updated utilities to version 4.3.11.

Changes in Reporter 0.2.7 (January 8. 2016):

  • FEATURE IMPROVEMENT: Updated the ISAS logo in the Welcome dialog.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.3.6.
  • LIBRARY UPDATE: Updated utilities to version 4.3.8.

Changes in Reporter 0.2.6 (January 6. 2016):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.3.4.
  • LIBRARY UPDATE: Updated utilities to version 4.3.7.

Changes in Reporter 0.2.5 (January 5. 2016):

  • FEATURE IMPROVEMENT: Improved the handling of missing mgf and FASTA files.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.3.3.
  • LIBRARY UPDATE: Updated utilities to version 4.3.6.

Changes in Reporter 0.2.4 (December 31. 2015):

  • FEATURE IMPROVEMENT: Updated the ISAS logo in the splash screen.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.3.2.
  • LIBRARY UPDATE: Updated utilities to version 4.3.5.

Changes in Reporter 0.2.3 (December 28. 2015):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.3.1.
  • LIBRARY UPDATE: Updated utilities to version 4.3.4.

Changes in Reporter 0.2.2 (December 23. 2015):

  • BUG FIX: Added a fix for a Java bug where the button for the scroll bar could disappear on certain Java versions.
  • BUG FIX: Fixed a bug that made it impossible to save Reporter projects.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.3.0.
  • LIBRARY UPDATE: Updated utilities to version 4.3.3.

Changes in Reporter 0.2.1 (December 7. 2015):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.2.2.
  • LIBRARY UPDATE: Updated utilities to version 4.1.15.

Changes in Reporter 0.2.0 (December 2. 2015):

  • BUG FIX: Fixed issues that could occur for peptides without modifications.
  • BUG FIX: Fixed issues with the progress bars not being updated properly when normalizing the ratios.
  • BUG FIX: Fixed a column alignment issue in the default PSM export.
  • BUG FIX: Fixed incorrect references to the log file.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.2.0.
  • LIBRARY UPDATE: Updated utilities to version 4.1.13.

Changes in Reporter 0.1.6 (October 22. 2015):

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

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.1.3.
  • LIBRARY UPDATE: Updated utilities to version 4.1.8.

Changes in Reporter 0.1.6 (October 14. 2015):

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

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.1.1.
  • LIBRARY UPDATE: Updated utilities to version 4.0.15.

Changes in Reporter 0.1.5 (October 12. 2015):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.1.0.
  • LIBRARY UPDATE: Updated utilities to version 4.0.14.

Changes in Reporter 0.1.4 (October 3. 2015):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.0.9.
  • LIBRARY UPDATE: Updated utilities to version 4.0.13.

Changes in Reporter 0.1.3 (October 1. 2015):

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.0.6.
  • LIBRARY UPDATE: Updated utilities to version 4.0.10.

Changes in Reporter 0.1.2 (September 23. 2015):

  • BUG FIX: If all proteins are removed by the protein filter, all proteins are now shown instead.

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.0.3.
  • LIBRARY UPDATE: Updated utilities to version 4.0.8.

Changes in Reporter 0.1.1 (September 5. 2015):

  • BUG FIX: Fixed path issues on Linux/Mac.
  • BUG FIX: Fixed an issue with the waiting icon in the progress bar when loading PeptideShaker projects.

Changes in Reporter 0.1.0 (September 4. 2015):

  • NEW FEATURE: Added support for k-means clustering.
  • NEW FEATURE: Added normalization settings.
  • NEW FEATURE: Added the find/search option to the results frame.

  • FEATURE IMPROVEMENT: Added a Welcome Dialog and made various other GUI improvements.
  • FEATURE IMPROVEMENT: Sped up the protein filtering and ratio extraction.
  • FEATURE IMPROVEMENT: Better error handling if the loading is canceled by the user.

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

  • LIBRARY UPDATE: Updated PeptideShaker to version 1.0.1.
  • LIBRARY UPDATE: Updated jsparklines to version 1.0.5.
  • LIBRARY UPDATE: Updated utilities to version 4.0.4.

Changes in Reporter 0.0.5 (June 22. 2015):

  • BUG FIX: Fixed a bug in the setting of the desktop icon.

Changes in Reporter 0.0.4 (June 21. 2015):

  • FEATURE IMPROVEMENT: Refactored the GUI in the New Project Dialog.

  • BUG FIX: Fixed a bug in the loading of isotope correction factors from file.

  • LIBRARY UPDATE: Updated PeptideShaker to version 0.40.2.
  • LIBRARY UPDATE: Updated utilities to version 3.49.19.

Changes in Reporter 0.0.3 (June 3. 2015):

  • BUG FIX: Fixed bugs related to saving the reporter methods.

  • LIBRARY UPDATE: Updated PeptideShaker to version 0.39.1.
  • LIBRARY UPDATE: Updated utilities to version 3.49.4.

Changes in Reporter 0.0.2 (June 2. 2015):

  • FEATURE IMPROVEMENT: Made it possible to edit and save the reagent details via the GUI.

  • LIBRARY UPDATE: Updated PeptideShaker to version 0.39.0.
  • LIBRARY UPDATE: Updated utilities to version 3.49.2.

Changes in Reporter 0.0.1 (May 6. 2015):

  • First public beta release of Reporter.