PRIDE Converter Changelog

What's new in PRIDE Converter 2.5.6

Aug 23, 2013
  • BUG FIX: Fixed an issue with the wrapper on the newer Java versions.
  • BUG FIX: Fixed an issue with missing icons in the data source selection dialog.
  • BUG FIX: Fixed an issue with a possible null pointer in MS_LimsConverter related to strange PTMs.
  • BUG FIX: Replaced paths to CvMappingRules.xsl as the file had moved.
  • LIBRARY UPDATE: Updated cv-rule-reader to version 2.0.3.

New in PRIDE Converter 2.5.5 (May 29, 2012)

  • BUG FIX: Updated to support new fragment ion types reported by Mascot dat file parser

New in PRIDE Converter 2.5.3 (Aug 12, 2011)

  • Removed support for DTASelect files, never properly implemented

New in PRIDE Converter 2.5.2 (Jun 21, 2011)

  • BUG FIX: Added 2 new FragmentIon accessions

New in PRIDE Converter 2.5.1 (Apr 20, 2011)

  • Improved the GUI of the SpectraSelection panels by reducing the size of the "Load Spectra" button (and moving it), as this was pressed by some users even when not doing manual selection, thus slowing down the process.

New in PRIDE Converter 2.5.0 (Mar 14, 2011)

  • Replacement of PSI with MS ontology.
  • Fixed unhandled case in modification mapping when mass was not specified.
  • See ReleaseNotes for complete list of changes.

New in PRIDE Converter 2.4.9 (Dec 16, 2010)

  • Bug Fix: Removed 'percent_coverage' value parsing from TPP protXML files (since we don't know how these percentage values are encoded).
  • Bug Fix: Update JRAP library (external dependency) to latest version jrap_StAX_v5.2.

New in PRIDE Converter 2.4.7 (Nov 29, 2010)

  • Using Peptide Score Threshold has now been implemented for Mascot dat files.
  • See ReleaseNotes for complete list of changes.

New in PRIDE Converter 2.4.6 (Nov 23, 2010)

  • Fixed an issue in ms_lims interface.

New in PRIDE Converter 2.3.2 (May 4, 2010)

  • Turned the ErrorLog back on again.
  • Converting Mascot Dat files is now working again.
  • omssa-parser library updated to version 1.3.6.

New in PRIDE Converter 2.2.1 (Feb 16, 2010)

  • Added support for multiple charges in mgf files when the charge values are separated by "and".
  • Added support for Terminal Modifications in PeptideProphet files.

New in PRIDE Converter 2.1.1 (Oct 12, 2009)

  • FEATURE IMPROVEMENT: Updated the default subject in the mailto links.
  • BUG FIX: When parsing decoy proteins from PeptideProphet XML files the total number of proteins can now be 0.
  • LIBRARY UPDATE: OMSSA Parser updated to version 1.3.4.
  • LIBRARY UPDATE: OLS Dialog updated to version 3.2.2, which includes new search options and additional features.

New in PRIDE Converter 2.1 (Oct 1, 2009)

  • FEATURE IMPROVEMENT: The RequestFtpAccess dialog now includes a mailto link with a default e-mail for requesting FTP access.
  • FEATURE IMPROVEMENT: The text in the JOptionPane dialogs has been by simplified and shortened. Some minor typos have also been fixed.
  • FEATURE IMPROVEMENT: Reduced the size of the PRIDE Converter zip file by removing unused libraries.
  • FEATURE IMPROVEMENT: Improved the radio button renderer.
  • FEATURE IMPROVEMENT: The default browser launcher now recognizes more browsers.
  • BUG FIX: Fixed a problem in the spectra selection frame where the selection in the table was not always updated correctly if sorting was turned on.
  • BUG FIX: The PSI-MOD modification mass check is now working again. (The DiffMono mass value had been moved back to the PSI-MOD metadata section after being in the xrefs section for a while.)
  • BUG FIX: Fixed a GUI bug in the peptide counter for DTASelect and TPP data sets. (Note: The bug did not affect the contents of the file.)
  • BUG FIX: Clicking cancel when mapping OMSSA modifications to PSI-MOD modifications now cancels the conversion process.
  • BUG FIX: Fixed two Mac and Linux GUI bugs where the content in the first and list frame was not shown correctly.
  • LIBRARY UPDATE: ols-dialog updated to v2.0.1 which includes modification mass search when mapping PSI-MOD modifications.

New in PRIDE Converter 2.0.3 (Sep 21, 2009)

  • BUG FIX: Fixed a serious bug for OMSSA conversion where integer division was used when scaling the mz and intensity peak values, and the precursor mz value.