Release Notes

Changes in omssa-parser v2.0.4 - (January 5. 2022):

• LIBRARY UPDATE: Updated log4j-core to version 2.17.1.
• LIBRARY UPDATE: Updated log4j-api to version 2.17.1.
• LIBRARY UPDATE: Updated utilities to version 5.0.35.

Changes in omssa-parser v2.0.3 - (November 15. 2021):

• LIBRARY UPDATE: Updated utilities to version 5.0.34.

Changes in omssa-parser v2.0.1 - (November 20. 2020):

• FEATURE IMPROVEMENT: Added support for parsing spectrum titles with leading or trailing white space.
• LIBRARY UPDATE: Updated utilities to version 5.0.1.

Changes in omssa-parser v2.0.0 - (November 4. 2020):

• FEATURE IMPROVEMENT: Made the code compatible with Java 9 and newer.
• LIBRARY UPDATE: Updated JSparklines to version 1.0.12.
• LIBRARY UPDATE: Updated utilities to version 5.0.0.

Changes in omssa-parser v1.9.0 - (January 31. 2017):

• LIBRARY UPDATE: Updated utilities to version 4.10.0.

Changes in omssa-parser v1.8.0 - (December 11. 2016):

• FEATURE IMPROVEMENT: Removed the references to the deprecated EBI Nexus repository.
• LIBRARY UPDATE: Updated utilities to version 4.8.7.

Changes in omssa-parser v1.7.1 - (October 12. 2015):

• FEATURE IMPROVEMENT: Removed the peptide map from the IdfileReader to speed up the processing.
• LIBRARY UPDATE: Updated utilities to version 4.0.14.

Changes in omssa-parser v1.7.0 - (August 27. 2015):

• LIBRARY UPDATE: Updated utilities to version 4.0.0.

Changes in omssa-parser v1.6.12 - (December 11. 2014):

• LIBRARY UPDATE: Updated utilities to version 3.43.24.

Changes in omssa-parser v1.6.11 - (October 8. 2014):

• FEATURE IMPROVEMENT: Minor corrections in the ID file reader.

Changes in omssa-parser v1.6.10 - (September 8. 2014):

• LIBRARY UPDATE: Updated utilities to version 3.36.0.

Changes in omssa-parser v1.6.9 - (August 19. 2014):

• LIBRARY UPDATE: Updated utilities to version 3.35.0.

Changes in omssa-parser v1.6.6 - (August 11. 2014):

• LIBRARY UPDATE: Updated utilities to version 3.32.0.

Changes in omssa-parser v1.6.3 - (January 21. 2014):

• LIBRARY UPDATE: Updated utilities to version 3.21.6.

Changes in omssa-parser v1.6.2 - (January 14. 2014):

• LIBRARY UPDATE: Updated utilities to version 3.21.0.

Changes in omssa-parser 1.6.1 (November 18. 2013):

• LIBRARY UPDATE: Updated utilities to version 3.17.7.

Changes in omssa-parser 1.6.0 (August 25. 2013):

• NEW FEATURE: Created a new low memory usage mode.
• FEATURE IMPROVEMENT: Added some tests to escape null pointers that could occur when loading (corrupt?) omx files.
• LIBRARY UPDATE: Updated utilities to version 3.14.27.

Download count: 36

Changes in omssa-parser 1.5.11 (June 10. 2013):

• BUG FIX: Fixed a problem with starting the viewer on the latest Java release.

Download count: 16

Changes in omssa-parser 1.5.10 (April 26. 2013):

• BUG FIX: Fixed a problem with starting the viewer on the latest Java release.

Download count: 19

Changes in omssa-parser 1.5.9 (January 11. 2013):

• FEATURE IMPROVEMENT: Made a minor change to the pom file to handle recursive issues that can occur when opening the project in NetBeans 7.2.
• FEATURE IMPROVEMENT: Spectrum titles are now decoded in the id file reader.
• BUG FIX: Minor code cleanups.

Download count: 19

Changes in omssa-parser 1.5.8 (November 28. 2012):

• FEATURE IMPROVEMENT: Removed the fixed modifications from the OMSSAIdfileReader.
• BUG FIX: Fixed an issue with one of the constructors of OmxParser.
• LIBRARY UPDATE: Updated utilities to version 3.10.24.

Download count: 11

Changes in omssa-parser 1.5.6 (November 14. 2012):

• NEW FEATURE: The code now supports Maven 3.
• FEATURE IMPROVEMENT: Added new constructors to the OmxParser, making it possible to provide the input as files instead of the paths to the files.
• FEATURE IMPROVEMENT: Improved the fixMgfTitle method in the OMSSAIdfileReader.
• FEATURE IMPROVEMENT: The source and JavaDoc is now included when building.
• LIBRARY UPDATE: Updated utilities to version 3.10.8

Download count: 15

Changes in omssa-parser 1.5.2 (August 21. 2012):

• BUG FIX: Fixed a bug in the OMSSA Viewer were fixed n- and c-terminal PTMs were annotated more than once in the legend.

Download count: 29

Changes in omssa-parser 1.5.1 (August 20. 2012):

• BUG FIX: Fixed a bug in the OMSSA Viewer were fixed n- and c-terminal PTMs were not annotated.
• LIBRARY UPDATE: Updated utilities to version 3.7.6, improving the look and feel of the spectrum viewer.

Download count: 0

Changes in omssa-parser 1.5 (April 16. 2012):

• FEATURE IMPROVEMENT: Upgraded the OMSSA Viewer to the PeptideShaker look and feel.
• FEATURE IMPROVEMENT: Updated the help and about texts.
• LIBRARY UPDATE: Added jsparklines as a dependency.
• LIBRARY UPDATE: Removed jgoodies and swingx as a dependencies.

Download count: 36

Changes in omssa-parser 1.4.7 (January 31. 2012):

• BUG FIX: Changed the OMSSA abundance scale from a long to a double (as detailed in OMSSA.mod.xsd).

Download count: 61

Changes in omssa-parser 1.4.6 (September 9. 2011):

• NEW FEATURE: Added the possibility to not import peak lists.

Download count: 109

Changes in omssa-parser 1.4.5 (March 10. 2011):

• LIBRARY UPDATE: utilities library to version 3.0.46.

Download count: 117

Changes in omssa-parser 1.4.4 (February 27. 2011):

• BUG FIX: Fixed some minor GUI details in the OMSSA Viewer.
• LIBRARY UPDATE: utilities library to version 3.0.40.

Download count: 14

Changes in omssa-parser 1.4.3 (February 22. 2011):

• FEATURE IMPROVEMENT: Improved the parsing of the protein accession number details from the omx file in OMSSA Viewer.

Download count: 6

Changes in omssa-parser 1.4.2 (December 5. 2010):

• FEATURE IMPROVEMENT: Made some minor GUI changes to the viewer.
• BUG FIX: Fixed an index bug in Spectrum to HitSetMap that occurred if not all spectrum indices were used.
• LIBRARY UPDATE: utilities library to version 3.0.30.

Download count: 49

Changes in omssa-parser 1.4.1 (September 30. 2010):

• FEATURE IMPROVEMENT: Export option now includes spectral filenames (or ´not available´ if not specified).

Download count: 30

Changes in omssa-parser 1.4 (July 16. 2010):

• NEW FEATURE: OMSSA Parser has been extended to support OMSSA 2.1.9.
• NEW FEATURE: All variables corresponding to XML tags in the OMSSA.mod.xsd file are now annotated with Javadoc based on the annotation used in the OMSSA.mod.xsd file.
• NEW FEATURE: Mappings of all enumerations used in the OMSSA.mod.xsd file (see OmssaEnumerators.java) has been implemented, making it possible to map an integer ID to the corresponding text description.

Download count: 26

Changes in omssa-parser 1.3.7 (May 31. 2010):

• FEATURE IMPROVEMENT: In some files the abundance scale was too big for an int value. Has now been replaced by a long.
• LIBRARY UPDATE: utilities library to version 3.0.1

Download count: 15

Changes in omssa-parser 1.3.6 (Apr. 26. 2010):

• FEATURE IMPROVEMENT: All data classes are now serializable.

Download count: 6

Changes in omssa-parser 1.3.5 (Nov. 25. 2009):

• NEW FEATURE: On Windows platforms OMSSA Parser can now be run from paths containing spaces.
• FEATURE IMPROVEMENT: Updated the JOptionPane dialogs by simplifying and shortening the text. Also fixed some minor typos.
• BUG FIX: Altered the default subject in the mailto links in order to work on non-Windows platforms.

Download count: 39

Changes in omssa-parser 1.3.4 (Aug. 19. 2009):

• OMSSA Viewer: Fixed a bug where the neutral loss of ‘H2O’ was written using the number ‘0’ instead of the letter ‘O’.
• Updated the utilities library to version 2.9.9.

Download count: 31

Changes in omssa-parser 1.3.3 (July 28. 2009):

• OMSSA Parser: Extended the support for neutral losses. Instead of returning a boolean variable, it now returns -1 if no neutral loss or a number -> 0 for water, 1 for ammonium. As detailed in the annotation of OMSSA omx files.
• OMSSA Viewer: Updated the fragment ion annotations to support neutral losses and immonium ions.

Download count: 5

Changes in omssa-parser 1.3.2 (Jun. 03. 2009):

• Default MSResponse_scale (for scaling m/z values) is 100, if not given.
• OMSSA Viewer: Spectrum name is not mandatory, use spectrum number if no name is given.
• OMSSA Viewer: Increased the size of the first column in the Spectrum Files table somewhat to support longer row ids, i.e., bigger omx files.
• OMSSA Viewer: Fixed a bug where the OMSSA Viewer tried to validate the modification files. Validation is now turned off.
• OMSSA Viewer: Added an export all identifications (best hits only) feature.
• OMSSA Viewer: Fixed a bug that resulted in the parser crashing when encountering multiple modifications on the same residue.
• OMSSA Viewer: Fixed a couple of minor gui bugs.

Download count: 12

Changes in omssa-parser 1.3.1 (May 29. 2009):

• OMSSA Viewer: Fixed a bug in the dta export function. The m/z values have to be converted to MH+ values, and this was previously not done (the m/z values were used directly).

Download count: 1

Changes in omssa-parser 1.3.0 (Apr. 26. 2009):

• Now only requires Java version 1.5 (previously 1.6).
• Two new dependencies added (swingx-0.9.1 (for JXTable) and swing-layout-1.0.3 (for Java 1.6 GUI stuff).
• Fixed a minor bug in the “automatic check for updates” feature.

Download count: 3

Changes in omssa-parser 1.2.1 (Mar. 26. 2009):

• Updated the check for new versions, due to a minor change in the way google code annotated deprecated downloads.

Download count: 8

Changes in omssa-parser 1.2.0 (Mar. 16. 2009):

• Fixed a bug in the overloading of constructors in the OmssaOmxFile class. Now all constructors should work.

Changes in omssa-parser 1.1.2 (Feb. 04. 2009):

• The automatic check for new versions now also handles deprecated downloads.
• Minor updates of the help files.

Changes in omssa-parser 1.1.1 (Jan. 16. 2009):

• A dialog with details about the error now appears if an exception is caught.

Changes in omssa-parser 1.1.0 (Jan. 15. 2009):

• OMSSA Viewer: Modified peptide terminals are now supported.
• OMSSA Viewer: Modification that are not found in mods.xml or usermods.xml (when these files are provided), no longer results in an error. The modification is simply labeled as “unknown”.
• OMSSA Viewer: Fixed a bug that resulted in an incorrect mapping of modifications that had modification numbers higher than 9.
• OMSSA Viewer: Fixed a bug that occured when opening a new omx file after having sorted the previous file in the Spectra Files table. (An exception was previously thrown.)
• OMSSA Viewer: Fixed a bug that resulted in making it imposible to update the ion coverage annotations by using the ion type selection or by selecting a different hit in the Identification table.
• OMSSA Viewer The Spectrum panel ion coverage now also displays parent, internal, immonium and unknown ions if they are annotated in the omx file.
• Fixed the lockstack issue in the XML parsing.

Changes in omssa-parser 1.0.0 (Jan. 14. 2009):

• The m/z-axis now starts at 0.0 and not at the lowest m/z value in the spectrum.
• Changed the export format from csv files to tab separated text files.
• Updated OMSSA Viewer to version 1.3.
• Increased the default height of the Spectrum table.
• Added some tooltips to the File and Export menus.
• Improved the representation of the E- and P-values in the Identifications table by using scientific notation.
• If more than one charge is found the charge is now considered as unknown and is set to 0 in the Spectra Files table.

Changes in omssa-parser 0.9.7 (Jan. 11. 2009):

• Fixed a bug that resulted in the OMSSA Viewer not being able to start.
• Upgraded the OMSSA Viewer to version 1.2

Changes in omssa-parser 0.9.6 (Jan. 7. 2009):

• Removed two unused libs (mail and activation).
• Fixed the problem with the labels on the vertical axis in the SpectrumPanel where the font size was too small to read.
• Updated the utilites jar to version 2.9.1.

Changes in omssa-parser 0.9.5 (Dec. 16. 2008):

• Added a way of turning on/off the different annotations in the spectrum panel.
• Fixed the scale issue yet again. Now individual MSSpectrum_iscale scales are used for each spectrum.
• Added charge to the spectrum panel ion coverage.
• The ion coverage in the spectrum panel now changes relative to the identification selected in the identification table.
• Added theoretical and experimental mass to the identification table.
• Added file filters when doing file selection.
• Added export functionality: all spectra file details (to csv files), all identifications (to csv files), all spectra (to dta files) and selected spectrum (to csv file).

Changes in omssa-parser 0.9.4 (Dec. 14. 2008):

• Added a simple, lightweight viewer for omx files: OMSSA Viewer v1.0.
• Removed the hardcoding of the scale value. The scale is now extracted from the omx file.
• The OMSSA modifications are now also parsed if the mods.xml and usermods.xml files are provided.

Changes in omssa-parser 0.9.3:

• Cleaned up the package structure.

Changes in omssa-parser 0.9.2:

• Javadoc added and extended.

Changes in omssa-parser 0.9.1:

• Logging functionality added (log4j)
• Added methods for extracting the “real” m/z and abundance values. (The original values can still be extracted, but have to be divided by 1000 to get the “real” values.)
• Javadoc added for the methods and variables involved in the previous point.