Release notes

Starting from MascotDatfile version 3.0, all subsequent versions of the library are listed here.

3.6.0 (31 January 2017)

  • Minor change in the compomics id file reader.
  • Updated utilities to version 4.10.0.

3.5.0 (12 December 2016)

  • Removed the references to the deprecated EBI Nexus repository.
  • Fixed https://github.com/compomics/mascotdatfile/issues/14.
  • Updated utilities to version 4.8.7.

3.4.32 (12 October 2015)

  • Removed the peptide map from the IdfileReader to speed up the processing.
  • Updated utilities to version 4.0.0.

3.4.31 (27 August 2015)

  • Updated utilities to version 4.0.0.

3.4.19 (21 January 2014)

  • Disabled the error logging in the getAllSpectrumMatches method in the MascotIdfileReader class.
  • Corrected a JavaDoc error where the Mascot version was annotated as the database version.
  • Updated utilities to version 3.21.6.

3.4.18 (16 January 2014)

  • Removed the protein mappings from the IdfileReader class.

3.4.17 (16 January 2014)

  • Fixed a logic bug in the parsing of the compound number.

3.4.16 (15 January 2014)

  • Updated utilities to version 3.21.0.

3.4.15 (1 August 2013)

  • Removed spectrum file renaming for Mascot distiller files which should not be needed anymore.
  • Update utilities to version 3.14.16.

3.4.14 (9 July 2013)

  • Updated utilities to version 3.14.13.

3.4.13 (25 June 2013)

  • Started with refactoring.
  • Fixed a problem which allowed nulls in a List to not be removed.

3.4.11 (21 May 2013)

  • Fixed a bug where the first element in a vector was used without checking that the vector actually contained any elements first.

3.4.10 (14 March 2013)

  • The PeptideHit object’s warning “Warning, more than two ‘;’ semicolons used in the peptidehit String” is now only shown if the debug variable is turned on.
  • Fixed an issue with recursive folder generation when building the project using Maven 3 and NetBeans.
  • Fixed JavaDoc warnings.

3.4.9 (13 February 2013)

  • The secondary databases (if searching with more than one database) can now be extracted from the search parameters using the new getSecondaryDatabases() method.

3.4.8 (13 February 2013)

  • Prevented an exception thrown in the id file reader due to empty peptide assumption lists returned by the parser.

3.4.7 (6 December 2012)

  • Changed the location of the iText dependency from the Genesis repository to the common Maven repository, as there were some issues using the Genesis version.

3.4.6 (13 November 2012)

  • The code now works with Maven 3
  • Improved the formatting of a peptide hit warning message.

3.3 (26 July 2012)

  • Support for mascot 2.4

###3.2.9 (20 January 2012)

  • Added boolean parameter for getDecoyQueryToPeptideMap() method which will or will not throw an exception if the Decoy section is not in the Mascot result file.

3.2.8 (20 December 2011)

  • Fixed an issue with temp file indexing, introduced while fixing bug with newline auto-detection.

3.2.7 (19 December 2011)

  • Fixed an issue with Distiller filename parsing

3.2.6 (11 October 2011)

  • Fixed an issue where different kinds of newlines at the beginning would upset the indexing of a file

3.2.5 (22 July 2011)

  • Removed the maven filter for generating the log4j configuration file as this lead to NumberFormatExceptions.

3.2.4 (4 July 2011)

  • Created a dedicated tmp directory that is automatically cleaned.

3.2.3 (1 May 2011)

  • Added new optional parameters to be used by the MSF parser.

3.2.2 (27 October 2010)

  • Created a MascotDatfileException for library specific RuntimeExceptions.

3.2.1 (21 September 2010)

  • Create a setter for the ModifiacationMap so that this can be adapted from ms-lims.

3.2 (18 September 2010)

  • Add support for protein like ‘“DDI00062040.1”:0:325:329:1,”DDI00100151.4”:0:642:646:1’.

3.1 (23 April 2010)

  • Introduced log4j framework into MascotDatfile.

3.0.2 (1 April 2010)

  • Bugfix from Pride submission. When the unimod.xml section encompassed in a Mascot results file contains a custom modification with a accented ‘é’ character, the indexing algorithm failed on UNIX.
  • Bugfix from Pride submission. IPI protein accessions with multiple Trembl references are separated by a “;” character, and this caused an error while parsing the second half of a peptidehit String.

3.0.1 (24 February 2010)

  • When more then 10 variable modifications are applied, the modification id becomes hexadecimal (‘A’ for the tenth modification) and caused an parsing error in MascotDatfile.

3.0

  • Initial import of the MascotDatfile library into google code.
  • Note that all MascotDatfile packages have been changed from be.proteomics.mascotdatfile to com.compomics.mascotdatfile.