Release notes
Starting from MascotDatfile version 3.0, all subsequent versions of the library are listed here.
3.6.1 (4 September 2019)
- fix for new distiller version in the processMGFTitleToFilename method. Support for the new “Sum of 2 scans. Range” title format as well as the old “Sum of 2 scans in range”.
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
getAllSpectrumMatchesmethod in theMascotIdfileReaderclass. - 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
IdfileReaderclass.
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.mascotdatfiletocom.compomics.mascotdatfile.