Converter from mzData to MGF

[Fredrik Levander]

There is need for a converter from mzData to MGF files for OMSSA searches #470, #471. Only searches using MGF will give a spectrum identifier in the response. The MGF files produced needs to have the spectrumID in the title.

[Fredrik Levander]

(In [2937]) Fixes #490. Added converter from mzData to MGF. It will currently only work with MSMS files.

[Fredrik Levander]

(In [2958]) Refs #493, refs #490. Support for MGF retention time and total intensity

[olle]

(In [3379]) Refs #591. Refs #471. Refs #490. First version of support for performing OMSSA search for input mzData files by using data converted to MGF (Mascot Generic Format):

1. OMSSA search properties template file conf/omssa.properties.in

in client/servlet/ updated with new parameters omssa.web.convert.mzdata_to_mgf and omssa.local.convert.mzdata_to_mgf, indicating if mzData data converted to MGF should be used for OMSSA search. Valid values are "true" and "false", although the software may be lenient and accept other alternatives.

2. Class/file action/omssa/SearchOMSSA.java in client/servlet/

updated:

1. New private static constant

Job.ExecutionTime ESTIMATED_EXECUTION_TIME added, set to Job.ExecutionTime.SHORT.

2. Protected method void runMe() updated by obtaining the values

of new configuration parameters omssa.web.convert.mzdata_to_mgf and omssa.local.convert.mzdata_to_mgf from configuration file omssa.properties, and the relevant one is used as value for new variable Boolean convertMzDataToMgfFlag. If input spectrum file should be converted before OMSSA search, a conversion job is created, if the needed converted file does not already exist. If a conversion job is created, it is set as blocker for the created search job. The value of variable Boolean convertMzDataToMgfFlag is transferred to the created search job via job parameters.

3. New private method

boolean convertedMzDataToMgfFileExists(DbControl dc, File spectrumFile) added. It calls new private method File fetchConvertedMzDataToMgfFile(DbControl dc, File spectrumFile) to check if a converted mzData to MGF file exists.

4. New private method

File fetchConvertedMzDataToMgfFile(DbControl dc, File spectrumFile) added. It fetches the converted mzData to MGF file.

5. New private method

Job createMzDataToMgfConvertJob(DbControl dc, File spectrumFile) added. It creates an mzData file to MGF file conversion job. The conversion job is set to the same estimated execution time ESTIMATED_EXECUTION_TIME as the search job.

3. Class/file plugins/SearchOMSSAPlugin.java in plugin/ updated:
4. Private method

void execute(Request request, Response response, ProgressReporter progress) updated by obtaining the value of variable Boolean convertMzDataToMgfFlag from job parameters. The value is transferred to private methods void omssaSearchViaWebInterface(Request request, ...) and void omssaSearchLocal(Request request, ...) via new arguments.

2. Private method

void omssaSearchViaWebInterface(Request request, ...) updated with new argument Boolean convertMzDataToMgfFlag. If mzData data converted to MGF should be used for search, the spectrum file is obtained by calling new private method File fetchConvertedMzDataToMgfFile(DbControl dc, File spectrumFile), and a note reporting that converted data is used for search is added to the job message string.

3. Private method

void omssaSearchLocal(Request request, ...) updated with new argument Boolean convertMzDataToMgfFlag. If mzData data converted to MGF should be used for search, the spectrum file is obtained by calling new private method File fetchConvertedMzDataToMgfFile(DbControl dc, File spectrumFile), and a note reporting that converted data is used for search is added to the job message string. When spectrum file data is copied to a temporary local file to be used for the OMSSA search, the file is given the same name as the original input spectrum file, even if converted data from another file is copied.

4. New private method

File fetchConvertedMzDataToMgfFile(DbControl dc, File spectrumFile) added. It fetches the converted mzData to MGF file.