Package eu.isas.searchgui.processbuilders

Class OmssaclProcessBuilder

java.lang.Object
eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder
eu.isas.searchgui.processbuilders.OmssaclProcessBuilder
All Implemented Interfaces:
Runnable
public class OmssaclProcessBuilder extends SearchGUIProcessBuilder
This class takes care of building the omssacl process.
Author:
Lennart Martens, Marc Vaudel, Harald Barsnes

  • Field Details

    • EXECUTABLE_FILE_NAME

      public static final String EXECUTABLE_FILE_NAME
      The name of the OMSSA executable.
      See Also:

  • Constructor Details

    • OmssaclProcessBuilder

      public OmssaclProcessBuilder(File omssacl_directory, File aOmssaTempFolder, File mgfFile, File fastaFile, File outputFile, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, Double refMass, int nThreads) throws IOException, ClassNotFoundException
      Constructor.
      Parameters:
      omssacl_directory - directory location of omssacl.exe
      aOmssaTempFolder - the OMSSA temp folder
      mgfFile - the spectrum file
      fastaFile - the FASTA file
      outputFile - string location where to send omx/csv/pepxml formatted results file
      searchParameters - the search parameters
      waitingHandler - the waiting handler
      exceptionHandler - the handler of exceptions
      refMass - the reference mass to convert the fragment ion tolerance from ppm to Dalton
      nThreads - the number of threads to use
      Throws:
      IOException - exception thrown whenever an error occurred while reading or writing a file.
      ClassNotFoundException - exception thrown whenever an error occurred while saving the search parameters

  • Method Details

    • getType

      public String getType()
      Description copied from class: SearchGUIProcessBuilder
      Returns the type of the process.
      Specified by:
      getType in class SearchGUIProcessBuilder
      Returns:
      the type of the process

    • getCurrentlyProcessedFileName

      public String getCurrentlyProcessedFileName()
      Description copied from class: SearchGUIProcessBuilder
      Returns the file name of the currently processed file.
      Specified by:
      getCurrentlyProcessedFileName in class SearchGUIProcessBuilder
      Returns:
      the file name of the currently processed file

    • getIonId

      public int getIonId(String letter)
      Returns the ion type. zdot is considered as z. adot, x-CO2 and adot-CO2 are ignored as long as nobody complains.
      Parameters:
      letter - ion letter
      Returns:
      ion number

    • getSearchedModificationsIds

      public ArrayList<Integer> getSearchedModificationsIds(ArrayList<String> modificationsNames, com.compomics.util.parameters.identification.tool_specific.OmssaParameters omssaParameters)
      Returns an array of OMSSA indexes corresponding to the list of given modification names.
      Parameters:
      modificationsNames - the modification names
      omssaParameters - the OMSSA parameters
      Returns:
      the corresponding list of OMSSA modification indexes

    • writeOmssaUserModificationsFile

      public static void writeOmssaUserModificationsFile(File omssaFile, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, File identificationParametersFile) throws IOException, ClassNotFoundException
      Writes the OMSSA modification file corresponding to the PTMs loaded in the factory in the given file. Stores the PTM indexes in the OMSSA specific parameters.
      Parameters:
      omssaFile - the file where to write the OMSSA modification files
      identificationParameters - the identification parameters
      identificationParametersFile - the file where to save the identification parameters
      Throws:
      IOException - exception thrown whenever an error occurred while writing the file
      ClassNotFoundException - exception thrown whenever an error occurred while saving the search parameters

    • getOmssaUserModBloc

      public static String getOmssaUserModBloc(com.compomics.util.experiment.biology.modifications.Modification modification, int cpt, int omssaIndex)
      Returns an MSModSpec bloc as present in the OMSSA user modification files for a given PTM. Only the amino acids targeted by the pattern of the modification will be considered.
      Parameters:
      modification - the modification
      cpt - the index of this modification in the list
      omssaIndex - the OMSSA index of this modification
      Returns:
      a string containing the XML bloc