Package com.compomics.util.experiment.io.identification.idfilereaders

Class XTandemIdfileReader

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader
All Implemented Interfaces:
IdfileReader, Serializable, AutoCloseable
public class XTandemIdfileReader extends ExperimentObject implements IdfileReader
This IdfileReader reads identifications from an X! Tandem xml result file.
Author:
Dominik Kopczynski, Harald Barsnes
See Also:

  • Constructor Details

    • XTandemIdfileReader

      public XTandemIdfileReader()
      Default constructor for the purpose of instantiation.

    • XTandemIdfileReader

      public XTandemIdfileReader(File inputFile) throws IOException
      Constructor for an X!Tandem xml result file reader.
      Parameters:
      inputFile - the Mascot dat file
      Throws:
      IOException - if an IOException occurs

    • XTandemIdfileReader

      public XTandemIdfileReader(File inputFile, WaitingHandler waitingHandler) throws IOException
      Constructor for an X!Tandem xml result file reader.
      Parameters:
      inputFile - the Mascot dat file
      waitingHandler - the waiting handler
      Throws:
      IOException - if an IOException occurs

  • Method Details

    • getExtension

      public String getExtension()
      Description copied from interface: IdfileReader
      Returns the extension of the file for which this IdfileReader can be used.
      Specified by:
      getExtension in interface IdfileReader
      Returns:
      String with the extension (taken to make up the end of the filename) of the file that this IdfileReader can read.

    • getAllSpectrumMatches

      public ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters) throws IOException, SQLException, ClassNotFoundException, InterruptedException, JAXBException, XMLStreamException
      Description copied from interface: IdfileReader
      Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum. It is very important to close the file reader after creation. Using this method secondary maps are not filled.
      Specified by:
      getAllSpectrumMatches in interface IdfileReader
      Parameters:
      spectrumProvider - A spectrum provider with the spectra of the file loaded.
      waitingHandler - The waiting handler displaying the progress (can be null). The secondary progress methods will be called.
      searchParameters - The search parameters.
      Returns:
      a list of spectrum matches
      Throws:
      IOException - if an IOException occurs
      SQLException - if an SQLException occurs
      ClassNotFoundException - if an\ ClassNotFoundException occurs
      InterruptedException - if an InterruptedException occurs
      JAXBException - if a JAXBException occurs
      XMLStreamException - if an XMLStreamException occurs

    • getAllSpectrumMatches

      public ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations) throws IOException, SQLException, ClassNotFoundException, InterruptedException, JAXBException, XMLStreamException
      Description copied from interface: IdfileReader
      Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum.It is very important to close the file reader after creation. Secondary peptide and tag maps are filled according to the file content and the sequence matching preferences. If the sequence matching preferences are null, the maps are not filled.
      Specified by:
      getAllSpectrumMatches in interface IdfileReader
      Parameters:
      spectrumProvider - A spectrum provider with the spectra of the file loaded.
      waitingHandler - The waiting handler displaying the progress (can be null). The secondary progress methods will be called.
      searchParameters - The search parameters.
      sequenceMatchingPreferences - The sequence matching preferences to use for the creation of the secondary maps.
      expandAaCombinations - If true, a peptide assumption (not implemented for tag assumptions) will be created for all possible amino acid combination for peptide sequences containing an ambiguity like an X.
      Returns:
      the spectrum matches
      Throws:
      IOException - if an IOException occurs
      SQLException - if an SQLException occurs
      ClassNotFoundException - if an\ ClassNotFoundException occurs
      InterruptedException - if an InterruptedException occurs
      JAXBException - if a JAXBException occurs
      XMLStreamException - if an XMLStreamException occurs

    • close

      public void close() throws IOException
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface IdfileReader
      Throws:
      IOException

    • getSoftwareVersions

      public HashMap<String,ArrayList<String>> getSoftwareVersions()
      Description copied from interface: IdfileReader
      Returns the names and versions of the software used to generate the identification file in a map, e.g., Mascot > (2.2 and 2.3) and X!Tandem > Sledgehammer (2013.09.01.1). Null if not known.
      Specified by:
      getSoftwareVersions in interface IdfileReader
      Returns:
      the version of the software used to generate the identification file, null if not known

    • hasDeNovoTags

      public boolean hasDeNovoTags()
      Description copied from interface: IdfileReader
      Returns a boolean indicating whether the file contains de novo results as tags.
      Specified by:
      hasDeNovoTags in interface IdfileReader
      Returns:
      a boolean indicating whether the file contains de novo results as tags