Interface IdfileReader

All Superinterfaces:
AutoCloseable
All Known Implementing Classes:
AndromedaIdfileReader, CossIdfileReader, DirecTagIdfileReader, MascotIdfileReader, MsAmandaIdfileReader, MzIdentMLIdfileReader, NovorIdfileReader, OnyaseIdfileReader, PepNovoIdfileReader, PepxmlIdfileReader, PNovoIdfileReader, TideIdfileReader, XTandemIdfileReader

public interface IdfileReader
extends AutoCloseable
Generic interface for the parser of a file containing PSMs.
Author:
Marc Vaudel, Harald Barsnes
  • Method Details

    • getSoftwareVersions

      HashMap<String,​ArrayList<String>> getSoftwareVersions()
      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.
      Returns:
      the version of the software used to generate the identification file, null if not known
    • getExtension

      String getExtension()
      Returns the extension of the file for which this IdfileReader can be used.
      Returns:
      String with the extension (taken to make up the end of the filename) of the file that this IdfileReader can read.
    • close

      void close() throws IOException
      Specified by:
      close in interface AutoCloseable
      Throws:
      IOException
    • getAllSpectrumMatches

      ArrayList<SpectrumMatch> getAllSpectrumMatches​(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters) throws IOException, SQLException, ClassNotFoundException, InterruptedException, JAXBException, org.xmlpull.v1.XmlPullParserException, XMLStreamException
      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.
      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
      org.xmlpull.v1.XmlPullParserException - if an XmlPullParserException occurs
      XMLStreamException - if an XMLStreamException occurs
    • getAllSpectrumMatches

      ArrayList<SpectrumMatch> getAllSpectrumMatches​(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations) throws IOException, SQLException, ClassNotFoundException, InterruptedException, JAXBException, org.xmlpull.v1.XmlPullParserException, org.xmlpull.v1.XmlPullParserException, XMLStreamException
      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.
      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
      org.xmlpull.v1.XmlPullParserException - if an XmlPullParserException occurs
      XMLStreamException - if an XMLStreamException occurs
    • hasDeNovoTags

      boolean hasDeNovoTags()
      Returns a boolean indicating whether the file contains de novo results as tags.
      Returns:
      a boolean indicating whether the file contains de novo results as tags