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

Class DirecTagIdfileReader

java.lang.Object
com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader
All Implemented Interfaces:
IdfileReader, AutoCloseable
public class DirecTagIdfileReader extends Object implements IdfileReader
An identification file reader for Direct tag results.
Author:
Marc Vaudel

  • Field Details

    • cTermCorrection

      public final double cTermCorrection
      The mass to add to the C-terminal gap so that is corresponds to a peptide fragment.
      See Also:

    • nTermCorrection

      public final double nTermCorrection
      The mass to add to the N-terminal gap so that is corresponds to a peptide fragment.
      See Also:

  • Constructor Details

    • DirecTagIdfileReader

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

    • DirecTagIdfileReader

      public DirecTagIdfileReader(File tagFile)
      Constructors, parses a file.
      Parameters:
      tagFile - the file to parse

  • Method Details

    • getTagsParametersNames

      public Set<String> getTagsParametersNames()
      Returns the name of the different parameters names found.
      Returns:
      the name of the different parameters names found

    • getTagParameter

      public String getTagParameter(String tagParameterName)
      Returns the tagging parameter corresponding to a given parameter name.
      Parameters:
      tagParameterName - the name of the parameter of interest
      Returns:
      the parameter of interest

    • getAllSpectrumMatches

      public ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters) throws IOException, SQLException, ClassNotFoundException, InterruptedException, JAXBException
      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

    • getAllSpectrumMatches

      public ArrayList<SpectrumMatch> getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations) throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, JAXBException
      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
      IllegalArgumentException

    • getTagsGenerator

      public String getTagsGenerator()
      Returns the tags generator used to create the file.
      Returns:
      the tags generator used to create the file

    • getTagsGeneratorVersion

      public String getTagsGeneratorVersion()
      Returns the version of the tags generator used to create the file.
      Returns:
      the version of the tags generator used to create the file

    • getCopyRight

      public String getCopyRight()
      Returns the copyright.
      Returns:
      the copyright

    • getLicense

      public String getLicense()
      Returns the license information of this file.
      Returns:
      the license information of this file

    • getTimeStart

      public String getTimeStart()
      Returns the starting time of the tagging as given in the file.
      Returns:
      the starting time of the tagging

    • getTimeEnd

      public String getTimeEnd()
      Returns the ending time of the tagging as given in the file.
      Returns:
      the ending time of the tagging

    • getTaggingTimeSeconds

      public Double getTaggingTimeSeconds()
      Returns the tagging time in seconds as listed in the file.
      Returns:
      the tagging time in seconds as listed in the file

    • getnProcessingNode

      public Integer getnProcessingNode()
      Returns the number of processing nodes used.
      Returns:
      the number of processing nodes used

    • getInputFile

      public File getInputFile()
      Returns the spectrum file name as found in the parameters section.
      Returns:
      the spectrum file name

    • 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.

    • 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