java.lang.Object
com.compomics.util.experiment.biology.genes.go.GoDomains

public class GoDomains
extends Object
Class parsing go domains and storing them in a map.
Author:
Marc Vaudel, Harald Barsnes
  • Field Details

  • Constructor Details

  • Method Details

    • laodMappingFromFile

      public void laodMappingFromFile​(File file, WaitingHandler waitingHandler) throws IOException
      Reads go mappings from a file. The structure of the file should go accession go name Previous mappings are silently overwritten.
      Parameters:
      file - the file containing the GO mapping
      waitingHandler - a waiting handler allowing canceling of the process.
      Throws:
      IOException - if an exception occurs while reading the file
    • getTermDomain

      public String getTermDomain​(String goAccession)
      Returns the description of a GO term.
      Parameters:
      goAccession - the accession number of the GO term of interest
      Returns:
      the first description found, null if not found
    • addDomain

      public void addDomain​(String goAccession, String goDomain)
      Adds a go domain to the mapping.
      Parameters:
      goAccession - the accession of the GO term
      goDomain - the domain of the GO term
    • saveMapping

      public void saveMapping​(File destinationFile) throws IOException
      Saves the mapping to the given file.
      Parameters:
      destinationFile - the destination file
      Throws:
      IOException - exception thrown whenever an error occurred while writing the file