java.lang.Object
com.compomics.util.experiment.io.biology.protein.converters.DecoyConverter

public class DecoyConverter
extends Object
This class appends decoy sequences to the given FASTA file.
Author:
Marc Vaudel, Harald Barsnes
  • Constructor Details

  • Method Details

    • appendDecoySequences

      public static void appendDecoySequences​(File fastaIn, File fastaOut, FastaParameters fastaParameters, WaitingHandler waitingHandler) throws IOException
      Appends decoy sequences to the provided FASTA file.
      Parameters:
      fastaIn - the FASTA file to read
      fastaOut - the FASTA file to write
      fastaParameters - the FASTA parameters
      waitingHandler - a handler to allow canceling the import and displaying progress
      Throws:
      IOException - exception thrown whenever an error happened while reading or writing a FASTA file
    • getDecoyParameters

      public static FastaParameters getDecoyParameters​(FastaParameters targetParameters)
      Returns the FASTA parameters of the target-decoy database based on the parameters of the target database.
      Parameters:
      targetParameters - the parameters of the target database
      Returns:
      the FASTA parameters of the target-decoy database
    • getDecoySummary

      public static FastaSummary getDecoySummary​(File newFastaFile, FastaSummary targetSummary)
      Returns the FASTA summary of the target-decoy database based on the summary of the target database.
      Parameters:
      newFastaFile - the new FASTA file
      targetSummary - the summary of the target database
      Returns:
      the FASTA summary of the target-decoy database