Class FastaParametersInputBean

java.lang.Object
com.compomics.cli.fasta.FastaParametersInputBean

public class FastaParametersInputBean
extends Object
This class gathers command line parameters for the parsing of FASTA files.
Author:
Marc Vaudel, Harald Barsnes
  • Constructor Details

    • FastaParametersInputBean

      public FastaParametersInputBean​(org.apache.commons.cli.CommandLine aLine, File fastaFile, WaitingHandler waitingHandler) throws IOException
      Parses all the arguments from a command line.
      Parameters:
      aLine - the command line
      fastaFile - the FASTA file to infer the parameters from if not provided in the command line arguments
      waitingHandler - the waiting handler
      Throws:
      IOException - if an error occurs while reading or writing a file.
  • Method Details

    • isValidStartup

      public static boolean isValidStartup​(org.apache.commons.cli.CommandLine aLine)
      Verifies the command line start parameters.
      Parameters:
      aLine - the command line to validate
      Returns:
      true if the startup was valid
    • getFastaParameters

      public FastaParameters getFastaParameters()
      Returns the FASTA parameters as parsed from the command line.
      Returns:
      the FASTA parameters as parsed from the command line