Package com.compomics.cli.fasta

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 Summary

Constructors

Constructor	Description
FastaParametersInputBean(org.apache.commons.cli.CommandLine aLine, File fastaFile, WaitingHandler waitingHandler)	Parses all the arguments from a command line.

Method Summary

Modifier and Type	Method	Description
FastaParameters	getFastaParameters()	Returns the FASTA parameters as parsed from the command line.
static boolean	isValidStartup(org.apache.commons.cli.CommandLine aLine)	Verifies the command line start parameters.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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