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