public class IdentificationParametersInputBean extends Object
Constructor and Description |
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IdentificationParametersInputBean(org.apache.commons.cli.CommandLine aLine)
Takes all the arguments from a command line.
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Modifier and Type | Method and Description |
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File |
getDestinationFile()
Returns the file where to save the identification parameters.
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IdentificationParameters |
getIdentificationParameters()
Returns the identification parameters.
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File |
getInputFile()
Returns the input parameters file.
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Boolean |
isListEnzymes()
Indicates whether the enzymes should be printed.
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Boolean |
isListMods()
Indicates whether the modifications should be printed.
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static boolean |
isValidModifications(org.apache.commons.cli.CommandLine aLine)
Verifies that modifications are correctly recognized.
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static boolean |
isValidStartup(org.apache.commons.cli.CommandLine aLine,
boolean checkMandatoryParameters)
Verifies the command line start parameters.
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void |
setIdentificationParameters(IdentificationParameters identificationParameters)
Sets the identification parameters.
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void |
updateIdentificationParameters()
Updates the identification parameters according to the command line.
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public IdentificationParametersInputBean(org.apache.commons.cli.CommandLine aLine) throws IOException, ClassNotFoundException
aLine
- the command lineIOException
- if an IOException occursClassNotFoundException
- if aClassNotFoundException
ClassNotFoundException occurspublic static boolean isValidStartup(org.apache.commons.cli.CommandLine aLine, boolean checkMandatoryParameters)
aLine
- the command line to validatecheckMandatoryParameters
- if true, check if mandatory parameters
are includedpublic void updateIdentificationParameters()
public void setIdentificationParameters(IdentificationParameters identificationParameters)
identificationParameters
- the identification parameterspublic IdentificationParameters getIdentificationParameters()
public File getInputFile()
public File getDestinationFile()
public Boolean isListMods()
public Boolean isListEnzymes()
public static boolean isValidModifications(org.apache.commons.cli.CommandLine aLine) throws IOException
aLine
- the command line to validateIOException
- if an IOException occursCopyright © 2021. All rights reserved.