Class DecoyConverter
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
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Constructor Summary
Constructors Constructor Description DecoyConverter()
Empty default constructor. -
Method Summary
Modifier and Type Method Description static void
appendDecoySequences(File fastaIn, File fastaOut, FastaParameters fastaParameters, WaitingHandler waitingHandler)
Appends decoy sequences to the provided FASTA file.static FastaParameters
getDecoyParameters(FastaParameters targetParameters)
Returns the FASTA parameters of the target-decoy database based on the parameters of the target database.static FastaSummary
getDecoySummary(File newFastaFile, FastaSummary targetSummary)
Returns the FASTA summary of the target-decoy database based on the summary of the target database.
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Constructor Details
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DecoyConverter
public DecoyConverter()Empty default constructor.
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Method Details
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appendDecoySequences
public static void appendDecoySequences(File fastaIn, File fastaOut, FastaParameters fastaParameters, WaitingHandler waitingHandler) throws IOExceptionAppends decoy sequences to the provided FASTA file.- Parameters:
fastaIn
- the FASTA file to readfastaOut
- the FASTA file to writefastaParameters
- the FASTA parameterswaitingHandler
- 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
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getDecoyParameters
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
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getDecoySummary
Returns the FASTA summary of the target-decoy database based on the summary of the target database.- Parameters:
newFastaFile
- the new FASTA filetargetSummary
- the summary of the target database- Returns:
- the FASTA summary of the target-decoy database
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