public class DecoyConverter extends Object
Modifier and Type | Field and Description |
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static String |
decoyFlag
The flag to append to the accessions of decoy proteins.
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Constructor and Description |
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DecoyConverter() |
Modifier and Type | Method and Description |
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static void |
appendDecoySequences(File fastaIn,
File fastaOut,
WaitingHandler waitingHandler)
Appends decoy sequences to the provided FASTA file.
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static FastaParameters |
getDecoyParameters(FastaParameters targetParameters)
Returns the FASTA parameters of the target-decoy database based on the parameters of the target database.
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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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public static final String decoyFlag
public static void appendDecoySequences(File fastaIn, File fastaOut, WaitingHandler waitingHandler) throws IOException
fastaIn
- the FASTA file to readfastaOut
- the FASTA file to writewaitingHandler
- a handler to allow canceling the import and
displaying progressIOException
- exception thrown whenever an error happened while
reading or writing a FASTA filepublic static FastaParameters getDecoyParameters(FastaParameters targetParameters)
targetParameters
- the parameters of the target databasepublic static FastaSummary getDecoySummary(File newFastaFile, FastaSummary targetSummary)
newFastaFile
- the new FASTA filetargetSummary
- the summary of the target databaseCopyright © 2018. All rights reserved.