Package com.compomics.util.experiment.io.biology.protein.converters

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

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.

Methods inherited from class java.lang.Object

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

Constructor Details

DecoyConverter

public DecoyConverter()

Empty default constructor.

Method Details

appendDecoySequences

public static void appendDecoySequences(File fastaIn,
 File fastaOut,
 FastaParameters fastaParameters,
 WaitingHandler waitingHandler)
                                 throws IOException

Appends decoy sequences to the provided FASTA file.

Parameters:

fastaIn - the FASTA file to read

fastaOut - the FASTA file to write

fastaParameters - the FASTA parameters

waitingHandler - 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

getDecoyParameters

public static FastaParameters getDecoyParameters(FastaParameters targetParameters)

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

getDecoySummary

public static FastaSummary getDecoySummary(File newFastaFile,
 FastaSummary targetSummary)

Returns the FASTA summary of the target-decoy database based on the summary of the target database.

Parameters:

newFastaFile - the new FASTA file

targetSummary - the summary of the target database

Returns:

the FASTA summary of the target-decoy database