public class FastaParameters extends Object
Modifier and Type | Field and Description |
---|---|
static String[] |
decoyFlags
The decoy flags used to infer the fasta parameters.
|
static char[] |
separators
The decoy separators used to infer the fasta parameters.
|
Constructor and Description |
---|
FastaParameters() |
Modifier and Type | Method and Description |
---|---|
String |
getDecoyFlag()
Returns the decoy flag.
|
String |
getDescription()
Returns the description for this database.
|
String |
getName()
Returns the name of the database.
|
String |
getVersion()
Returns the database version.
|
static FastaParameters |
inferParameters(File fastaFile)
Infers the parameters used to parse the file.
|
static FastaParameters |
inferParameters(File fastaFile,
WaitingHandler waitingHandler)
Infers the parameters used to parse the file.
|
boolean |
isDecoySuffix()
Returns a boolean indicating whether the decoy flag is a suffix or a
prefix.
|
boolean |
isSameAs(FastaParameters fastaParameters)
Returns a boolean indicating whether the parsing parameters are the same as the given parameters.
|
boolean |
isTargetDecoy()
Returns a boolean indicating whether the database is concatenated target decoy.
|
void |
setDecoyFlag(String decoyFlag)
Sets the decoy flag.
|
void |
setDecoySuffix(boolean decoySuffix)
Sets whether the decoy flag is a suffix or a prefix.
|
void |
setDefaultAttributes(File fastaFile)
Sets default name and version from the given fasta file.
|
void |
setDescription(String description)
Sets the description for this database.
|
void |
setName(String name)
Sets a new name for the database.
|
void |
setTargetDecoy(boolean targetDecoy)
Sets whether the database is concatenated target decoy.
|
void |
setVersion(String version)
Sets the database version.
|
public static final String[] decoyFlags
public static final char[] separators
public String getDecoyFlag()
public void setDecoyFlag(String decoyFlag)
decoyFlag
- the decoy flagpublic boolean isDecoySuffix()
public void setDecoySuffix(boolean decoySuffix)
decoySuffix
- whether the decoy flag is a suffix or a prefixpublic String getName()
public void setName(String name)
name
- a new name for the databasepublic String getVersion()
public void setVersion(String version)
version
- the database versionpublic String getDescription()
public void setDescription(String description)
description
- the description for this databasepublic boolean isTargetDecoy()
public void setTargetDecoy(boolean targetDecoy)
targetDecoy
- a boolean indicating whether the database is concatenated target decoypublic boolean isSameAs(FastaParameters fastaParameters)
fastaParameters
- the other parameterspublic void setDefaultAttributes(File fastaFile)
fastaFile
- the fasta filepublic static FastaParameters inferParameters(File fastaFile) throws IOException
fastaFile
- a fasta fileIOException
- exception thrown if an error occurred while iterating the filepublic static FastaParameters inferParameters(File fastaFile, WaitingHandler waitingHandler) throws IOException
fastaFile
- a fasta filewaitingHandler
- a handler to allow canceling the importIOException
- exception thrown if an error occurred while iterating the fileCopyright © 2018. All rights reserved.