public class FastaParameters extends ExperimentObject
Modifier and Type | Field and Description |
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static String[] |
DECOY_FLAGS
The decoy flags used to infer the FASTA parameters.
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static char[] |
DECOY_SEPARATORS
The decoy separators used to infer the FASTA parameters.
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NO_KEY
Constructor and Description |
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FastaParameters()
Empty default constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(FastaParameters fastaParameters) |
String |
getDecoyFlag()
Returns the decoy flag.
|
String |
getShortDescription()
Returns a short description of the parameters.
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String |
getTargetDecoyFileNameSuffix()
Returns the target-decoy file name suffix.
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static FastaParameters |
inferParameters(String fastaFilePath,
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.
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boolean |
isTargetDecoy()
Returns a boolean indicating whether the FASTA file should be processed
as target-decoy or only target.
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void |
setDecoyFlag(String decoyFlag)
Sets the decoy flag.
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void |
setDecoySuffix(boolean decoySuffix)
Sets whether the decoy flag is a suffix or a prefix.
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void |
setTargetDecoy(boolean targetDecoy)
Sets whether the FASTA file should be processed as target-decoy or only
target.
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void |
setTargetDecoyFileNameSuffix(String targetDecoyFileNameSuffix)
Set the target-decoy file name suffix.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public static final String[] DECOY_FLAGS
public static final char[] DECOY_SEPARATORS
public boolean isTargetDecoy()
public void setTargetDecoy(boolean targetDecoy)
targetDecoy
- whether the FASTA file should be processed as
target-decoy or only targetpublic 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 getTargetDecoyFileNameSuffix()
public void setTargetDecoyFileNameSuffix(String targetDecoyFileNameSuffix)
targetDecoyFileNameSuffix
- the targetDecoyFileNameSuffix to setpublic boolean isSameAs(FastaParameters fastaParameters)
fastaParameters
- the other parameterspublic static FastaParameters inferParameters(String fastaFilePath, WaitingHandler waitingHandler) throws IOException
fastaFilePath
- path to a FASTA filewaitingHandler
- a handler to allow canceling the importIOException
- exception thrown if an error occurred while iterating
the filepublic boolean equals(FastaParameters fastaParameters)
public String getShortDescription()
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