public class UniformPositionPrior extends PositionPrior
motifLength
Constructor and Description |
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UniformPositionPrior()
This empty constructor creates an instance with motif length -1.
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UniformPositionPrior(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
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protected void |
extractAdditionalInformation(StringBuffer xml)
This method extracts additional information from a
StringBuffer . |
protected StringBuffer |
getAdditionalInformation()
This method returns a
StringBuffer containing additional
information for the XML representation. |
String |
getInstanceName()
Returns the instance name.
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int |
getLength()
Returns the length that is supported by this prior.
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double |
getLogPriorForPositions(int seqLength,
int... starts)
The logarithmic value of the prior for specified start positions of the
part motifs.
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clone, setMotifLength, toXML
public UniformPositionPrior()
public UniformPositionPrior(StringBuffer xml) throws NonParsableException
Storable
.
Creates a new UniformPositionPrior
out of its XML representation.xml
- the XML representation as StringBuffer
NonParsableException
- if the StringBuffer
can not be parsedpublic double getLogPriorForPositions(int seqLength, int... starts) throws IllegalArgumentException
PositionPrior
getLogPriorForPositions
in class PositionPrior
seqLength
- the length of the sequencestarts
- the start positions of the part motifsIllegalArgumentException
- if something went wrong, e.g. the motif length is not set.public final int getLength()
PositionPrior
getLength
in class PositionPrior
public String getInstanceName()
PositionPrior
getInstanceName
in class PositionPrior
protected StringBuffer getAdditionalInformation()
PositionPrior
StringBuffer
containing additional
information for the XML representation.getAdditionalInformation
in class PositionPrior
StringBuffer
containing additional information for the
XML representationprotected void extractAdditionalInformation(StringBuffer xml)
PositionPrior
StringBuffer
.extractAdditionalInformation
in class PositionPrior
xml
- the StringBuffer
containing the additional information
of the XML representation