public interface SequenceScore extends Cloneable, Storable
AbstractScoreBasedClassifier
to classify Sequence
s by chosing the class with the SequenceScore
yielding
the maximum score for the input Sequence
.
The most important sub-interfaces are the StatisticalModel
for SequenceScore
s that define a proper, i.e., normalized, likelihood
over the input Sequence
s, and DifferentiableSequenceScore
that can compute the derivation with respect to their parameters.Modifier and Type | Method and Description |
---|---|
SequenceScore |
clone()
Creates a clone (deep copy) of the current
SequenceScore instance. |
AlphabetContainer |
getAlphabetContainer()
Returns the container of alphabets that were used when constructing the instance.
|
ResultSet |
getCharacteristics()
Returns some information characterizing or describing the current
instance.
|
String |
getInstanceName()
Should return a short instance name such as iMM(0), BN(2), ...
|
int |
getLength()
Returns the length of sequences this instance can score.
|
double[] |
getLogScoreFor(DataSet data)
This method computes the logarithm of the scores of all sequences
in the given data set.
|
void |
getLogScoreFor(DataSet data,
double[] res)
This method computes and stores the logarithm of the scores for
any sequence in the data set in the given
double -array. |
double |
getLogScoreFor(Sequence seq)
Returns the logarithmic score for the
Sequence seq . |
double |
getLogScoreFor(Sequence seq,
int start)
|
double |
getLogScoreFor(Sequence seq,
int start,
int end)
|
NumericalResultSet |
getNumericalCharacteristics()
Returns the subset of numerical values that are also returned by
getCharacteristics() . |
boolean |
isInitialized()
This method can be used to determine whether the instance is initialized.
|
String |
toString(NumberFormat nf)
This method returns a
String representation of the instance. |
SequenceScore clone() throws CloneNotSupportedException
SequenceScore
instance.CloneNotSupportedException
- if something went wrong while cloningAlphabetContainer getAlphabetContainer()
String getInstanceName()
int getLength()
ResultSet getCharacteristics() throws Exception
StorableResult
.Exception
- if some of the characteristics could not be definedStorableResult
NumericalResultSet getNumericalCharacteristics() throws Exception
getCharacteristics()
.Exception
- if some of the characteristics could not be defineddouble getLogScoreFor(Sequence seq)
Sequence
seq
.seq
- the sequencedouble getLogScoreFor(Sequence seq, int start)
double[] getLogScoreFor(DataSet data) throws Exception
getLogScoreFor(Sequence)
.data
- the data set of sequencesException
- if something went wronggetLogScoreFor(Sequence)
void getLogScoreFor(DataSet data, double[] res) throws Exception
double
-array.
getLogScoreFor(Sequence)
.data
- the data set of sequencesres
- the array for the results, has to have length
data.getNumberOfElements()
(which returns the
number of sequences in the data set)Exception
- if something went wronggetLogScoreFor(Sequence)
,
getLogScoreFor(DataSet)
boolean isInitialized()
getLogScoreFor(Sequence)
.true
if the instance is initialized, false
otherwiseString toString(NumberFormat nf)
String
representation of the instance.nf
- the NumberFormat
for the String
representation of parameters or probabilitiesString
representation of the instance