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SUMMARY: NESTED  FIELD  CONSTR  METHOD  DETAIL: FIELD  CONSTR  METHOD 
public interface SequenceScore
This interface defines a scoring function that assigns a score to each input sequence. Such score can, for instance, be
used in a AbstractScoreBasedClassifier
to classify Sequence
s by chosing the class with the SequenceScore
yielding
the maximum score for the input Sequence
.
The most important subinterfaces 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.
Method Summary  

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)
Returns the logarithmic score for the Sequence seq
beginning at position start in the Sequence . 
double 
getLogScoreFor(Sequence seq,
int start,
int end)
Returns the logarithmic score for the Sequence seq
beginning at position start in the Sequence . 
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. 
Methods inherited from interface de.jstacs.Storable 

toXML 
Method Detail 

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 sequence
double getLogScoreFor(Sequence seq, int start)
Sequence
seq
beginning at position start
in the Sequence
.
seq
 the Sequence
start
 the start position in the Sequence
Sequence
double getLogScoreFor(Sequence seq, int start, int end) throws Exception
Sequence
seq
beginning at position start
in the Sequence
.
seq
 the Sequence
start
 the start position in the Sequence
end
 the end position (inclusive) in the Sequence
Sequence
Exception
 if, for instance, the subsequence length can not be handleddouble[] getLogScoreFor(DataSet data) throws Exception
getLogScoreFor(Sequence)
.
data
 the data set of sequences
Exception
 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 probabilities
String
representation of the instance


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