Modifier and Type | Field and Description |
---|---|
protected MEMConstraint[] |
constraints
The specific constraints of this MEM.
|
Constructor and Description |
---|
MEM(AbstractList<int[]> constr,
int[] allAlphLen,
int[] indices)
The main constructor of a MEM.
|
MEM(int[] constraint,
int[] allAlphLen,
int[][] cond)
The main constructor of a MEM.
|
MEM(StringBuffer representation)
The constructor for the
Storable interface. |
Modifier and Type | Method and Description |
---|---|
MEM |
clone() |
double |
getLogPriorPart(double ess)
This method compute the prior for the current parameter ignoring some constants.
|
double |
getLogScoreFor(Sequence seq,
int start)
Returns the logarithmic score for the
sequence beginning at start . |
double |
getScoreFor(Sequence seq,
int start)
Returns the score for the
sequence beginning at start . |
String |
toString(NumberFormat nf)
This method returns some
String using a given NumberFormat . |
StringBuffer |
toXML()
This method returns an XML representation as
StringBuffer of an
instance of the implementing class. |
void |
train(SequenceIterator s,
byte algo,
TerminationCondition condition,
SafeOutputStream sostream)
This method approximates the distribution either analytically or numerically.
|
protected MEMConstraint[] constraints
public MEM(AbstractList<int[]> constr, int[] allAlphLen, int[] indices)
constr
- the constraintsallAlphLen
- the alphabet length of all alphabetsindices
- the indices of the positions to be usedpublic MEM(int[] constraint, int[] allAlphLen, int[][] cond)
constraint
- the constraintallAlphLen
- the alphabet length of all alphabetscond
- the conditional fixed positionspublic MEM(StringBuffer representation) throws NonParsableException
Storable
interface.representation
- the representationNonParsableException
- if the the StringBuffer could not be parsed.public MEM clone() throws CloneNotSupportedException
clone
in class Object
CloneNotSupportedException
public double getScoreFor(Sequence seq, int start)
sequence
beginning at start
.seq
- the sequencestart
- the start positionsequence
beginning at start
public double getLogScoreFor(Sequence seq, int start)
sequence
beginning at start
.seq
- the sequencestart
- the start positionsequence
beginning at start
public double getLogPriorPart(double ess)
ess
- the ESS to be usedStatisticalModel.getLogPriorTerm()
public String toString(NumberFormat nf)
String
using a given NumberFormat
.nf
- the NumberFormat
.public StringBuffer toXML()
Storable
StringBuffer
of an
instance of the implementing class.public void train(SequenceIterator s, byte algo, TerminationCondition condition, SafeOutputStream sostream) throws Exception
s
- the SequenceIterator used in normalization and numerical approximationalgo
- the choice of numerical approximationcondition
- the TerminationCondition
for stopping the iterative algorithmsostream
- a possibility for writing some informationException
- if something went wrong inside the algorithmsMEMTools