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java.lang.Objectde.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint
public abstract class Constraint
The main class for all constraints on models. This class centralizes all specific constraints (e.g. P(X1=A,X2=A)) from a partitioning constraint (e.g. all specific constraints for some given positions).
Field Summary | |
---|---|
protected double[] |
counts
The counts for each specific constraint. |
protected double[] |
freq
The frequencies estimated from the counts. |
protected int[] |
usedPositions
The used positions. |
Constructor Summary | |
---|---|
protected |
Constraint(int[] usedPositions,
int n)
The main constructor. |
protected |
Constraint(StringBuffer xml)
The standard constructor for the interface Storable . |
Method Summary | |
---|---|
void |
add(int index,
double weight)
Adds the given weight to the count with index
index . |
void |
add(Sequence seq,
int start,
double weight)
This method determines the specific constraint that is fulfilled by the Sequence seq and adds the weight to the
specific counter. |
protected abstract void |
appendAdditionalInfo(StringBuffer xml)
This method appends additional information that is not stored in the base class to the StringBuffer . |
protected Constraint |
clone()
|
abstract void |
estimate(double ess)
Estimates the (smoothed) relative frequencies using the ess (equivalent sample size). |
protected void |
estimateUnConditional(int start,
int end,
double pc,
boolean exceptionWhenNoData)
Estimates unconditionally. |
protected abstract void |
extractAdditionalInfo(StringBuffer xml)
This method parses additional information from the StringBuffer
that is not parsed in the base class. |
double |
getCount(int index)
Returns the current count with index index . |
abstract String |
getDescription(AlphabetContainer con,
int i)
Returns the decoded symbol for the encoded symbol i . |
double |
getFreq(int index)
Returns the current frequency with index index . |
double |
getFreq(Sequence seq,
int start)
This method determines the specific constraint that is fulfilled by the Sequence seq beginning at position
start . |
String |
getFreqInfo(AlphabetContainer con)
Returns an information about the stored frequencies. |
int |
getMarginalOrder()
Returns the marginal order, i.e. the number of used random variables. |
int |
getNumberOfSpecificConstraints()
Returns the number of specific constraints. |
int |
getPosition(int index)
Returns the position with index index . |
int[] |
getPositions()
Returns a clone of the array of used positions. |
protected abstract String |
getXMLTag()
Returns the XML tag that is used for the class to en- or decode. |
void |
reset()
This method resets all member variables that are in some way counters, frequencies, ... |
void |
resetCounts()
This method allows to reset the internal field counts that is used for estimating the probabilities. |
abstract int |
satisfiesSpecificConstraint(Sequence seq,
int start)
This method returns the index of the specific constraint that is fulfilled by the Sequence seq beginning at position
start . |
abstract String |
toString()
|
StringBuffer |
toXML()
This method returns an XML representation as StringBuffer of an
instance of the implementing class. |
Methods inherited from class java.lang.Object |
---|
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
---|
protected double[] counts
protected double[] freq
protected int[] usedPositions
Constructor Detail |
---|
protected Constraint(int[] usedPositions, int n) throws IllegalArgumentException
Constraint
and checks that
each position is used maximally once.
usedPositions
- the used positions (will be cloned), have to be non-negativen
- the number of specific constraints
IllegalArgumentException
- if there are some fundamental errors in the arguments for the positionsprotected Constraint(StringBuffer xml) throws NonParsableException
Storable
.
Creates a new Constraint
out of its XML representation.
xml
- the XML representation as StringBuffer
NonParsableException
- if the Constraint
could not be reconstructed out of
the XML representation (the StringBuffer
could not be
parsed)Storable
,
extractAdditionalInfo(StringBuffer)
Method Detail |
---|
public final void add(int index, double weight)
weight
to the count with index
index
.
index
- the indexweight
- the weightpublic void add(Sequence seq, int start, double weight)
Sequence
seq
and adds the weight
to the
specific counter.
seq
- the sequencestart
- the start positionweight
- the weight for the sequencesatisfiesSpecificConstraint(Sequence, int)
,
add(int, double)
protected Constraint clone() throws CloneNotSupportedException
clone
in class Object
CloneNotSupportedException
public abstract void estimate(double ess)
ess
- the essprotected void estimateUnConditional(int start, int end, double pc, boolean exceptionWhenNoData)
start
- the start indexend
- the end indexpc
- the pseudocount for each parameterexceptionWhenNoData
- indicates if an (runtime) exception is thrown if no data was
available to estimate the parametersprotected abstract void appendAdditionalInfo(StringBuffer xml)
StringBuffer
.
xml
- the StringBuffer
that is used for appending additional
informationpublic double getCount(int index)
index
.
index
- the index
public double getFreq(int index)
index
.
index
- the index
public double getFreq(Sequence seq, int start)
Sequence
seq
beginning at position
start
.
seq
- the Sequence
start
- the start position
satisfiesSpecificConstraint(Sequence, int)
,
getFreq(int)
public int getMarginalOrder()
public int getNumberOfSpecificConstraints()
public int getPosition(int index)
index
.
index
- the index
index
public int[] getPositions()
protected abstract String getXMLTag()
public void reset()
public abstract int satisfiesSpecificConstraint(Sequence seq, int start)
Sequence
seq
beginning at position
start
.
seq
- the sequencestart
- the start position
protected abstract void extractAdditionalInfo(StringBuffer xml) throws NonParsableException
StringBuffer
that is not parsed in the base class.
xml
- the StringBuffer
to be parsed
NonParsableException
- if something with the parsing went wrongpublic abstract String toString()
toString
in class Object
public StringBuffer toXML()
Storable
StringBuffer
of an
instance of the implementing class.
toXML
in interface Storable
public abstract String getDescription(AlphabetContainer con, int i)
i
.
con
- the AlphabetContainer
i
- the encoded symbol
i
public String getFreqInfo(AlphabetContainer con)
con
- the AlphabetContainer
public void resetCounts()
counts
that is used for estimating the probabilities.
add(int, double)
,
add(Sequence, int, double)
,
estimate(double)
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