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java.lang.Objectde.jstacs.models.discrete.Constraint
de.jstacs.models.discrete.inhomogeneous.InhConstraint
de.jstacs.models.discrete.inhomogeneous.MEMConstraint
public class MEMConstraint
The constraint can be used for any MEM application.
Field Summary |
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Fields inherited from class de.jstacs.models.discrete.inhomogeneous.InhConstraint |
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offset |
Fields inherited from class de.jstacs.models.discrete.Constraint |
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counts, freq, usedPositions |
Constructor Summary | |
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MEMConstraint(int[] pos,
int[] alphabetLength)
Creates a MEMConstraint as part of a (whole) model |
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MEMConstraint(int[] pos,
int[] alphabetLength,
int[] corrected_positions)
Creates a MEMConstraint as part of a model |
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MEMConstraint(StringBuffer xml)
Creates a MEMConstraint from a StringBuffer |
Method Summary | |
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protected void |
appendAdditionalInfo(StringBuffer xml)
This method appends additional information that are not stored in the base class to the StringBuffer. |
MEMConstraint |
clone()
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void |
estimate(double ess)
Estimates the (smoothed) relative frequencies using the ess. |
protected void |
extractAdditionalInfo(StringBuffer xml)
This method parses additional information from the StringBuffer that are not parsed in the base class. |
int |
getCorrectedPosition(int index)
Returns the value of the corrected position |
double |
getExpLambda(int index)
Returns \exp(\lambda_{index}). |
double |
getFreq(int index)
Returns the current frequency with index index |
double |
getLambda(int index)
Returns \lambda_{index}. |
protected String |
getXMLTag()
Returns the XML-tag that is used for the class to en- or decode. |
void |
multiplyExpLambdaWith(int index,
double val)
Multiplies \exp(\lambda_{index}) with val |
void |
reset()
This method resets all member variables the are in someway counters, frequencies, ... |
int |
satisfiesSpecificConstraint(SequenceIterator sequence)
Returns the index of that constraint that is satiesfied by sequence |
void |
setExpLambda(int index,
double val)
Sets the value of exp(\lambda_{index}) |
void |
setLambda(int index,
double val)
Sets the value of \lambda_{index} |
String |
toString()
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Methods inherited from class de.jstacs.models.discrete.inhomogeneous.InhConstraint |
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satisfiesSpecificConstraint |
Methods inherited from class de.jstacs.models.discrete.Constraint |
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add, add, estimateUnConditional, getCount, getFreq, getMarginalOrder, getNumberOfSpecificConstraints, getPosition, getPositions, toXML |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public MEMConstraint(int[] pos, int[] alphabetLength) throws IllegalArgumentException
pos
- the used positions (have to be sorted)alphabetLength
- an array containing the length of the the alphabet for each position (of the whole model)
IllegalArgumentException
- if pos
is not sortedpublic MEMConstraint(int[] pos, int[] alphabetLength, int[] corrected_positions) throws IllegalArgumentException
pos
- the used positions (have to be sorted)alphabetLength
- an array containing the length of the the alphabet for each position (of the whole model)corrected_positions
- an array containing the corrected positions
IllegalArgumentException
- if pos
is not sorted or pos.length!=corrected_positions.length
public MEMConstraint(StringBuffer xml) throws NonParsableException
xml
- the buffer
NonParsableException
- if the buffer is not parsableMethod Detail |
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public MEMConstraint clone() throws CloneNotSupportedException
clone
in class InhConstraint
CloneNotSupportedException
public void estimate(double ess)
Constraint
estimate
in class Constraint
ess
- the ESSpublic int getCorrectedPosition(int index)
index
-
public double getExpLambda(int index)
index
- the index
public double getLambda(int index)
index
- the index
public void multiplyExpLambdaWith(int index, double val)
val
index
- the indexval
- the factor/valuepublic void reset()
Constraint
reset
in class Constraint
public int satisfiesSpecificConstraint(SequenceIterator sequence)
sequence
sequence
- the SequenceIterator
public double getFreq(int index)
Constraint
index
getFreq
in class Constraint
index
- the index
public void setExpLambda(int index, double val)
index
- the indexval
- the valuepublic void setLambda(int index, double val)
index
- the indexval
- the valuepublic String toString()
toString
in class Constraint
protected void appendAdditionalInfo(StringBuffer xml)
Constraint
appendAdditionalInfo
in class InhConstraint
xml
- the StringBuffer that is used for appending additional informationprotected String getXMLTag()
Constraint
getXMLTag
in class Constraint
protected void extractAdditionalInfo(StringBuffer xml) throws NonParsableException
Constraint
extractAdditionalInfo
in class InhConstraint
xml
- the StringBuffer to parse
NonParsableException
- if something with the parsing went wrong
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