Package org.snpeff.motif
Class Pwm
- java.lang.Object
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- org.snpeff.motif.Pwm
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- Direct Known Subclasses:
PwmAndSeqs
public class Pwm extends java.lang.Object
Create a DNA motif count matrix Refrence http://en.wikipedia.org/wiki/Position-specific_scoring_matrix- Author:
- pcingola
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
calcLogOddsWeight()
Calculate log odds matrix from counts Reference: http://en.wikipedia.org/wiki/Position-specific_scoring_matrixchar[]
getBestSequence()
Get best matching sequence (highest score)java.lang.String
getBestSequenceStr()
int
getCount(char base, int position)
Get counts for a given positionjava.lang.String
getId()
double
getLogOdds(char base, int position)
java.lang.String
getName()
int
getTotalCount()
boolean
isConserved(int pos)
Is position 'pos' conserved (only one base has non-zero counts)int
length()
double
score(java.lang.String dna)
Calculate PWM score for a stringvoid
set(java.lang.String dna)
Set PWM as a perfect match to a dna sequencevoid
setCounts(char base, int[] counts)
Set counts for one basevoid
setId(java.lang.String id)
void
setName(java.lang.String name)
java.lang.String
toString()
void
updateCounts(java.lang.String dna)
void
updateCounts(java.lang.String dna, int inc)
Update counts matrix.
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Field Detail
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SCALE
public static final int SCALE
- See Also:
- Constant Field Values
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BASES
public static final char[] BASES
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Method Detail
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calcLogOddsWeight
public void calcLogOddsWeight()
Calculate log odds matrix from counts Reference: http://en.wikipedia.org/wiki/Position-specific_scoring_matrix
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getBestSequence
public char[] getBestSequence()
Get best matching sequence (highest score)- Returns:
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getBestSequenceStr
public java.lang.String getBestSequenceStr()
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getCount
public int getCount(char base, int position)
Get counts for a given position
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getId
public java.lang.String getId()
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getLogOdds
public double getLogOdds(char base, int position)
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getName
public java.lang.String getName()
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getTotalCount
public int getTotalCount()
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isConserved
public boolean isConserved(int pos)
Is position 'pos' conserved (only one base has non-zero counts)
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length
public int length()
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score
public double score(java.lang.String dna)
Calculate PWM score for a string
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set
public void set(java.lang.String dna)
Set PWM as a perfect match to a dna sequence
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setCounts
public void setCounts(char base, int[] counts)
Set counts for one base
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setId
public void setId(java.lang.String id)
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setName
public void setName(java.lang.String name)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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updateCounts
public void updateCounts(java.lang.String dna)
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updateCounts
public void updateCounts(java.lang.String dna, int inc)
Update counts matrix.
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