Package org.snpeff.spliceSites
Class AcgtTree
java.lang.Object
org.snpeff.spliceSites.AcgtTree
ACGT tree
- Author:
- pcingola
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final char[]
static final int
static final double
static final double
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
static int
base2index
(char base) double
entropy()
Calculate the entropyentropyAll
(int thresholdCount) findNodeNames
(double thresholdEntropy, double thresholdP, int thresholdCount) Find node names that are within the thresholdsget
(char base) Get a nodeGet node indexed by this stringgetOrCreate
(char base) Get a node (create it if it doesn't exist)int
void
inc
(char base) Increment counter for a basepAll
(int thresholdCount) protected void
double
void
Set a nodetoString()
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Field Details
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BASES
public static final char[] BASES -
LOG2
public static final double LOG2 -
FAKE_COUNTS
public static final int FAKE_COUNTS- See Also:
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MAX_ENTROPY
public static final double MAX_ENTROPY- See Also:
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Constructor Details
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AcgtTree
public AcgtTree() -
AcgtTree
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Method Details
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base2index
public static int base2index(char base) -
add
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entropy
public double entropy()Calculate the entropy -
entropyAll
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findNodeNames
Find node names that are within the thresholds -
get
Get a node -
get
Get node indexed by this string -
getOrCreate
Get a node (create it if it doesn't exist) -
getTotalCount
public int getTotalCount() -
inc
public void inc(char base) Increment counter for a base -
pAll
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pAll
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seqConservation
public double seqConservation() -
set
Set a node -
toString
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toString
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