Package org.snpeff.nmer
Class Nmer
java.lang.Object
org.snpeff.nmer.Nmer
Binary packed N-mer (i.e. DNA sequence of length N)
In this implementation N has to be less than 32
- Author:
- pcingola
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionlong
getNmer()
Set nmer (binary coded)int
hashCode()
int
length()
Get nmer's lengthint
read
(InputStream outputStream) void
rol
(char base) Rotate sequence left and append a base at the end Note: The first base is dropped, so the total length is still 'n'void
Set nmer's sequencevoid
setLength
(int length) Set nmer's lengthvoid
setNmer
(long nmer) Set nmer (binary coded)toString()
long
wc()
Watson-Cricks complement of this nmer Since {A, C, G, T} is translated into binary {00, 01, 10, 11}.void
write
(OutputStream outputStream)
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Field Details
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MAX_NMER_SIZE
public static final int MAX_NMER_SIZE- See Also:
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Constructor Details
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Nmer
public Nmer(int length) -
Nmer
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Method Details
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getNmer
public long getNmer()Set nmer (binary coded)- Parameters:
nmer
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hashCode
public int hashCode() -
length
public int length()Get nmer's length- Returns:
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read
- Throws:
IOException
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rol
public void rol(char base) Rotate sequence left and append a base at the end Note: The first base is dropped, so the total length is still 'n'- Parameters:
cq
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set
Set nmer's sequence- Parameters:
seqStr
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setLength
public void setLength(int length) Set nmer's length- Parameters:
length
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setNmer
public void setNmer(long nmer) Set nmer (binary coded)- Parameters:
nmer
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toString
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wc
public long wc()Watson-Cricks complement of this nmer Since {A, C, G, T} is translated into binary {00, 01, 10, 11}. The complement is: baseWc = XOR(11, base)- Returns:
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write
- Throws:
IOException
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