Package org.snpeff.binseq.coder
Class Coder
- java.lang.Object
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- org.snpeff.binseq.coder.Coder
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- All Implemented Interfaces:
java.io.Serializable
- Direct Known Subclasses:
DnaCoder
public abstract class Coder extends java.lang.Object implements java.io.Serializable
Class used to encode & decode sequences into binary and vice-versa They are usually stored in 'long' words- Author:
- pcingola
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static int
BITS_PER_LONGWORD
static int
BYTES_PER_LONGWORD
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Constructor Summary
Constructors Constructor Description Coder()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description abstract int
basesPerWord()
How many bases can we pack in a wordabstract int
baseToBits(char c)
Encode a base using a binary representationabstract int
bitsPerBase()
How many bits do we need for each baseabstract int
decodeWord(long word, int pos)
Decode bits from a given position in a wordabstract int
lastBaseinWord()
Index of the last base coded in a wordabstract long
mask(int baseIndexInWord)
Bitmask for a base in a wordint
qualityToBits(int q)
Encode a quality using a binary representationabstract char
toBase(int code)
Decode a base using a binary representationabstract char
toBase(long word, int pos)
Decode a base from a given position in a wordint
toQuality(int code)
Decode a quality
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Field Detail
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BITS_PER_LONGWORD
public static final int BITS_PER_LONGWORD
- See Also:
- Constant Field Values
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BYTES_PER_LONGWORD
public static final int BYTES_PER_LONGWORD
- See Also:
- Constant Field Values
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Method Detail
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basesPerWord
public abstract int basesPerWord()
How many bases can we pack in a word- Returns:
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baseToBits
public abstract int baseToBits(char c)
Encode a base using a binary representation- Parameters:
c
-- Returns:
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bitsPerBase
public abstract int bitsPerBase()
How many bits do we need for each base- Returns:
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decodeWord
public abstract int decodeWord(long word, int pos)
Decode bits from a given position in a word- Parameters:
word
-pos
-- Returns:
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lastBaseinWord
public abstract int lastBaseinWord()
Index of the last base coded in a word- Returns:
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mask
public abstract long mask(int baseIndexInWord)
Bitmask for a base in a word- Returns:
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qualityToBits
public int qualityToBits(int q)
Encode a quality using a binary representation- Parameters:
c
-- Returns:
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toBase
public abstract char toBase(int code)
Decode a base using a binary representation- Parameters:
c
-- Returns:
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toBase
public abstract char toBase(long word, int pos)
Decode a base from a given position in a word- Parameters:
word
-pos
-- Returns:
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toQuality
public int toQuality(int code)
Decode a quality- Parameters:
c
-- Returns:
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