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Class iubio.bioseq.BaseKind
java.lang.Object
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+----iubio.bioseq.BaseKind
- public class BaseKind
- extends java.lang.Object
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allprintflag
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alnumseqflag
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alphaseqflag
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aminoflag
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crctab
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digitflag
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indelEdge
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indelHard
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indelSoft
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iubextraflag
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iubnucflag
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iubsymflag
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kBit5
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kBit6
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kBit7
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kBitA
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kBitC
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kBitExtra
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kBitG
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kBitT
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kMask5
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kMask6
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kMask7
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kMaskA
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kMaskB
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kMaskC
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kMaskD
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kMaskExtra
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kMaskG
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kMaskH
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kMaskIndel
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kMaskK
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kMaskM
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kMaskN
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kMaskNucs
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kMaskR
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kMaskRna
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kMaskS
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kMaskT
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kMaskU
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kMaskV
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kMaskW
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kMaskY
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otherprintflag
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primenucflag
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protonlyflag
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seqsymflag
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BaseKind()
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Amino123(char)
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Amino321(String)
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aminoConsensus(byte, byte)
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isAlnumseq(int)
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isAlphaseq(int)
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isAmino(int)
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isAnyChar(int)
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isBasekind(int, int)
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isDnanuc(int)
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isGCGSeqChar(int)
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isIndel(int)
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isIUBsym(int)
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isNucleicMatch(int, int)
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isPrimenuc(int)
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isPrint(int)
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isProtonly(int)
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isRnanuc(int)
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isSeqChar(int)
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isSeqNumChar(int)
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isSeqsym(int)
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nucleicBits(byte)
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nucleicBits(char)
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nucleicComplement(byte, boolean)
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nucleicConsensus(int, int)
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indelHard
public static char indelHard
indelSoft
public static char indelSoft
indelEdge
public static char indelEdge
kBitA
public static final int kBitA
kMaskA
public static final int kMaskA
kBitC
public static final int kBitC
kMaskC
public static final int kMaskC
kBitG
public static final int kBitG
kMaskG
public static final int kMaskG
kBitT
public static final int kBitT
kMaskT
public static final int kMaskT
kMaskY
public static final int kMaskY
kMaskK
public static final int kMaskK
kMaskS
public static final int kMaskS
kMaskR
public static final int kMaskR
kMaskM
public static final int kMaskM
kMaskW
public static final int kMaskW
kMaskH
public static final int kMaskH
kMaskB
public static final int kMaskB
kMaskV
public static final int kMaskV
kMaskD
public static final int kMaskD
kMaskN
public static final int kMaskN
kBitExtra
public static final int kBitExtra
kMaskExtra
public static final int kMaskExtra
kMaskIndel
public static final int kMaskIndel
kMaskU
public static final int kMaskU
kMaskRna
public static final int kMaskRna
kMaskNucs
public static final int kMaskNucs
kBit5
public static final int kBit5
kMask5
public static final int kMask5
kBit6
public static final int kBit6
kMask6
public static final int kMask6
kBit7
public static final int kBit7
kMask7
public static final int kMask7
primenucflag
public static final int primenucflag
iubextraflag
public static final int iubextraflag
aminoflag
public static final int aminoflag
protonlyflag
public static final int protonlyflag
seqsymflag
public static final int seqsymflag
digitflag
public static final int digitflag
otherprintflag
public static final int otherprintflag
iubnucflag
public static final int iubnucflag
iubsymflag
public static final int iubsymflag
alphaseqflag
public static final int alphaseqflag
alnumseqflag
public static final int alnumseqflag
allprintflag
public static final int allprintflag
crctab
public static long crctab[]
BaseKind
public BaseKind()
isPrimenuc
public static boolean isPrimenuc(int c)
isIUBsym
public static boolean isIUBsym(int c)
isDnanuc
public static boolean isDnanuc(int c)
isRnanuc
public static boolean isRnanuc(int c)
isAmino
public static boolean isAmino(int c)
isProtonly
public static boolean isProtonly(int c)
isSeqsym
public static boolean isSeqsym(int c)
isAlphaseq
public static boolean isAlphaseq(int c)
isAlnumseq
public static boolean isAlnumseq(int c)
isPrint
public static boolean isPrint(int c)
isIndel
public static boolean isIndel(int c)
isBasekind
public static boolean isBasekind(int c,
int flag)
isSeqChar
public static int isSeqChar(int c)
isGCGSeqChar
public static int isGCGSeqChar(int c)
isSeqNumChar
public static int isSeqNumChar(int c)
isAnyChar
public static int isAnyChar(int c)
nucleicBits
public static final int nucleicBits(char nuc)
nucleicBits
public static int nucleicBits(byte nuc)
nucleicComplement
public static byte nucleicComplement(byte b,
boolean isrna)
isNucleicMatch
public static boolean isNucleicMatch(int xNucBits,
int yNucBits)
nucleicConsensus
public static byte nucleicConsensus(int xNucBits,
int yNucBits)
Amino123
public static java.lang.String Amino123(char amino1)
Amino321
public static char Amino321(java.lang.String amino)
aminoConsensus
public static byte aminoConsensus(byte x,
byte y)
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