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Class iubio.bioseq.BaseKind

java.lang.Object
   |
   +----iubio.bioseq.BaseKind

public class BaseKind
extends java.lang.Object

Variable Index

 o allprintflag
 o alnumseqflag
 o alphaseqflag
 o aminoflag
 o crctab
 o digitflag
 o indelEdge
 o indelHard
 o indelSoft
 o iubextraflag
 o iubnucflag
 o iubsymflag
 o kBit5
 o kBit6
 o kBit7
 o kBitA
 o kBitC
 o kBitExtra
 o kBitG
 o kBitT
 o kMask5
 o kMask6
 o kMask7
 o kMaskA
 o kMaskB
 o kMaskC
 o kMaskD
 o kMaskExtra
 o kMaskG
 o kMaskH
 o kMaskIndel
 o kMaskK
 o kMaskM
 o kMaskN
 o kMaskNucs
 o kMaskR
 o kMaskRna
 o kMaskS
 o kMaskT
 o kMaskU
 o kMaskV
 o kMaskW
 o kMaskY
 o otherprintflag
 o primenucflag
 o protonlyflag
 o seqsymflag

Constructor Index

 o BaseKind()

Method Index

 o Amino123(char)
 o Amino321(String)
 o aminoConsensus(byte, byte)
 o isAlnumseq(int)
 o isAlphaseq(int)
 o isAmino(int)
 o isAnyChar(int)
 o isBasekind(int, int)
 o isDnanuc(int)
 o isGCGSeqChar(int)
 o isIndel(int)
 o isIUBsym(int)
 o isNucleicMatch(int, int)
 o isPrimenuc(int)
 o isPrint(int)
 o isProtonly(int)
 o isRnanuc(int)
 o isSeqChar(int)
 o isSeqNumChar(int)
 o isSeqsym(int)
 o nucleicBits(byte)
 o nucleicBits(char)
 o nucleicComplement(byte, boolean)
 o nucleicConsensus(int, int)

Variables

 o indelHard
 public static char indelHard
 o indelSoft
 public static char indelSoft
 o indelEdge
 public static char indelEdge
 o kBitA
 public static final int kBitA
 o kMaskA
 public static final int kMaskA
 o kBitC
 public static final int kBitC
 o kMaskC
 public static final int kMaskC
 o kBitG
 public static final int kBitG
 o kMaskG
 public static final int kMaskG
 o kBitT
 public static final int kBitT
 o kMaskT
 public static final int kMaskT
 o kMaskY
 public static final int kMaskY
 o kMaskK
 public static final int kMaskK
 o kMaskS
 public static final int kMaskS
 o kMaskR
 public static final int kMaskR
 o kMaskM
 public static final int kMaskM
 o kMaskW
 public static final int kMaskW
 o kMaskH
 public static final int kMaskH
 o kMaskB
 public static final int kMaskB
 o kMaskV
 public static final int kMaskV
 o kMaskD
 public static final int kMaskD
 o kMaskN
 public static final int kMaskN
 o kBitExtra
 public static final int kBitExtra
 o kMaskExtra
 public static final int kMaskExtra
 o kMaskIndel
 public static final int kMaskIndel
 o kMaskU
 public static final int kMaskU
 o kMaskRna
 public static final int kMaskRna
 o kMaskNucs
 public static final int kMaskNucs
 o kBit5
 public static final int kBit5
 o kMask5
 public static final int kMask5
 o kBit6
 public static final int kBit6
 o kMask6
 public static final int kMask6
 o kBit7
 public static final int kBit7
 o kMask7
 public static final int kMask7
 o primenucflag
 public static final int primenucflag
 o iubextraflag
 public static final int iubextraflag
 o aminoflag
 public static final int aminoflag
 o protonlyflag
 public static final int protonlyflag
 o seqsymflag
 public static final int seqsymflag
 o digitflag
 public static final int digitflag
 o otherprintflag
 public static final int otherprintflag
 o iubnucflag
 public static final int iubnucflag
 o iubsymflag
 public static final int iubsymflag
 o alphaseqflag
 public static final int alphaseqflag
 o alnumseqflag
 public static final int alnumseqflag
 o allprintflag
 public static final int allprintflag
 o crctab
 public static long crctab[]

Constructors

 o BaseKind
 public BaseKind()

Methods

 o isPrimenuc
 public static boolean isPrimenuc(int c)
 o isIUBsym
 public static boolean isIUBsym(int c)
 o isDnanuc
 public static boolean isDnanuc(int c)
 o isRnanuc
 public static boolean isRnanuc(int c)
 o isAmino
 public static boolean isAmino(int c)
 o isProtonly
 public static boolean isProtonly(int c)
 o isSeqsym
 public static boolean isSeqsym(int c)
 o isAlphaseq
 public static boolean isAlphaseq(int c)
 o isAlnumseq
 public static boolean isAlnumseq(int c)
 o isPrint
 public static boolean isPrint(int c)
 o isIndel
 public static boolean isIndel(int c)
 o isBasekind
 public static boolean isBasekind(int c,
                                  int flag)
 o isSeqChar
 public static int isSeqChar(int c)
 o isGCGSeqChar
 public static int isGCGSeqChar(int c)
 o isSeqNumChar
 public static int isSeqNumChar(int c)
 o isAnyChar
 public static int isAnyChar(int c)
 o nucleicBits
 public static final int nucleicBits(char nuc)
 o nucleicBits
 public static int nucleicBits(byte nuc)
 o nucleicComplement
 public static byte nucleicComplement(byte b,
                                      boolean isrna)
 o isNucleicMatch
 public static boolean isNucleicMatch(int xNucBits,
                                      int yNucBits)
 o nucleicConsensus
 public static byte nucleicConsensus(int xNucBits,
                                     int yNucBits)
 o Amino123
 public static java.lang.String Amino123(char amino1)
 o Amino321
 public static char Amino321(java.lang.String amino)
 o aminoConsensus
 public static byte aminoConsensus(byte x,
                                   byte y)

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