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Class iubio.bioseq.Bioseq

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

public class Bioseq
extends java.lang.Object
implements java.lang.Cloneable

Variable Index

 o baseOnly
 o gBaseType
 o gUseByteArray
 o kAmino
 o kDNA
 o kNucleic
 o kOtherSeq
 o kRNA
 o maskOnly
 o maskOnlyAsText
 o nucAndMask

Constructor Index

 o Bioseq()
 o Bioseq(byte[])
 o Bioseq(byte[], int, int)
 o Bioseq(char[])
 o Bioseq(char[], int, int)
 o Bioseq(int)
 o Bioseq(Object)
 o Bioseq(String)

Method Index

 o base(int, int)
 o basebyte(int)
 o basechar(int)
 o bases()
 o clone()
 o cmp(Bioseq, int)
 o cmp(byte[], byte[], int)
 o compress(byte)
 o compress(byte[], int, int, byte)
 o compress(int, int, byte)
 o copy(byte[], int, byte[], int, int)
 o copy(byte[], int, int)
 o copyFrom(byte[])
 o copyFrom(byte[], int, int)
 o copyFrom(char[])
 o copyFrom(char[], int, int)
 o copyFrom(Object)
 o copyFrom(String)
 o dup()
 o dup(byte[])
 o equals(Bioseq)
 o equals(byte[], byte[])
 o equalsIgnoreCase(Bioseq)
 o equalsIgnoreCase(byte[], byte[])
 o expand(byte[], int)
 o expand(int)
 o getSeqStats()
 o getSeqStats(int, int)
 o getSeqtype()
 o getSeqtype(byte[], int, int)
 o getSeqtype(String, int, int)
 o indexOf(byte, int)
 o indexOf(byte[], byte, int)
 o isBytes()
 o length()
 o replace(Bioseq, int, char, char)
 o replace(Bioseq, int, String, String)
 o replace(int, char, char)
 o replace(int, String, String)
 o reverseComplement()
 o reverseComplement(int, int)
 o setbase(int, byte)
 o setbase(int, char)
 o setbases(byte[])
 o toBytes()
 o toBytes(int)
 o toBytes(int, int, int)
 o toChars()
 o toChars(int)
 o toChars(int, int, int)
 o toString()

Variables

 o kOtherSeq
 public static final short kOtherSeq
 o kDNA
 public static final short kDNA
 o kRNA
 public static final short kRNA
 o kNucleic
 public static final short kNucleic
 o kAmino
 public static final short kAmino
 o baseOnly
 public static final int baseOnly
 o maskOnly
 public static final int maskOnly
 o nucAndMask
 public static final int nucAndMask
 o maskOnlyAsText
 public static final int maskOnlyAsText
 o gUseByteArray
 public static boolean gUseByteArray
 o gBaseType
 public int gBaseType

Constructors

 o Bioseq
 public Bioseq()
 o Bioseq
 public Bioseq(int maxlen)
 o Bioseq
 public Bioseq(byte b[])
 o Bioseq
 public Bioseq(byte b[],
               int offs,
               int len)
 o Bioseq
 public Bioseq(char c[])
 o Bioseq
 public Bioseq(char c[],
               int offs,
               int len)
 o Bioseq
 public Bioseq(java.lang.String s)
 o Bioseq
 public Bioseq(java.lang.Object ob)

Methods

 o copyFrom
 public void copyFrom(java.lang.Object ob)
 o copyFrom
 public final void copyFrom(byte b[])
 o copyFrom
 public void copyFrom(byte b[],
                      int offs,
                      int len)
 o copyFrom
 public final void copyFrom(char c[])
 o copyFrom
 public void copyFrom(char c[],
                      int offs,
                      int len)
 o copyFrom
 public void copyFrom(java.lang.String s)
 o length
 public int length()
 o setbases
 public void setbases(byte theBases[])
 o setbase
 public void setbase(int i,
                     byte b)
 o setbase
 public void setbase(int i,
                     char c)
 o basebyte
 public byte basebyte(int i)
 o basechar
 public char basechar(int i)
 o base
 public char base(int i,
                  int basepart)
 o isBytes
 public boolean isBytes()
 o bases
 public byte[] bases()
 o toBytes
 public final byte[] toBytes()
 o toBytes
 public byte[] toBytes(int basepart)
 o toBytes
 public byte[] toBytes(int offset,
                       int count,
                       int basepart)
 o toChars
 public final char[] toChars()
 o toChars
 public final char[] toChars(int basepart)
 o toChars
 public char[] toChars(int offset,
                       int count,
                       int basepart)
 o toString
 public java.lang.String toString()
Overrides:
toString in class java.lang.Object
 o clone
 public java.lang.Object clone()
Overrides:
clone in class java.lang.Object
 o getSeqtype
 public int getSeqtype()
 o getSeqtype
 public static int getSeqtype(java.lang.String s,
                              int offset,
                              int seqlen)
 o getSeqtype
 public static int getSeqtype(byte ba[],
                              int offset,
                              int seqlen)
 o getSeqStats
 public final iubio.bioseq.SeqInfo getSeqStats()
 o getSeqStats
 public iubio.bioseq.SeqInfo getSeqStats(int offset,
                                         int seqlen)
 o reverseComplement
 public void reverseComplement()
 o reverseComplement
 public void reverseComplement(int offset,
                               int count)
 o equals
 public final boolean equals(iubio.bioseq.Bioseq b)
 o equals
 public static boolean equals(byte a[],
                              byte b[])
 o equalsIgnoreCase
 public final boolean equalsIgnoreCase(iubio.bioseq.Bioseq b)
 o equalsIgnoreCase
 public static boolean equalsIgnoreCase(byte a[],
                                        byte b[])
 o compress
 public final void compress(byte gapc)
 o compress
 public final void compress(int offset,
                            int seqlen,
                            byte gapc)
 o compress
 public static byte[] compress(byte src[],
                               int offset,
                               int seqlen,
                               byte gapc)
 o replace
 public final void replace(int len,
                           char oldbase,
                           char newbase)
 o replace
 public static void replace(iubio.bioseq.Bioseq seq,
                            int len,
                            char oldbase,
                            char newbase)
 o replace
 public final void replace(int len,
                           java.lang.String oldbases,
                           java.lang.String newbases)
 o replace
 public static void replace(iubio.bioseq.Bioseq seq,
                            int len,
                            java.lang.String oldbases,
                            java.lang.String newbases)
 o expand
 public final void expand(int newlen)
 o expand
 public static byte[] expand(byte src[],
                             int newlen)
 o dup
 public final byte[] dup()
 o dup
 public static byte[] dup(byte src[])
 o cmp
 public final int cmp(iubio.bioseq.Bioseq b,
                      int len)
 o cmp
 public static int cmp(byte a[],
                       byte b[],
                       int len)
 o indexOf
 public final int indexOf(byte b,
                          int len)
 o indexOf
 public static int indexOf(byte a[],
                           byte b,
                           int len)
 o copy
 public final void copy(byte dst[],
                        int dstOffset,
                        int len)
 o copy
 public static void copy(byte src[],
                         int srcOffset,
                         byte dst[],
                         int dstOffset,
                         int len)

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