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Class iubio.bioseq.Bioseq
java.lang.Object
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+----iubio.bioseq.Bioseq
- public class Bioseq
- extends java.lang.Object
- implements java.lang.Cloneable
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baseOnly
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gBaseType
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gUseByteArray
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kAmino
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kDNA
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kNucleic
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kOtherSeq
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kRNA
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maskOnly
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maskOnlyAsText
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nucAndMask
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Bioseq()
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Bioseq(byte[])
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Bioseq(byte[], int, int)
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Bioseq(char[])
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Bioseq(char[], int, int)
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Bioseq(int)
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Bioseq(Object)
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Bioseq(String)
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base(int, int)
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basebyte(int)
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basechar(int)
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bases()
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clone()
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cmp(Bioseq, int)
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cmp(byte[], byte[], int)
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compress(byte)
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compress(byte[], int, int, byte)
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compress(int, int, byte)
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copy(byte[], int, byte[], int, int)
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copy(byte[], int, int)
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copyFrom(byte[])
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copyFrom(byte[], int, int)
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copyFrom(char[])
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copyFrom(char[], int, int)
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copyFrom(Object)
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copyFrom(String)
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dup()
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dup(byte[])
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equals(Bioseq)
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equals(byte[], byte[])
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equalsIgnoreCase(Bioseq)
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equalsIgnoreCase(byte[], byte[])
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expand(byte[], int)
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expand(int)
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getSeqStats()
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getSeqStats(int, int)
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getSeqtype()
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getSeqtype(byte[], int, int)
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getSeqtype(String, int, int)
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indexOf(byte, int)
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indexOf(byte[], byte, int)
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isBytes()
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length()
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replace(Bioseq, int, char, char)
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replace(Bioseq, int, String, String)
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replace(int, char, char)
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replace(int, String, String)
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reverseComplement()
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reverseComplement(int, int)
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setbase(int, byte)
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setbase(int, char)
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setbases(byte[])
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toBytes()
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toBytes(int)
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toBytes(int, int, int)
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toChars()
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toChars(int)
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toChars(int, int, int)
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toString()
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kOtherSeq
public static final short kOtherSeq
kDNA
public static final short kDNA
kRNA
public static final short kRNA
kNucleic
public static final short kNucleic
kAmino
public static final short kAmino
baseOnly
public static final int baseOnly
maskOnly
public static final int maskOnly
nucAndMask
public static final int nucAndMask
maskOnlyAsText
public static final int maskOnlyAsText
gUseByteArray
public static boolean gUseByteArray
gBaseType
public int gBaseType
Bioseq
public Bioseq()
Bioseq
public Bioseq(int maxlen)
Bioseq
public Bioseq(byte b[])
Bioseq
public Bioseq(byte b[],
int offs,
int len)
Bioseq
public Bioseq(char c[])
Bioseq
public Bioseq(char c[],
int offs,
int len)
Bioseq
public Bioseq(java.lang.String s)
Bioseq
public Bioseq(java.lang.Object ob)
copyFrom
public void copyFrom(java.lang.Object ob)
copyFrom
public final void copyFrom(byte b[])
copyFrom
public void copyFrom(byte b[],
int offs,
int len)
copyFrom
public final void copyFrom(char c[])
copyFrom
public void copyFrom(char c[],
int offs,
int len)
copyFrom
public void copyFrom(java.lang.String s)
length
public int length()
setbases
public void setbases(byte theBases[])
setbase
public void setbase(int i,
byte b)
setbase
public void setbase(int i,
char c)
basebyte
public byte basebyte(int i)
basechar
public char basechar(int i)
base
public char base(int i,
int basepart)
isBytes
public boolean isBytes()
bases
public byte[] bases()
toBytes
public final byte[] toBytes()
toBytes
public byte[] toBytes(int basepart)
toBytes
public byte[] toBytes(int offset,
int count,
int basepart)
toChars
public final char[] toChars()
toChars
public final char[] toChars(int basepart)
toChars
public char[] toChars(int offset,
int count,
int basepart)
toString
public java.lang.String toString()
- Overrides:
- toString in class java.lang.Object
clone
public java.lang.Object clone()
- Overrides:
- clone in class java.lang.Object
getSeqtype
public int getSeqtype()
getSeqtype
public static int getSeqtype(java.lang.String s,
int offset,
int seqlen)
getSeqtype
public static int getSeqtype(byte ba[],
int offset,
int seqlen)
getSeqStats
public final iubio.bioseq.SeqInfo getSeqStats()
getSeqStats
public iubio.bioseq.SeqInfo getSeqStats(int offset,
int seqlen)
reverseComplement
public void reverseComplement()
reverseComplement
public void reverseComplement(int offset,
int count)
equals
public final boolean equals(iubio.bioseq.Bioseq b)
equals
public static boolean equals(byte a[],
byte b[])
equalsIgnoreCase
public final boolean equalsIgnoreCase(iubio.bioseq.Bioseq b)
equalsIgnoreCase
public static boolean equalsIgnoreCase(byte a[],
byte b[])
compress
public final void compress(byte gapc)
compress
public final void compress(int offset,
int seqlen,
byte gapc)
compress
public static byte[] compress(byte src[],
int offset,
int seqlen,
byte gapc)
replace
public final void replace(int len,
char oldbase,
char newbase)
replace
public static void replace(iubio.bioseq.Bioseq seq,
int len,
char oldbase,
char newbase)
replace
public final void replace(int len,
java.lang.String oldbases,
java.lang.String newbases)
replace
public static void replace(iubio.bioseq.Bioseq seq,
int len,
java.lang.String oldbases,
java.lang.String newbases)
expand
public final void expand(int newlen)
expand
public static byte[] expand(byte src[],
int newlen)
dup
public final byte[] dup()
dup
public static byte[] dup(byte src[])
cmp
public final int cmp(iubio.bioseq.Bioseq b,
int len)
cmp
public static int cmp(byte a[],
byte b[],
int len)
indexOf
public final int indexOf(byte b,
int len)
indexOf
public static int indexOf(byte a[],
byte b,
int len)
copy
public final void copy(byte dst[],
int dstOffset,
int len)
copy
public static void copy(byte src[],
int srcOffset,
byte dst[],
int dstOffset,
int len)
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