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Class iubio.bioseq.SeqRange
java.lang.Object
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+----iubio.bioseq.SeqRange
- public class SeqRange
- extends java.lang.Object
- implements java.lang.Cloneable
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kBetween
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kChange
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kDelete
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kEndless
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kEndMatchend
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kEndmore
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kInsert
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kNoValue
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kReorder
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kStartless
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kStartMatchend
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kStartmore
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kZero
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opComplement
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opGroup
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opJoin
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opMax
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opNull
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opOneof
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opOrder
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sOperators
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SeqRange()
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SeqRange(int, int)
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SeqRange(int, int, int)
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SeqRange(int, int, int, String)
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SeqRange(int, int, int, String, String, SeqRange)
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SeqRange(String)
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add(SeqRange)
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clone()
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compareTo(SeqRange)
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contains(SeqRange)
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copy(SeqRange)
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equals(Object)
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intersection(SeqRange)
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intersection0(SeqRange)
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intersects(SeqRange)
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intersectsMax(SeqRange)
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invert(int)
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isComplement()
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isComplex()
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isEmpty()
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isRemote()
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joinRange(SeqRange)
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max()
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nbases()
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newRange()
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newRange(int, int)
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next()
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operation()
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opint()
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origin()
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parse(String)
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parse1(String)
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remoteSeq()
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reverse()
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set(int, int)
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setDisplayOrigin(int)
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setNbases(int)
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setStart(int)
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start()
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startIsEnd()
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stop()
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stopIsEnd()
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subrange(SeqRange)
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toString()
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uncertain()
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updateRange(int, int, int)
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updateRange(int, int, int, byte[])
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kDelete
public static final int kDelete
kInsert
public static final int kInsert
kReorder
public static final int kReorder
kChange
public static final int kChange
kNoValue
public static final int kNoValue
kZero
public static final int kZero
kStartless
public static final int kStartless
kStartmore
public static final int kStartmore
kEndless
public static final int kEndless
kEndmore
public static final int kEndmore
kBetween
public static final int kBetween
kStartMatchend
public static final int kStartMatchend
kEndMatchend
public static final int kEndMatchend
sOperators
public static final java.lang.String sOperators[]
opJoin
public static final byte opJoin
opComplement
public static final byte opComplement
opOrder
public static final byte opOrder
opGroup
public static final byte opGroup
opOneof
public static final byte opOneof
opMax
public static final byte opMax
opNull
public static final byte opNull
SeqRange
public SeqRange()
SeqRange
public SeqRange(int start,
int nbases)
SeqRange
public SeqRange(int start,
int nbases,
int uncertain)
SeqRange
public SeqRange(int start,
int nbases,
int uncertain,
java.lang.String refid)
SeqRange
public SeqRange(int start,
int nbases,
int uncertain,
java.lang.String refid,
java.lang.String soperation,
iubio.bioseq.SeqRange next)
SeqRange
public SeqRange(java.lang.String range) throws iubio.bioseq.SeqRangeException
set
public final void set(int start,
int nbases)
start
public final int start()
nbases
public final int nbases()
stop
public final int stop()
uncertain
public final int uncertain()
next
public final iubio.bioseq.SeqRange next()
operation
public final java.lang.String operation()
opint
public final int opint()
remoteSeq
public final java.lang.String remoteSeq()
isRemote
public final boolean isRemote()
isEmpty
public final boolean isEmpty()
isComplex
public final boolean isComplex()
isComplement
public final boolean isComplement()
origin
public final int origin()
stopIsEnd
public final boolean stopIsEnd()
startIsEnd
public final boolean startIsEnd()
setStart
public final void setStart(int start)
setNbases
public final void setNbases(int nbases)
setDisplayOrigin
public int setDisplayOrigin(int zerobase)
max
public int max()
copy
public void copy(iubio.bioseq.SeqRange sr)
add
public void add(iubio.bioseq.SeqRange sr)
clone
public java.lang.Object clone()
- Overrides:
- clone in class java.lang.Object
updateRange
public final boolean updateRange(int changeflags,
int astart,
int length)
updateRange
public boolean updateRange(int changeflags,
int astart,
int length,
byte basechanges[])
toString
public java.lang.String toString()
- Overrides:
- toString in class java.lang.Object
equals
public boolean equals(java.lang.Object ob)
- Overrides:
- equals in class java.lang.Object
contains
public boolean contains(iubio.bioseq.SeqRange sr)
intersects
public boolean intersects(iubio.bioseq.SeqRange sr)
intersectsMax
public boolean intersectsMax(iubio.bioseq.SeqRange sr)
intersection0
public iubio.bioseq.SeqRange intersection0(iubio.bioseq.SeqRange sr)
intersection
public iubio.bioseq.SeqRange intersection(iubio.bioseq.SeqRange sr)
compareTo
public int compareTo(iubio.bioseq.SeqRange sr)
invert
public iubio.bioseq.SeqRange invert(int maxlen)
joinRange
public iubio.bioseq.SeqRange joinRange(iubio.bioseq.SeqRange sr)
subrange
public iubio.bioseq.SeqRange subrange(iubio.bioseq.SeqRange subr)
reverse
public iubio.bioseq.SeqRange reverse()
newRange
public iubio.bioseq.SeqRange newRange()
newRange
public iubio.bioseq.SeqRange newRange(int start,
int nbases)
parse1
public void parse1(java.lang.String s) throws iubio.bioseq.SeqRangeException
parse
public static iubio.bioseq.SeqRange parse(java.lang.String s) throws iubio.bioseq.SeqRangeException
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