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Class iubio.bioseq.SeqRange

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

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

Variable Index

 o kBetween
 o kChange
 o kDelete
 o kEndless
 o kEndMatchend
 o kEndmore
 o kInsert
 o kNoValue
 o kReorder
 o kStartless
 o kStartMatchend
 o kStartmore
 o kZero
 o opComplement
 o opGroup
 o opJoin
 o opMax
 o opNull
 o opOneof
 o opOrder
 o sOperators

Constructor Index

 o SeqRange()
 o SeqRange(int, int)
 o SeqRange(int, int, int)
 o SeqRange(int, int, int, String)
 o SeqRange(int, int, int, String, String, SeqRange)
 o SeqRange(String)

Method Index

 o add(SeqRange)
 o clone()
 o compareTo(SeqRange)
 o contains(SeqRange)
 o copy(SeqRange)
 o equals(Object)
 o intersection(SeqRange)
 o intersection0(SeqRange)
 o intersects(SeqRange)
 o intersectsMax(SeqRange)
 o invert(int)
 o isComplement()
 o isComplex()
 o isEmpty()
 o isRemote()
 o joinRange(SeqRange)
 o max()
 o nbases()
 o newRange()
 o newRange(int, int)
 o next()
 o operation()
 o opint()
 o origin()
 o parse(String)
 o parse1(String)
 o remoteSeq()
 o reverse()
 o set(int, int)
 o setDisplayOrigin(int)
 o setNbases(int)
 o setStart(int)
 o start()
 o startIsEnd()
 o stop()
 o stopIsEnd()
 o subrange(SeqRange)
 o toString()
 o uncertain()
 o updateRange(int, int, int)
 o updateRange(int, int, int, byte[])

Variables

 o kDelete
 public static final int kDelete
 o kInsert
 public static final int kInsert
 o kReorder
 public static final int kReorder
 o kChange
 public static final int kChange
 o kNoValue
 public static final int kNoValue
 o kZero
 public static final int kZero
 o kStartless
 public static final int kStartless
 o kStartmore
 public static final int kStartmore
 o kEndless
 public static final int kEndless
 o kEndmore
 public static final int kEndmore
 o kBetween
 public static final int kBetween
 o kStartMatchend
 public static final int kStartMatchend
 o kEndMatchend
 public static final int kEndMatchend
 o sOperators
 public static final java.lang.String sOperators[]
 o opJoin
 public static final byte opJoin
 o opComplement
 public static final byte opComplement
 o opOrder
 public static final byte opOrder
 o opGroup
 public static final byte opGroup
 o opOneof
 public static final byte opOneof
 o opMax
 public static final byte opMax
 o opNull
 public static final byte opNull

Constructors

 o SeqRange
 public SeqRange()
 o SeqRange
 public SeqRange(int start,
                 int nbases)
 o SeqRange
 public SeqRange(int start,
                 int nbases,
                 int uncertain)
 o SeqRange
 public SeqRange(int start,
                 int nbases,
                 int uncertain,
                 java.lang.String refid)
 o SeqRange
 public SeqRange(int start,
                 int nbases,
                 int uncertain,
                 java.lang.String refid,
                 java.lang.String soperation,
                 iubio.bioseq.SeqRange next)
 o SeqRange
 public SeqRange(java.lang.String range) throws iubio.bioseq.SeqRangeException

Methods

 o set
 public final void set(int start,
                       int nbases)
 o start
 public final int start()
 o nbases
 public final int nbases()
 o stop
 public final int stop()
 o uncertain
 public final int uncertain()
 o next
 public final iubio.bioseq.SeqRange next()
 o operation
 public final java.lang.String operation()
 o opint
 public final int opint()
 o remoteSeq
 public final java.lang.String remoteSeq()
 o isRemote
 public final boolean isRemote()
 o isEmpty
 public final boolean isEmpty()
 o isComplex
 public final boolean isComplex()
 o isComplement
 public final boolean isComplement()
 o origin
 public final int origin()
 o stopIsEnd
 public final boolean stopIsEnd()
 o startIsEnd
 public final boolean startIsEnd()
 o setStart
 public final void setStart(int start)
 o setNbases
 public final void setNbases(int nbases)
 o setDisplayOrigin
 public int setDisplayOrigin(int zerobase)
 o max
 public int max()
 o copy
 public void copy(iubio.bioseq.SeqRange sr)
 o add
 public void add(iubio.bioseq.SeqRange sr)
 o clone
 public java.lang.Object clone()
Overrides:
clone in class java.lang.Object
 o updateRange
 public final boolean updateRange(int changeflags,
                                  int astart,
                                  int length)
 o updateRange
 public boolean updateRange(int changeflags,
                            int astart,
                            int length,
                            byte basechanges[])
 o toString
 public java.lang.String toString()
Overrides:
toString in class java.lang.Object
 o equals
 public boolean equals(java.lang.Object ob)
Overrides:
equals in class java.lang.Object
 o contains
 public boolean contains(iubio.bioseq.SeqRange sr)
 o intersects
 public boolean intersects(iubio.bioseq.SeqRange sr)
 o intersectsMax
 public boolean intersectsMax(iubio.bioseq.SeqRange sr)
 o intersection0
 public iubio.bioseq.SeqRange intersection0(iubio.bioseq.SeqRange sr)
 o intersection
 public iubio.bioseq.SeqRange intersection(iubio.bioseq.SeqRange sr)
 o compareTo
 public int compareTo(iubio.bioseq.SeqRange sr)
 o invert
 public iubio.bioseq.SeqRange invert(int maxlen)
 o joinRange
 public iubio.bioseq.SeqRange joinRange(iubio.bioseq.SeqRange sr)
 o subrange
 public iubio.bioseq.SeqRange subrange(iubio.bioseq.SeqRange subr)
 o reverse
 public iubio.bioseq.SeqRange reverse()
 o newRange
 public iubio.bioseq.SeqRange newRange()
 o newRange
 public iubio.bioseq.SeqRange newRange(int start,
                                       int nbases)
 o parse1
 public void parse1(java.lang.String s) throws iubio.bioseq.SeqRangeException
 o parse
 public static iubio.bioseq.SeqRange parse(java.lang.String s) throws iubio.bioseq.SeqRangeException

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