mobios.type
Class Sequence
java.lang.Object
mobios.type.Sequence
- All Implemented Interfaces:
- Serializable
- Direct Known Subclasses:
- DNA, Peptide, RNA
public abstract class Sequence
- extends Object
- implements Serializable
A compact representation of sequences of small alphabets whose indices fit within a valid
byte range. The general contract of Sequence
implementations in this package is that all instances be immutable. This class has constructors that make
references to external objects in instances. It is the responsibility
of the user to ensure that the external objects are immutable!
- Version:
- 2003.06.05
- Author:
- Jack, Neha, Rui Mao, Weijia Xu, Willard
- See Also:
- Serialized Form
size
public final int size()
- Returns:
- the size of the
Sequence
.
numFragments
public int numFragments(int fragmentLength)
- The number of fragments a given
Sequence
can be divided up into.
- Parameters:
fragmentLength
- the length of the fragments to split the Sequence
into
- Returns:
- the number of fragments for the given
Sequence
get
public abstract Symbol get(int index)
- Parameters:
index
- an integer index value
- Returns:
- the
Symbol
corresponding to that index.
toString
public abstract String toString()
- Overrides:
toString
in class Object
getAlphabet
public abstract Alphabet getAlphabet()
- Returns:
getSequenceID
public String getSequenceID()
(C) 2002 - 2006 The MoBIoS Group