net.sf.octet.model
Class BasicGammaSequence

java.lang.Object
  net.sf.octet.model.AtomGraphDecorator
      net.sf.octet.model.BasicGammaSequence

All Implemented Interfaces:

AtomCollection, AtomGraph, AtomPairCollection, GammaSequence

public class BasicGammaSequence

extends AtomGraphDecorator

implements GammaSequence

A default implementation of the BasicGammaSequence interface.

Author:

Richard Apodaca

Constructor Summary

BasicGammaSequence(AtomPair axis, AtomPairCollection pairs)
Constructs a BasicGammaSequence from axis and pairs.

Method Summary

AtomPair

getAxis() Returns the AtomPair that contains the first Atom in this sequence as its source and the last Atom as its target.

Methods inherited from class net.sf.octet.model.AtomGraphDecorator

containsAtom, containsAtomPair, containsAtomPair, countAtomPairs, countAtoms, countNeighbors, getAtom, getAtomIndex, getAtomPair, getAtomPair, getAtomPairIndex, iterateAtomPairs, iterateAtoms, iterateNeighbors, toAtomArray, toAtomPairArray

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.sf.octet.model.AtomGraph

countNeighbors, iterateNeighbors

Methods inherited from interface net.sf.octet.collection.AtomCollection

containsAtom, countAtoms, getAtom, getAtomIndex, iterateAtoms, toAtomArray

Methods inherited from interface net.sf.octet.collection.AtomPairCollection

containsAtomPair, containsAtomPair, countAtomPairs, getAtomPair, getAtomPair, getAtomPairIndex, iterateAtomPairs, toAtomPairArray

Constructor Detail

BasicGammaSequence

public BasicGammaSequence(AtomPair axis,
                          AtomPairCollection pairs)

Constructs a BasicGammaSequence from axis and pairs.

Parameters:

axis - the axis to use

pairs - the AtomPairCollection on which to base the underlying AtomGraph

Throws:

IllegalRepresentationException - if pairs descibes any topology other than an unbranched linear chain (currently only cycles)

Method Detail

getAxis

public AtomPair getAxis()

Description copied from interface: GammaSequence

Returns the AtomPair that contains the first Atom in this sequence as its source and the last Atom as its target.

Specified by:

getAxis in interface GammaSequence

Returns:

the AtomPair that contains the first Atom in this sequence as its source and the last Atom as its target