jprotein.data.datatype
Class Sequence

java.lang.Object
  java.util.AbstractCollection
      java.util.AbstractList
          java.util.Vector
              jprotein.data.datatype.Sequence

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

Direct Known Subclasses:

Alignment, BlastSequenceInfo, Sequence3D, SequenceInformation

public class Sequence
extends java.util.Vector

See Also:

Serialized Form

Constructor Summary

Sequence()

Sequence(java.lang.String sequenceName)

Sequence(java.lang.String sequenceName, java.lang.String residueSequence)

Method Summary

boolean	equals(java.lang.Object o)
int	getNonGappedPosition(int index)
int	getNonGappedSequenceLength()
Residue	getResidue(int pos)
java.util.Vector	getSequence()
int	getSequenceLength()
java.lang.String	getSequenceName()
boolean	isIdentical(Sequence seq)
void	setSequence(java.lang.String residueSequence)
void	setSequenceName(java.lang.String sequenceName)
java.lang.String	toFasta()
java.lang.String	toString()

Methods inherited from class java.util.Vector

add, add, addAll, addAll, addElement, capacity, clear, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, firstElement, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, lastElement, lastIndexOf, lastIndexOf, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, retainAll, set, setElementAt, setSize, size, subList, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

iterator, listIterator, listIterator

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

iterator, listIterator, listIterator

Constructor Detail

Sequence

public Sequence()

Sequence

public Sequence(java.lang.String sequenceName)

Sequence

public Sequence(java.lang.String sequenceName,
                java.lang.String residueSequence)

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.util.Vector

setSequence

public void setSequence(java.lang.String residueSequence)

getSequence

public java.util.Vector getSequence()

getSequenceName

public java.lang.String getSequenceName()

getSequenceLength

public int getSequenceLength()

getResidue

public Residue getResidue(int pos)

setSequenceName

public void setSequenceName(java.lang.String sequenceName)

equals

public boolean equals(java.lang.Object o)

Specified by:

equals in interface java.util.Collection

Specified by:

equals in interface java.util.List

Overrides:

equals in class java.util.Vector

toFasta

public java.lang.String toFasta()

getNonGappedSequenceLength

public int getNonGappedSequenceLength()

getNonGappedPosition

public int getNonGappedPosition(int index)

isIdentical

public boolean isIdentical(Sequence seq)