edu.mssm.crover.webapps.dimlib.datamodel
Class ArcadiaAlignedSequence

java.lang.Object
  |
  +--edu.mssm.crover.webapps.dimlib.datamodel.ArcadiaAlignedSequence

All Implemented Interfaces:

BiologicalSequence, RootObject

public class ArcadiaAlignedSequence

extends java.lang.Object

implements BiologicalSequence

Stores the BiologicalSequence of sequences stored in an alignment, and a reference to its WildTypeProtein.

Author:

luce

Field Summary

Sequence	aseq
WildTypeProtein	wtp

Constructor Summary

ArcadiaAlignedSequence()

ArcadiaAlignedSequence(BiologicalSequence seq, WildTypeProtein wtp)

Method Summary

int	getLength() Returns the length of this sequence.
java.lang.String	getResidueCodes() Returns the residue codes of the sequence.
Sequence	getSeq()
java.lang.String	getShortName() Returns the short name of this sequence.
WildTypeProtein	getWTP()
void	setResidueCodes(java.lang.String residues)
void	setSeq(BiologicalSequence seq)
void	setShortName(java.lang.String name) Sets the short name of this sequence.
void	setWTP(WildTypeProtein wtp)

Methods inherited from class java.lang.Object

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

Field Detail

aseq

public Sequence aseq

wtp

public WildTypeProtein wtp

Constructor Detail

ArcadiaAlignedSequence

public ArcadiaAlignedSequence()

ArcadiaAlignedSequence

public ArcadiaAlignedSequence(BiologicalSequence seq,
                              WildTypeProtein wtp)

Method Detail

setSeq

public void setSeq(BiologicalSequence seq)

getSeq

public Sequence getSeq()

setWTP

public void setWTP(WildTypeProtein wtp)

getWTP

public WildTypeProtein getWTP()

setResidueCodes

public void setResidueCodes(java.lang.String residues)

Specified by:

setResidueCodes in interface BiologicalSequence

getResidueCodes

public java.lang.String getResidueCodes()

Description copied from interface: BiologicalSequence

Returns the residue codes of the sequence. The residues should be encoded following IUPAC-IUB, symbols for amino-acid nomemclature, Cornish-Bowden (1985). The returned String only contains valid sequence characters or gaps encoded as '-'. The following characters are considered valid: ACDEFGHIKLMNPQRSTVWY-

Specified by:

getResidueCodes in interface BiologicalSequence

setShortName

public void setShortName(java.lang.String name)

Description copied from interface: BiologicalSequence

Sets the short name of this sequence.

Specified by:

setShortName in interface BiologicalSequence

See Also:

for a definition of the shortname.

getShortName

public java.lang.String getShortName()

Description copied from interface: BiologicalSequence

Returns the short name of this sequence. The short name is a short sequence of character that is designed to be seen by the user to remind himself about what this sequence object represents.

Specified by:

getShortName in interface BiologicalSequence

getLength

public int getLength()

Description copied from interface: BiologicalSequence

Returns the length of this sequence. The gaps are ignored if presents.

Specified by:

getLength in interface BiologicalSequence