edu.mssm.crover.representation
Interface BiologicalSequence

All Superinterfaces:

RootObject

All Known Subinterfaces:

AnnotatedBioSequence

All Known Implementing Classes:

ArcadiaAlignedSequence, Sequence

public interface BiologicalSequence

extends RootObject

Interface to a represent a biological protein sequence.

Author:

Fabien Campagne

Method Summary

int	getLength() Returns the length of this sequence.
java.lang.String	getResidueCodes() Returns the residue codes of the sequence.
java.lang.String	getShortName() Returns the short name of this sequence.
void	setResidueCodes(java.lang.String arg0)
void	setShortName(java.lang.String arg0) Sets the short name of this sequence.

Method Detail

getResidueCodes

public java.lang.String getResidueCodes()

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-

setResidueCodes

public void setResidueCodes(java.lang.String arg0)

getShortName

public java.lang.String getShortName()

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.

getLength

public int getLength()

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

setShortName

public void setShortName(java.lang.String arg0)

Sets the short name of this sequence.

See Also:

for a definition of the shortname.