RbDe rbde-349 (20120127151154)

edu.mssm.crover.representation
Interface BiologicalSequence

All Superinterfaces:
Serializable
All Known Subinterfaces:
AnnotatedBioSequence
All Known Implementing Classes:
Sequence

public interface BiologicalSequence
extends Serializable

Interface to a represent a biological protein sequence.

Author:
Fabien Campagne

Method Summary
 int getLength()
          Returns the length of this sequence.
 String getResidueCodes()
          Returns the residue codes of the sequence.
 String getShortName()
          Returns the short name of this sequence.
 void setResidueCodes(String resiudeCodes)
          Set the residue codes of the sequence.
 void setShortName(String name)
          Set the short name of this sequence.
 

Method Detail

getResidueCodes

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

Returns:
the residue codes that make up this sequence

setResidueCodes

void setResidueCodes(String resiudeCodes)
Set the residue codes of the sequence.

Parameters:
resiudeCodes - The residue codes for the sequence

getShortName

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.

Returns:
The name of this sequence

getLength

int getLength()
Returns the length of this sequence. The gaps are ignored if present.

Returns:
the length of the sequence not including any gaps

setShortName

void setShortName(String name)
Set 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.

Parameters:
name - The name to use for this sequence

RbDe rbde-349 (20120127151154)

Copyright © 2003-2012 Institute for Computational Biomedicine, All Rights Reserved.