edu.mssm.crover.representation
Interface BiologicalSequence

All Superinterfaces:
RootObject
All Known Subinterfaces:
AnnotatedBioSequence
All Known Implementing Classes:
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

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

void setResidueCodes(java.lang.String arg0)

getShortName

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

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


setShortName

void setShortName(java.lang.String arg0)
Sets the short name of this sequence.

See Also:
for a definition of the shortname.


Copyright © 2003-2013 Institute for Computational Biomedicine, All Rights Reserved.