Class pmr.cml.ProteinSequence 
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Class pmr.cml.ProteinSequence 

java.lang.Object
   |
   +----pmr.simplegraph.DrawableObject
           |
           +----pmr.cml.BasicSequence
                   |
                   +----pmr.cml.ProteinSequence
public class ProteinSequence
extends BasicSequence
a simple Protein Sequence class
Author:
(C) P.Murray-Rust, 1996

Constructor Index

o ProteinSequence()
o ProteinSequence(String)
create from an ungapped string of 1-letter symbols

Method Index

o display(Graphics)
simple output of sequence - normally overwritten
o displayHydrophobicity()
o getHydrophobicity()
Eisenberg's hydrophobicity is hardcoded in
o getMolecularWeight()
sums the NEUTRAL residues and adds H2O.
o main(String[])
test routine
o process()
complex objects may require processing; override this
o readSwissProt(String)
create from a SwissProt file

Constructors

o ProteinSequence 
  public ProteinSequence()
o ProteinSequence 
  public ProteinSequence(String s)
create from an ungapped string of 1-letter symbols

Methods

o readSwissProt 
  public static ProteinSequence readSwissProt(String filename)
create from a SwissProt file
o process 
  public void process()
complex objects may require processing; override this
Overrides:
process in class BasicSequence
o getMolecularWeight 
  public double getMolecularWeight()
sums the NEUTRAL residues and adds H2O. Does NOT cater for S-S bonds or other chemical modifications or effect of charge
o getHydrophobicity 
  public RealArray getHydrophobicity()
Eisenberg's hydrophobicity is hardcoded in
o displayHydrophobicity 
  public void displayHydrophobicity()
o display 
  public void display(Graphics g)
simple output of sequence - normally overwritten
Overrides:
display in class BasicSequence
o main 
  public static void main(String args[])
test routine 
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