Class pmr.chemime.SwissProt 
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Class pmr.chemime.SwissProt 

java.lang.Object
   |
   +----java.awt.Component
           |
           +----java.awt.Container
                   |
                   +----java.awt.Panel
                           |
                           +----java.applet.Applet
                                   |
                                   +----pmr.simplegraph.SimpleApplet
                                           |
                                           +----pmr.sgml.SGMLApplet
                                                   |
                                                   +----pmr.sgml.SGMLTree
                                                           |
                                                           +----pmr.cml.CMLTree
                                                                   |
                                                                   +----pmr.chemime.ChemTree
                                                                           |
                                                                           +----pmr.chemime.SwissProt
public class SwissProt
extends ChemTree
holds a Swissprot file as a CMLTree

Probably not complete, but easily extendable

Author:
(C) P. Murray-Rust, 1996

Constructor Index

o SwissProt(String, StringList)
reads a local SwissProt file and creates a SwissProt object.

Method Index

o display()
displays the sequence automatically
o getSEQUENCENodes()
extract SEQUENCENodes from PDB object
o process()
o showHelp()
display help

Constructors

o SwissProt 
  public SwissProt(String filename,
                   StringList lines) throws BadSwissProtFileException
reads a local SwissProt file and creates a SwissProt object.
Parameters:
filename - name of file to read from (or title if lines != null)
lines - if lines != null, use this as file content instead of filename
Throws: BadSwissProtFileException
file does not correspond to the published format, or is corrupt, or we have misimplemented the standard(!)

Methods

o showHelp 
  public void showHelp()
display help
Overrides:
showHelp in class ChemTree
o process 
  protected void process() throws BadSwissProtFileException
o getSEQUENCENodes 
  public SEQUENCENode[] getSEQUENCENodes()
extract SEQUENCENodes from PDB object
o display 
  public void display()
displays the sequence automatically
Overrides:
display in class CMLTree 
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