Class pmr.cml.FEATURENode 
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Class pmr.cml.FEATURENode 

java.lang.Object
   |
   +----pmr.sgml.SGMLNode
           |
           +----pmr.sgml.DrawableSGMLNode
                   |
                   +----pmr.cml.DrawableX_Node
                           |
                           +----pmr.cml.FEATURENode
public class FEATURENode
extends DrawableX_Node
FEATURENode holds 'features' for macromolecules. This maps fairly directly onto SwissProt FT and various fields in PDB. Still being thrashed out!
Author:
(C) P. Murray-Rust, 1996

Constructor Index

o FEATURENode(String, SGMLTree)

Method Index

o announce(DrawableX_Node)
called (at least) by SEQUENCENode.
o contains(int)
does a feature contain a given residue number?
o createAdd0(SGMLTree, int, String, FEATURENode, String, String, String)
o createAndAdd(SGMLTree, int, String, String, DrawableX_Node, int, int, String, String)
create from a data entry; this has to add it to the tree as well

The target is a node such as a SEQUENCENode or ATOMSNode

o createAndAdd(SGMLTree, int, String, String, Vector, String, String)
this adds a range of addresses to the Feature
o debug()
for debug
o display()
displays the nodes.
o display(Graphics)
no routine yet to display the relationships...
o getColor()
color of SGMLNode text - overridden by subclasses?
o getEnd()
end of the feature (counts from ONE!)
o getFeatureString()
description of the Feature
o getKeyword()
o getStart()
start of the feature (counts from ONE!)
o getTitle()
get title from TITLE, DICTNAME, BUILTIN if present, else TITLE
o isDisulfide()
is the feature a disulfide?
o isNotMature()
is the feature not in the mature protein? (e.g.
o isStructural()
is the feature structural?
o mayContain(SGMLNode)
can this node contain others.
o process()
complex objects may require processing; override this.
o processKeywords()
o showHelp()
display Help

Constructors

o FEATURENode 
  public FEATURENode(String giName,
                     SGMLTree tree)

Methods

o createAndAdd 
  public static int createAndAdd(SGMLTree tree,
                                 int parentIndex,
                                 String title,
                                 String keyword,
                                 DrawableX_Node target,
                                 int start,
                                 int end,
                                 String description,
                                 String convention)
create from a data entry; this has to add it to the tree as well

The target is a node such as a SEQUENCENode or ATOMSNode

o createAndAdd 
  public static int createAndAdd(SGMLTree tree,
                                 int parentIndex,
                                 String title,
                                 String keyword,
                                 Vector fullAddresses,
                                 String description,
                                 String convention)
this adds a range of addresses to the Feature
o createAdd0 
  public static void createAdd0(SGMLTree tree,
                                int index,
                                String title,
                                FEATURENode node,
                                String keyword,
                                String description,
                                String convention)
o getFeatureString 
  public String getFeatureString()
description of the Feature
o getStart 
  public int getStart()
start of the feature (counts from ONE!)
o getEnd 
  public int getEnd()
end of the feature (counts from ONE!)
o contains 
  public boolean contains(int resno)
does a feature contain a given residue number?
o isDisulfide 
  public boolean isDisulfide()
is the feature a disulfide?
o isStructural 
  public boolean isStructural()
is the feature structural?
o isNotMature 
  public boolean isNotMature()
is the feature not in the mature protein? (e.g. PROPEP or SIGNAL)?
o getColor 
  public Color getColor()
color of SGMLNode text - overridden by subclasses?
Overrides:
getColor in class SGMLNode
o getTitle 
  public String getTitle()
get title from TITLE, DICTNAME, BUILTIN if present, else TITLE
Overrides:
getTitle in class DrawableX_Node
o getKeyword 
  public String getKeyword()
o showHelp 
  public void showHelp()
display Help
Overrides:
showHelp in class DrawableX_Node
o mayContain 
  public boolean mayContain(SGMLNode n)
can this node contain others.
Overrides:
mayContain in class DrawableX_Node
o process 
  public void process()
complex objects may require processing; override this.
Overrides:
process in class DrawableSGMLNode
o processKeywords 
  public void processKeywords()
o announce 
  public void announce(DrawableX_Node node)
called (at least) by SEQUENCENode. Tells the user about the FEATURE. At present uses postMessage()
o display 
  public void display()
displays the nodes. Doesn't yet clear subaddresses in nodes before it starts... see RELATION
Overrides:
display in class DrawableSGMLNode
o display 
  public void display(Graphics g)
no routine yet to display the relationships...
Overrides:
display in class DrawableX_Node
o debug 
  public void debug()
for debug
Overrides:
debug in class DrawableX_Node 
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