Class pmr.cml.SEQUENCENode 
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Class pmr.cml.SEQUENCENode 

java.lang.Object
   |
   +----pmr.sgml.SGMLNode
           |
           +----pmr.sgml.DrawableSGMLNode
                   |
                   +----pmr.cml.DrawableX_Node
                           |
                           +----pmr.cml.SEQUENCENode
public class SEQUENCENode
extends DrawableX_Node
implements SubAddressable
a macromolecular sequence. At present I have only tested it with proteins

I am still undecided as to whether to hold one chain per sequence or multiple chains. For example interchain disulphides cause a problem! Start with one chain per SEQUENCE Where do the FEATUREs then live??? Perhaps both under MOL (for molecular features - including interchain disulphides and active sites) and under SEQUENCE for chain-only features.

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

Constructor Index

o SEQUENCENode(String, SGMLTree)

Method Index

o addSubAddress(IntRange)
o addSubAddresses(IntRangeVector)
o clearSubAddresses()
o createAndAdd(SGMLTree, int, String, String, int, String)
o debug()
for debug
o display(Graphics)
used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
o drawFeature(Graphics, FEATURENode, int, int, int)
o drawFeature0(Graphics, FEATURENode, int, int, int, int, int, int)
o drawFeatures(Graphics)
o drawIcon(Graphics, int, int)
draw a CML icon
o drawSequenceString(Graphics)
o drawVLine(Graphics, int, int, int)
o getChainID()
o getChainLength()
o getFeatures()
o getFreeBar(int, int, int)
get first free bar and reserve it for this feature.
o getResiduesPerLine()
o getSequenceString()
get the sequence as a 1-letter string
o getSubAddresses()
o highlightRegion(Graphics, int, int, int)
o highlightResidue(Graphics, int, int)
o highlightSubAddresses(boolean)
o mayContain(SGMLNode)
can this node contain others.
o mouseUp(Event, int, int)
action when mouse is unclicked; if not overridden, no action
o process()
complex objects may require processing; override this.
o process1()
o showHelp()
display Help

Constructors

o SEQUENCENode 
  public SEQUENCENode(String giName,
                      SGMLTree tree)

Methods

o createAndAdd 
  public static int createAndAdd(SGMLTree tree,
                                 int parentIndex,
                                 String id,
                                 String chainString,
                                 int length,
                                 String convention)
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 getChainID 
  public String getChainID()
o getChainLength 
  public int getChainLength()
o getFeatures 
  public FEATURENode[] getFeatures()
o getResiduesPerLine 
  public int getResiduesPerLine()
o display 
  public void display(Graphics g)
used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
Overrides:
display in class DrawableX_Node
o debug 
  public void debug()
for debug
Overrides:
debug in class DrawableX_Node
o process1 
  public void process1()
o getSequenceString 
  public String getSequenceString()
get the sequence as a 1-letter string
o getFreeBar 
  public int getFreeBar(int featureIndex,
                        int start,
                        int end)
get first free bar and reserve it for this feature. If no bars free, use the last one (nbars-1).
o drawFeatures 
  public void drawFeatures(Graphics g)
o highlightResidue 
  public void highlightResidue(Graphics g,
                               int featureIndex,
                               int index)
o highlightRegion 
  public void highlightRegion(Graphics g,
                              int featureIndex,
                              int start,
                              int end)
o drawFeature 
  public void drawFeature(Graphics g,
                          FEATURENode feat,
                          int start,
                          int end,
                          int featureIndex)
o drawFeature0 
  public void drawFeature0(Graphics g,
                           FEATURENode feat,
                           int x0,
                           int y0,
                           int yoffset,
                           int x1,
                           int lbar,
                           int rbar)
o drawVLine 
  public void drawVLine(Graphics g,
                        int x,
                        int y,
                        int dy)
o drawSequenceString 
  public void drawSequenceString(Graphics g)
o mouseUp 
  public boolean mouseUp(Event evt,
                         int x,
                         int y)
action when mouse is unclicked; if not overridden, no action
Overrides:
mouseUp in class DrawableX_Node
o clearSubAddresses 
  public void clearSubAddresses()
o addSubAddress 
  public void addSubAddress(IntRange ir)
o addSubAddresses 
  public void addSubAddresses(IntRangeVector irv)
o getSubAddresses 
  public IntRangeVector getSubAddresses()
o highlightSubAddresses 
  public void highlightSubAddresses(boolean onOff)
o drawIcon 
  public int drawIcon(Graphics g,
                      int x,
                      int y)
draw a CML icon
Overrides:
drawIcon in class DrawableX_Node 
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