org.proteinshader.structure.visitor
Class ModifierVisitor

java.lang.Object
  org.proteinshader.structure.visitor.Visitor
      org.proteinshader.structure.visitor.ModifierVisitor

public class ModifierVisitor
extends Visitor

Knows how to modify multiple Drawable objects while traversing the hierarchy of objects contained in a Structure.

An AtomModifier, BondModifier, or SegmentModifier can be added to this Visitor. A newly created Visitor (or a Visitor on which clear() has been called) will have its RegionMode set to NO_REGIONS, its ResidueMode set to ALL, and its AAPortionMode set to ENTIRE_AA. Any of these modes can be changed with the setMode() method on Visitor.

Usage

The following code will set all Atoms and Bonds belonging to a Helix as invisible.

// Set up Atom and Bond modifications.
AtomModifier atomModifier = new AtomModifier();
atomModifier.setVisibility( VisibilityEnum.INVISIBLE );
BondModifier bondModifier = new BondModifier();
bondModifier.setVisibility( VisibilityEnum.INVISIBLE );

// Add the modifiers to the visitor.
ModifierVisitor visitor = new ModifierVisitor();
visitor.add( atomModifier );
visitor.add( bondModifier );
visitor.setMode( RegionMode.HELICES );

// Use the visitor to modify a Chain.
chain.accept( visitor );

Constructor Summary

ModifierVisitor()
Constructs a ModifierVisitor.

Method Summary

void	add(AtomModifier modifier) Adds a AtomModifier.
void	add(BondModifier modifier) Adds a BondModifier.
void	add(SegmentModifier modifier) Adds a SegmentModifier.
void	clear() Clears all memory of previously added Modifiers.
boolean	hasAtomModifier() Returns true if this ModifierVisitor holds an AtomModifier object.
boolean	hasBondModifier() Returns true if this ModifierVisitor holds a BondModifier object.
boolean	hasSegmentModifier() Returns true if this ModifierVisitor holds a SegmentModifier object.
void	visit(Atom atom) If an AtomModifier has been added, it will be used to modify the Atom.
void	visit(Bond bond) If a BondModifier has been added, it will be used to modify the Bond.
void	visit(Segment segment) If a SegmentModifier has been added, it will be used to modify the Segment.

Methods inherited from class org.proteinshader.structure.visitor.Visitor

includeAAHetAndWater, setDebug, setMode, setMode, setMode, setMode, setMode, setMode, setVisitSegments, visit, visit, visit, visit, visit, visit, visit, visit, visit

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ModifierVisitor

public ModifierVisitor()

Constructs a ModifierVisitor.

Method Detail

clear

public void clear()

Clears all memory of previously added Modifiers. Also calls clear() on the Visitor superclass, which will reset it to its default start-up state of RegionMode.NO_REGIONS, ResidueMode.ALL, AAPortionMode.ENTIRE_AA, and restrictions set to null.

Overrides:

clear in class Visitor

add

public void add(AtomModifier modifier)

Adds a AtomModifier. An argument of null can be used to clear the memory of the last AtomModifier added.

Parameters:

modifier - the AtomModifier to use.

add

public void add(BondModifier modifier)

Adds a BondModifier. An argument of null can be used to clear the memory of the last BondModifier added.

Parameters:

modifier - the BondModifier to use.

add

public void add(SegmentModifier modifier)

Adds a SegmentModifier. An argument of null can be used to clear the memory of the last BondModifier added.

Parameters:

modifier - the SegmentModifier to use.

visit

public void visit(Segment segment)
           throws VisitorException

If a SegmentModifier has been added, it will be used to modify the Segment.

Overrides:

visit in class Visitor

Parameters:

segment - the Segment to modify.

Throws:

VisitorException - if an error occurs during modifications.

visit

public void visit(Atom atom)
           throws VisitorException

If an AtomModifier has been added, it will be used to modify the Atom. The traversal will only be continued to Bonds if a BondModifier has been added.

Overrides:

visit in class Visitor

Parameters:

atom - the Atom to modify.

Throws:

VisitorException - if an error occurs during modifications.

visit

public void visit(Bond bond)
           throws VisitorException

If a BondModifier has been added, it will be used to modify the Bond.

Overrides:

visit in class Visitor

Parameters:

bond - the Bond to modify.

Throws:

VisitorException - if an error occurs during modifications.

hasAtomModifier

public boolean hasAtomModifier()

Returns true if this ModifierVisitor holds an AtomModifier object. Otherwise, returns false.

Returns:

True if there is an AtomModifier. Otherwise, false.

hasBondModifier

public boolean hasBondModifier()

Returns true if this ModifierVisitor holds a BondModifier object. Otherwise, returns false.

Returns:

True if there is an BondModifier. Otherwise, false.

hasSegmentModifier

public boolean hasSegmentModifier()

Returns true if this ModifierVisitor holds a SegmentModifier object. Otherwise, returns false.

Returns:

True if there is an SegmentModifier. Otherwise, false.