Uses of Class
org.proteinshader.structure.Segment

Packages that use Segment

org.proteinshader.graphics	Holds the drawing classes: Ribbon, Tube, FrenetFrames, Sphere, and Cylinder.
org.proteinshader.graphics.adapter	Holds the StructureToGraphics class, which is used to manage the use of the drawing classes and OpenGL display lists.
org.proteinshader.graphics.displaylists	Holds the classes needed to manage OpenGL display lists, which are used to cache reusable geometry for spheres, cylinders, ribbon segments, and tube segments.
org.proteinshader.graphics.utils	Holds a testing utility, class SegmentRenderer, which can be used for drawing ribbon and tube segments on-the-fly, rather than using cached geometry in the form of OpenGL display lists.
org.proteinshader.structure	Holds the classes that store information from a Protein Data Bank file: Structure, Model, Chain, AminoAcid, Heterogen, Water, Atom, Bond, Helix, BetaStrand, Loop, etc.
org.proteinshader.structure.factory	Holds the factory classes needed for generating the Segment objects that hold the information needed for rendering ribbon and tube segments.
org.proteinshader.structure.visitor	Holds Visitor classes that know how to traverse the hierarchy of objects held by class Structure.
org.proteinshader.structure.visitor.modifiers	Holds helper classes for the ModifierVisitor class, which is used to modify Drawable objects (Atoms, Bonds, and Segments).

Uses of Segment in org.proteinshader.graphics

Methods in org.proteinshader.graphics with parameters of type Segment

void	Silhouette.drawRibbon(GL gl, Segment s, SegmentListInfo info, boolean extraLines) Draws a translucent black silhoutte of a ribbon segment using jitter.
void	Silhouette.drawTube(GL gl, Segment s, SegmentListInfo info, boolean extraLines) Draws a translucent black silhoutte of a tube segment using jitter.

Uses of Segment in org.proteinshader.graphics.adapter

Methods in org.proteinshader.graphics.adapter with parameters of type Segment

void	StructureToGraphics.draw(GL gl, Segment segment) Draws a Segment of a Region (GeneralLoop, Helix, or BetaStrand).

Uses of Segment in org.proteinshader.graphics.displaylists

Methods in org.proteinshader.graphics.displaylists with parameters of type Segment

SegmentListInfo

SegmentReferences.getSegmentListInfo(Segment segment) Returns the SegmentListInfo object that stores information on the OpenGL display lists that have been cached for the Segment given as an argument.

Uses of Segment in org.proteinshader.graphics.utils

Methods in org.proteinshader.graphics.utils with parameters of type Segment

void	SegmentRenderer.drawRibbon(GL gl, Segment s) Draws the broad surfaces of a ribbon segment and remembers info needed by any subsequent call to drawThinSidesOfRibbon(), drawStartCap(), or drawEndCap().
void	SegmentRenderer.drawTube(GL gl, Segment s) Draws the curved body of a tube segment and remembers info needed by any subsequent call to drawStartCap() or drawEndCap().

Uses of Segment in org.proteinshader.structure

Methods in org.proteinshader.structure that return Segment

Segment	Segment.getNextSegment() Returns a reference to the next Segment with the same region so that the visiblity status of the next Segment can be checked before deciding to render a start cap for the current tube or ribbon segment.
Segment[]	Model.getOpaqueSegments() Copies the list of opaque Segments into an array and returns the array.
Segment	Segment.getPrevSegment() Returns a reference to the previous Segment with the same region so that the visiblity status of the previous Segment can be checked before deciding to render a start cap for the current tube or ribbon segment.
Segment	Atom.getSegment() Returns the Segment the Atom is associated with (or null if the Atom is not associated with any Segment).
Segment	Bond.getSegment() Returns the Segment the Bond is associated with (or null if the Bond is not associated with any Segment).
Segment	Region.getSegment(String segmentID) Returns the Segment with the requested segmentID (if it exists).
Segment	Model.getSegment(String segmentID, String regionID, RegionEnum regionType) Returns the requested Segment if it exists.

Methods in org.proteinshader.structure that return types with arguments of type Segment

Iterator<Segment>

Region.iteratorSegments() Returns an Iterator for the Segments owned by this Region.

Methods in org.proteinshader.structure with parameters of type Segment

void	Segment.setNextSegment(Segment next) Stores a reference to the next Segment within the same Region.
void	Segment.setPrevSegment(Segment prev) Stores a reference to the previous Segment within the same Region.
void	Atom.setSegment(Segment s) Sets the Segment the Atom is associated with.
void	Bond.setSegment(Segment s) Sets the Segment the Bond is associated with.

Uses of Segment in org.proteinshader.structure.factory

Methods in org.proteinshader.structure.factory that return types with arguments of type Segment

LinkedHashMap<String,Segment>	SegmentFactory.createSegments(Region region) Creates the Segment objects for a Region.
LinkedHashMap<String,Segment>	BetaStrandSegmentFactory.createSegments(Region region) After using the superclass createSegments() method, the LocalFrames held by some of the Segment objects will be modified so that beta-strands will have a pleated effect rather than a twisted ribbon appearance.

Uses of Segment in org.proteinshader.structure.visitor

Methods in org.proteinshader.structure.visitor with parameters of type Segment

void	ModifierVisitor.visit(Segment segment) If a SegmentModifier has been added, it will be used to modify the Segment.
void	Visitor.visit(Segment segment) If debug is true, the segmentID will be printed to standard out.
void	SFWriterVisitor.visit(Segment segment) Writes information on a Segment.
void	VisibilityVisitor.visit(Segment segment) Tests the visiblity of the Segment in order to determine if it should be transferred to the opaque Segments or translucent Drawables list.

Method parameters in org.proteinshader.structure.visitor with type arguments of type Segment

void	VisibilityVisitor.setListsToFill(List<Segment> opaqueSegments, List<Drawable> opaqueAtomsAndBonds, List<Drawable> translucentList) Sets the lists to place opaque and translucent Drawable objects in.

Uses of Segment in org.proteinshader.structure.visitor.modifiers

Methods in org.proteinshader.structure.visitor.modifiers with parameters of type Segment

void	SegmentModifier.modify(Segment segment) Sets the patterns texture, halftoning texture, Segment color, or decoration type as requested by SegmentModifier methods, and then calls on modify() of the DrawableModifier superclass.