Uses of Class
edu.sdsc.mbt.StructureComponent

Packages that use StructureComponent

edu.sdsc.mbt
edu.sdsc.mbt.filters	This package provides classes which enable filtering or subsetting of a structure's constituent components.
edu.sdsc.mbt.util	This package provides classes which implement extra functionality on top of the core MBT classes (that is, capabilities that are not absolutely required by, or would otherwise overcomplicate, the core classes).
edu.sdsc.mbt.viewables	This package provides classes which enable molecular biology data to be represented as visible/renderable viewable objects, plus, this package defines a top-level StructureDocument object to encapsulate the complete state of these objects and properties.
edu.sdsc.mbt.viewers.GLViewerImpl
edu.sdsc.sirius.builder
edu.sdsc.sirius.dialogs
edu.sdsc.sirius.util
edu.sdsc.sirius.viewers
edu.sdsc.sirius.viewers.TreeViewer
edu.sdsc.sirius.workbench

Uses of StructureComponent in edu.sdsc.mbt

Subclasses of StructureComponent in edu.sdsc.mbt

class	Atom Implements a StructureComponent container for atom data.
class	Bond Implements a StructureComponent container for bond information.
class	Chain Implements a StructureComponent container for chain information.
class	Coil Implements a StructureComponent container for Coil conformation (secondary structure) data.
class	Conformation Implements a an abstract StructureComponent container for conformation (secondary structure) data.
class	Fragment Implements a StructureComponent container for secondary structure fragment information.
class	Helix Implements a StructureComponent container for Helix conformation (secondary structure) data.
class	Residue Implements a StructureComponent container for residue information.
class	Strand Implements a StructureComponent container for Strand conformation (secondary structure) data.
class	StructureInfo Implements a StructureComponent container for Structure information data.
class	Symmetry Implements a StructureComponent container for Symmetry data.
class	Turn Implements a StructureComponent container for Turn conformation (secondary structure) data.

Fields in edu.sdsc.mbt declared as StructureComponent

StructureComponent

StructureComponentEvent.structureComponent

Methods in edu.sdsc.mbt that return StructureComponent

abstract StructureComponent

Structure.getStructureComponentByIndex(java.lang.String structureComponentType, int index) Get the values for any StructureSomponent subclass by its type-specific index.

Methods in edu.sdsc.mbt with parameters of type StructureComponent

void	Turn.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
void	Symmetry.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
void	StructureInfo.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
boolean	StructureComponentRelation.isRelated(StructureComponent subject, StructureComponent object) Tests to see if one StructureComponent instance is related to another.
void	StructureComponentIterator.next(StructureComponent structureComponent) Iterates through a set of StructureComponent objects.
abstract void	StructureComponent.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
StructureComponentIterator	Structure.getStructureComponentRelations(java.lang.String relation_name, StructureComponent structureComponent) Given a StructureComponentRelation name and a StructureComponent, create and return a StructureComponentIterator which will selectively return the related subset of StructureComponent objects.
void	Strand.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
void	Residue.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
void	Helix.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
void	Fragment.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
void	Conformation.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
void	Coil.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
void	Chain.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
void	Bond.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
void	Atom.copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".

Uses of StructureComponent in edu.sdsc.mbt.filters

Methods in edu.sdsc.mbt.filters with parameters of type StructureComponent

boolean	StructureComponentFilter.accept(StructureComponent structureComponent) Return the StructureComponent type that this filter will match and return.
boolean	RelationFilter.accept(StructureComponent structureComponent) Ask the relation object if the object should be accepted or not.
boolean	CAlphaAtomFilter.accept(StructureComponent structureComponent) Accept only C-Alpha Atom objects.
boolean	AtomFilter.accept(StructureComponent structureComponent) Accept ALL Atom objects.

Constructors in edu.sdsc.mbt.filters with parameters of type StructureComponent

RelationFilter(StructureComponentRelation relation, StructureComponent subject)
Constructs a RelationFilter for the given StructureComponentRelation instance and StructureComponent subject parameters.

Uses of StructureComponent in edu.sdsc.mbt.util

Methods in edu.sdsc.mbt.util that return StructureComponent

static StructureComponent

PickUtils.pickLevelComponent(StructureComponent sc, double[] coord) Walk the data hierarchy (atom/bond-residue-fragment-chain-molecule) from the given structure component level toward the current pick level, and return the current pick level component.

Methods in edu.sdsc.mbt.util with parameters of type StructureComponent

static StructureComponent	PickUtils.pickLevelComponent(StructureComponent sc, double[] coord) Walk the data hierarchy (atom/bond-residue-fragment-chain-molecule) from the given structure component level toward the current pick level, and return the current pick level component.
static Atom	PickUtils.closestAtom(StructureComponent sc, double[] coord) Find the atom object within the specified structure component which is closest to the given coordinate.

Uses of StructureComponent in edu.sdsc.mbt.viewables

Fields in edu.sdsc.mbt.viewables declared as StructureComponent

StructureComponent

StructureStylesEvent.structureComponent The StructureComponent for which style changed.

Methods in edu.sdsc.mbt.viewables with parameters of type StructureComponent

void	StructureStyles.setRenderingStyle(StructureComponent structureComponent, short style, short quality, boolean batch) Set the style for the given structure component and then fire an event to all listeners.
AtomRadius	StructureStyles.getAtomRadius(StructureComponent structureComponent) Set the style for the given structure component and then fire an event to all listeners.
void	StructureStyles.setAtomRadius(StructureComponent structureComponent, AtomRadius atomRadius)
BondRadius	StructureStyles.getBondRadius(StructureComponent structureComponent)
void	StructureStyles.setBondRadius(StructureComponent structureComponent, BondRadius bondRadius)
AtomColor	StructureStyles.getAtomColor(StructureComponent structureComponent)
void	StructureStyles.setAtomColor(StructureComponent structureComponent, AtomColor atomColor, boolean fire, boolean batch)
BondColor	StructureStyles.getBondColor(StructureComponent structureComponent)
void	StructureStyles.setBondColor(StructureComponent structureComponent, BondColor bondColor)
ResidueColor	StructureStyles.getResidueColor(StructureComponent structureComponent)
void	StructureStyles.setResidueColor(StructureComponent structureComponent, ResidueColor residueColor, boolean fire, boolean batch) Flag "batch" indicates that the event being fired from this method should contain this flag: the viewers will then refrain from repainting after every residue until further update notice
RibbonColor	StructureStyles.getRibbonColor(StructureComponent structureComponent)
void	StructureStyles.setRibbonColor(StructureComponent structureComponent, RibbonColor ribbonColor, boolean fire, boolean batch)
void	StructureStyles.setRibbonColor(StructureComponent structureComponent, ResidueColor residueColor, boolean fire, boolean batch)
void	StructureStyles.setVisible(StructureComponent structureComponent, boolean newState, boolean fire, boolean batch) Set the visibility state for the given structure component and then fire an event to all listeners.
void	StructureStyles.setSelected(StructureComponent structureComponent, boolean newState, boolean fire, boolean batch) Set the selection state for the given structure component and then fire an event to all listeners.
boolean	StructureStyles.isSelected(StructureComponent structureComponent) Get the selection state for the given structure component.
void	StructureStyles.registerStructureComponentRemoval(StructureComponent structureComponent)
void	StructureStyles.deleteStructureComponent(StructureComponent structureComponent, boolean fire, boolean batch) TODO temporarily use StructureStyles as a handler of component events.
void	StructureStyles.replaceStructureComponent(StructureComponent structureComponent, java.lang.String replacement)
void	StructureStyles.addStructureComponent(StructureComponent structureComponent, short inputStyle, short inputQuality, boolean batch)
static RibbonColor	RibbonColorFactory.getRibbonColor(StructureComponent structureComponent, ResidueColor residueColor)

Uses of StructureComponent in edu.sdsc.mbt.viewers.GLViewerImpl

Fields in edu.sdsc.mbt.viewers.GLViewerImpl declared as StructureComponent

StructureComponent

MbtRenderable.structureComponent

Methods in edu.sdsc.mbt.viewers.GLViewerImpl that return StructureComponent

StructureComponent

MbtRenderable.getStructureComponent() Return the StructureComponent for this MbtRenderable.

Methods in edu.sdsc.mbt.viewers.GLViewerImpl with parameters of type StructureComponent

void	ResidueLabelGeometry.draw(StructureComponent comp, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut)
void	MonitorGeometry.draw(StructureComponent comp, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut)
void	LabelGeometry.draw(StructureComponent comp, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut)
abstract void	Geometry.draw(StructureComponent structureComponent, StructureStyles styles, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut) Please complete the missing tags for main
void	ChainGeometry.draw(StructureComponent structureComponent, StructureStyles styles, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut) Please complete the missing tags for main
void	BondGeometry.draw(StructureComponent structureComponent, StructureStyles styles, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut) Please complete the missing tags for main
void	AtomLineGeometry.draw(StructureComponent structureComponent, StructureStyles styles, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut) Please complete the missing tags for main
void	AtomGeometry.draw(StructureComponent structureComponent, StructureStyles styles, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut) Please complete the missing tags for main
void	ArrowGeometry.draw(StructureComponent comp, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut)

Constructors in edu.sdsc.mbt.viewers.GLViewerImpl with parameters of type StructureComponent

MbtRenderable(StructureComponent structureComponent, StructureStyles styles, Geometry geometry)
Construct a Renderable object.

Uses of StructureComponent in edu.sdsc.sirius.builder

Methods in edu.sdsc.sirius.builder with parameters of type StructureComponent

void	SaveFragmentDialog.processPick(java.lang.String data, StructureComponent structureComponent)

Uses of StructureComponent in edu.sdsc.sirius.dialogs

Fields in edu.sdsc.sirius.dialogs declared as StructureComponent

StructureComponent	WeightEvent.structureComponent
StructureComponent	VisibilityEvent.structureComponent
StructureComponent	ViewEvent.structureComponent
StructureComponent	RibbonEvent.structureComponent
StructureComponent	RibbonColorEvent.structureComponent
StructureComponent	RenderingEvent.structureComponent
StructureComponent	LabelEvent.structureComponent
StructureComponent	HydrogenEvent.structureComponent
StructureComponent	ColorEvent.structureComponent

Methods in edu.sdsc.sirius.dialogs with parameters of type StructureComponent

void	WeightDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	VisibilityDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	SuperimposeDialog.processPick(java.lang.String data, StructureComponent structureComponent) This method is called by StructureViewer in response to a mouse click and sets the currently active text field to the String representation of the clicked StructureComponent.
void	StructureSuperpositionAlignDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	StructureSetDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	StructureSelectionDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	StructureRenameDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	StructureEditDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	StructureAlignmentDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	SequenceRenameDialog.processPick(java.lang.String data, StructureComponent component)
void	SelectListDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	SelectionAreaDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	RotateBondDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	RibbonDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	RibbonColorDialog.processPick(java.lang.String data, StructureComponent structureComponent) This method is called by StructureViewer in response to a mouse click and sets the currently active text field to the String representation of the clicked StructureComponent.
void	ResidueRenameDialog.processPick(java.lang.String data, StructureComponent component)
void	ResidueLabelDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	ReplaceResidueDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	ReplaceAtomDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	RenderingDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	RayTracerDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	PdbLoadDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	PdbDialog.processPick(java.lang.String data, StructureComponent s)
void	MotionDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	LabelDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	ImageExportDialog.processPick(java.lang.String data, StructureComponent s)
void	HydrogenDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	HybridizationDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	HBDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	FogDialog.processPick(java.lang.String data, StructureComponent c)
void	DistanceDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	DisplayDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	DihedralDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	DataWBListerDialog.processPick(java.lang.String name, StructureComponent comp)
void	CreateSequenceDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	CreateBondDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	ComponentRibbonDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	ComponentRenderingDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	ComponentColorDialog.processPick(java.lang.String data, StructureComponent structureComponent) This method is called by StructureViewer in response to a mouse click and sets the currently active text field to the String representation of the clicked StructureComponent.
void	ColorDialog.processPick(java.lang.String data, StructureComponent structureComponent) This method is called by StructureViewer in response to a mouse click and sets the currently active text field to the String representation of the clicked StructureComponent.
void	ChargeDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	CenterDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	BumpDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	BreakBondDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	BondOrderDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	AtomRenameDialog.processPick(java.lang.String data, StructureComponent component)
void	AtomDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	AngleDialog.processPick(java.lang.String data, StructureComponent structureComponent) This method is called by StructureViewer in response to a mouse click and sets the currently active text field to the String representation of the clicked StructureComponent.
void	AlignmentSettingsDialog.processPick(java.lang.String data, StructureComponent structureComponent)

Constructors in edu.sdsc.sirius.dialogs with parameters of type StructureComponent

ComponentRenderingDialog(javax.swing.JFrame f, Manager p, StructureViewer s, java.lang.String title, StructureComponent sc)

ComponentColorDialog(javax.swing.JFrame f, Manager p, StructureViewer s, java.lang.String title, StructureComponent sc, boolean ribbon)
Constructor that builds the dialog.

Uses of StructureComponent in edu.sdsc.sirius.util

Methods in edu.sdsc.sirius.util with parameters of type StructureComponent

static java.lang.String

DataService.componentToLabel(StructureComponent sc)

Uses of StructureComponent in edu.sdsc.sirius.viewers

Methods in edu.sdsc.sirius.viewers with parameters of type StructureComponent

void	StructureViewer.saveCustomFragment(StructureComponent component, java.lang.String name, StructureComponent[] attachments) Creates a new fragment record for a user-defined structure.
void	StructureViewer.superimpose(StructureComponent[] set1, StructureComponent[] set2)
void	StructureViewer.setFormalCharge(StructureComponent sc, java.lang.String label, short charge)

Uses of StructureComponent in edu.sdsc.sirius.viewers.TreeViewer

Methods in edu.sdsc.sirius.viewers.TreeViewer that return StructureComponent

StructureComponent

InfoViewer.getActiveComponent()

Methods in edu.sdsc.sirius.viewers.TreeViewer with parameters of type StructureComponent

void	StructureBrowser.expandToNode(StructureComponent component)
void	InfoViewer.displayComponentInfo(StructureComponent sc)

Uses of StructureComponent in edu.sdsc.sirius.workbench

Methods in edu.sdsc.sirius.workbench with parameters of type StructureComponent

void	WBSaveDialog.processPick(java.lang.String data, StructureComponent structureComponent)
void	WBListDialog.processPick(java.lang.String name, StructureComponent component) This is a blank method included for compatibility with DisplayDialog tracking system (one modal dialog is displayed at a time, so we need to know what is open and what is closed).