A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

B

B - Static variable in class edu.sdsc.mbt.util.Element

BLACK_TO_WHITE - Static variable in class edu.sdsc.mbt.viewables.InterpolatedColorMap

BOTTOM_BORDER - Static variable in class edu.sdsc.mbt.viewables.ResidueAnnotation

BREAK_BOND - Static variable in class edu.sdsc.sirius.dialogs.StructureEventRegistry

BackboneLine - class edu.sdsc.mbt.viewers.GLViewerImpl.BackboneLine.

BackboneLine is a LineStripArray class optimized for representing a backbone trace.

BackboneLine(int, int[], Vector3f[], Color[], boolean[]) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.BackboneLine

Be - Static variable in class edu.sdsc.mbt.util.Element

BlastLineData - class edu.sdsc.sirius.dialogs.TableImpl.BlastLineData.

A container class for data displayed in one row of the table of ResultPanel.

BlastLineData() - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.BlastLineData

BlastLineData(String, String, String, String) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.BlastLineData

BlastResultPanel - class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel.

This class implements a panel used to display sequence data retrieved from a database.

BlastResultPanel(JPanel, DataSet) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel

Constructs the ResultPanel when created as in a frame typically storing search results.

BlastSettings - class edu.sdsc.sirius.util.BlastSettings.

BlastSettings() - Constructor for class edu.sdsc.sirius.util.BlastSettings

Bond - class edu.sdsc.mbt.Bond.

Implements a StructureComponent container for bond information.

Bond(Atom, Atom) - Constructor for class edu.sdsc.mbt.Bond

Constructor variant used when there will likely be no atom list (eg: when only sequence data is loaded).

BondColor - interface edu.sdsc.mbt.viewables.BondColor.

This interface defines how all BondColor implementation classes should fill in a color for a given atomIndex+Atom.

BondColorByAtomColor - class edu.sdsc.mbt.viewables.BondColorByAtomColor.

This class implements the BondColor interface by applying a color to the given Bond by using the Atom colors.

BondColorByElement - class edu.sdsc.mbt.viewables.BondColorByElement.

This class implements the BondColor interface by applying a color to the given bondIndex+Bond by using the ElementColor class.

BondColorRegistry - class edu.sdsc.mbt.viewables.BondColorRegistry.

A class used to register BondColor implementation objects.

BondColorRegistry() - Constructor for class edu.sdsc.mbt.viewables.BondColorRegistry

BondFactory - class edu.sdsc.mbt.util.BondFactory.

BondFactory() - Constructor for class edu.sdsc.mbt.util.BondFactory

BondForm - interface edu.sdsc.mbt.viewables.BondForm.

This interface defines how all BondForm implementation classes should fill in a form for a given bondIndex.

BondFormOrder - class edu.sdsc.mbt.viewables.BondFormOrder.

Implements the BondForm interface as a "Order" bond type.

BondFormRegistry - class edu.sdsc.mbt.viewables.BondFormRegistry.

A class used to register BondForm implementation objects.

BondFormRegistry() - Constructor for class edu.sdsc.mbt.viewables.BondFormRegistry

BondFormSimple - class edu.sdsc.mbt.viewables.BondFormSimple.

Implements the BondForm interface as a "Simple" bond type.

BondFormSplit - class edu.sdsc.mbt.viewables.BondFormSplit.

Implements the BondForm interface as a "Split" bond type.

BondGeometry - class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometry.

Construct a new object for generating bond geometry using default

BondGeometry() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometry

Construct a new BondGeometry object.

BondGeometryUtils - class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometryUtils.

BondGeometryUtils() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometryUtils

BondInfo - class edu.sdsc.mbt.util.BondInfo.

BondInfo class.

BondInfo() - Constructor for class edu.sdsc.mbt.util.BondInfo

BondInfo(int, int) - Constructor for class edu.sdsc.mbt.util.BondInfo

BondLabel - interface edu.sdsc.mbt.viewables.BondLabel.

This interface defines how all BondLabel implementation classes should generate a String label for a given Bond.

BondLabelByDistance - class edu.sdsc.mbt.viewables.BondLabelByDistance.

This class implements the BondLabel interface by producing a string label based upon the Bond atom's distance..

BondLabelNone - class edu.sdsc.mbt.viewables.BondLabelNone.

This class implements the BondLabel interface by producing a null string label.

BondLabelRegistry - class edu.sdsc.mbt.viewables.BondLabelRegistry.

A class used to register BondLabel implementation objects.

BondLabelRegistry() - Constructor for class edu.sdsc.mbt.viewables.BondLabelRegistry

BondOrderDialog - class edu.sdsc.sirius.dialogs.BondOrderDialog.

BondOrderDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.BondOrderDialog

BondRadius - interface edu.sdsc.mbt.viewables.BondRadius.

This interface defines how all BondRadius implementation classes should provide a radius for a given Bond.

BondRadiusAsStick - class edu.sdsc.mbt.viewables.BondRadiusAsStick.

This class implements the BondRadius interface by applying a fixed radius representing the width IN PIXELS of the wireframe bond.

BondRadiusAsWire - class edu.sdsc.mbt.viewables.BondRadiusAsWire.

This class implements the BondRadius interface by applying a fixed radius representing the width IN PIXELS of the wireframe bond.

BondRadiusByAtomRadius - class edu.sdsc.mbt.viewables.BondRadiusByAtomRadius.

This class implements the BondRadius interface by applying a radius to the given Bond by using the AtomRadius class.

BondRadiusByScaledAtomRadius - class edu.sdsc.mbt.viewables.BondRadiusByScaledAtomRadius.

This class implements the BondRadius interface by applying a radius to the given Bond by using the AtomRadius class.

BondRadiusRegistry - class edu.sdsc.mbt.viewables.BondRadiusRegistry.

A class used to register BondRadius implementation objects.

BondRadiusRegistry() - Constructor for class edu.sdsc.mbt.viewables.BondRadiusRegistry

Br - Static variable in class edu.sdsc.mbt.util.Element

BreakBondDialog - class edu.sdsc.sirius.dialogs.BreakBondDialog.

BreakBondDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.BreakBondDialog

BrowserControl - class edu.sdsc.sirius.util.BrowserControl.

A simple, static class to display a URL in the system browser.

BrowserControl() - Constructor for class edu.sdsc.sirius.util.BrowserControl

BrowserLauncher - class edu.sdsc.sirius.util.BrowserLauncher.

BrowserLauncher is a class that provides one static method, openURL, which opens the default web browser for the current user of the system to the given URL.

BuilderDialog - class edu.sdsc.sirius.builder.BuilderDialog.

BuilderDialog(JFrame, Manager) - Constructor for class edu.sdsc.sirius.builder.BuilderDialog

BuilderPanel - class edu.sdsc.sirius.builder.BuilderPanel.

BuilderPanel(Manager) - Constructor for class edu.sdsc.sirius.builder.BuilderPanel

BumpDialog - class edu.sdsc.sirius.dialogs.BumpDialog.

BumpDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.BumpDialog

bSlider - Variable in class edu.sdsc.sirius.dialogs.FogDialog

backbone - Variable in class edu.sdsc.mbt.Atom

Whether this atom is a part of the protein backbone

backgroundColor - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

Color of background in 3D viewer

backgroundColor - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache

ballRadius - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

ballRadiusOption - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

ballRadiusOption - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache

batch - Variable in class edu.sdsc.mbt.StructureComponentEvent

batch - Variable in class edu.sdsc.mbt.viewables.StructureStylesEvent

batch - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEvent

beginTile(GL) - Method in class edu.sdsc.mbt.image.TileRenderer

Begins rendering a tile.

bkgColor - Variable in class edu.sdsc.sirius.export.ViewerParameters

block - Variable in class edu.sdsc.mbt.util.Element

bondOrder - Variable in class edu.sdsc.sirius.dialogs.GeometryEvent

bondOrderImported - Variable in class edu.sdsc.mbt.StructureMap

bondOrderOptions - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache

bondOrderUserAssigned - Variable in class edu.sdsc.mbt.StructureMap

bondRadiusScale - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

bonds - Variable in class edu.sdsc.sirius.io.SideChain

book - Variable in class edu.sdsc.sirius.viewers.SequenceViewer

build() - Method in class edu.sdsc.mbt.util.Octree

Build the whole tree recursively.

build(OctreeDataItem[]) - Method in class edu.sdsc.mbt.util.Octree

Build a subtree recursively.

build() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Extrusion

button - Variable in class edu.sdsc.sirius.dialogs.TableImpl.LineData

buttonWidthCells - Variable in class edu.sdsc.sirius.viewers.SequenceViewer