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

I

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

INTERSET - Static variable in class edu.sdsc.sirius.dialogs.BumpDialog

INTERSET - Static variable in class edu.sdsc.sirius.dialogs.HBDialog

INTRASET - Static variable in class edu.sdsc.sirius.dialogs.BumpDialog

INTRASET - Static variable in class edu.sdsc.sirius.dialogs.HBDialog

IOHandler - class edu.sdsc.sirius.util.IOHandler.

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

ImageExportDialog - class edu.sdsc.sirius.dialogs.ImageExportDialog.

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

ImageFileChooser - class edu.sdsc.sirius.dialogs.ImageFileChooser.

ImageFileChooser(Component) - Constructor for class edu.sdsc.sirius.dialogs.ImageFileChooser

Construct a new ImageFileChooser object.

ImageHandler - class edu.sdsc.mbt.image.ImageHandler.

ImageHandler() - Constructor for class edu.sdsc.mbt.image.ImageHandler

ImagePreviewPanel - class edu.sdsc.sirius.ray.ImagePreviewPanel.

ImagePreviewPanel(JFrame, Manager) - Constructor for class edu.sdsc.sirius.ray.ImagePreviewPanel

ImageUtils - class edu.sdsc.mbt.image.ImageUtils.

Provides AWT-based (pure Java) image manipulation methods for cropping, scaling, and padding images.

ImageUtils() - Constructor for class edu.sdsc.mbt.image.ImageUtils

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

InfoViewer - class edu.sdsc.sirius.viewers.TreeViewer.InfoViewer.

This class encapsulates a table that lists information about the currently active structure component

InfoViewer(Manager) - Constructor for class edu.sdsc.sirius.viewers.TreeViewer.InfoViewer

IntRange - class edu.sdsc.mbt.util.IntRange.

This class implements a container for a range of two int values.

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

Constructor initialized with two values

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

Constructor creating an empty Range object

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

This class stores information about a database entry used to display it in search and loading dialogs.

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

InterpolatedColorMap - class edu.sdsc.mbt.viewables.InterpolatedColorMap.

This class implements the ColorMap interface by generating a linear interpolated color from a list of user-defined color knots.

InterpolatedColorMap(int) - Constructor for class edu.sdsc.mbt.viewables.InterpolatedColorMap

Construct an InterpolatedColorMap with one of the default maps.

InterpolatedColorMap(float[][]) - Constructor for class edu.sdsc.mbt.viewables.InterpolatedColorMap

Construct an InterpolatedColorMap with explicit knots.

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

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

Primary Constructor.

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

Utility Constructor.

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

IntrinsicCrossSection represents, geometrically, a closed poligon.

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

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

IntrinsicCrossSection(int, Vec3f[]) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection

IntrinsicCrossSection(int, Vec3f[], Vec3f[]) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection

IntrinsicCrossSection(int, Vec3f[], Vec3f[], Color3f[]) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection

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

iconPath - Static variable in class edu.sdsc.sirius.builder.FragmentRegistry

id - Variable in class edu.sdsc.mbt.Chain

id - Variable in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock

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

importPreferences(InputStream) - Method in class edu.sdsc.mbt.viewables.StylesPreferences

importState(Manager, StructureViewer, SequenceViewer, String) - Static method in class edu.sdsc.sirius.export.StateHandler

inRing(Atom, int) - Method in class edu.sdsc.mbt.StructureMap

inRing(Atom, int) - Static method in class edu.sdsc.sirius.util.StructureMath

This method determines whether a given Atom is in a ring system of the specified size

incrementAttachmentAtom() - Method in class edu.sdsc.sirius.builder.FragmentRecord

index - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell

index1 - Variable in class edu.sdsc.mbt.util.BondInfo

index2 - Variable in class edu.sdsc.mbt.util.BondInfo

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

init() - Method in class AppletLauncher3D

Applet initialization

init() - Method in class SiriusAppletLauncher

Applet initialization

init() - Method in class Viewer

init(GLAutoDrawable) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

GLEventListener interface - init method: Initialize the GlGeometryViewer class.

init - Variable in class edu.sdsc.sirius.viewers.StructureViewer

insertGappedColumn(int) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel

insertString(int, String, AttributeSet) - Method in class edu.sdsc.sirius.util.LimitedLengthDocument

Inserts a String in the field.

interaction - Variable in class edu.sdsc.sirius.dialogs.BumpDialog

interaction - Variable in class edu.sdsc.sirius.dialogs.HBDialog

interpolate(float, FrenetTrihedron, FrenetTrihedron) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron

interpolate(float[][], int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Interpolator

Interpolate the input knots with the specified number of subdivisions per input segment.

interpolate(Vector3f, Vector3f, float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f

interpolateByBinormal(float, FrenetTrihedron, FrenetTrihedron) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron

inverse(Quat4f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Quat4f

Sets the value of this quaternion to quaternion inverse of quaternion q1.

inverse() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Quat4f

Sets the value of this quaternion to the quaternion inverse of itself.

invertSelection() - Method in class edu.sdsc.mbt.viewables.StructureStyles

invertSelection() - Method in class edu.sdsc.sirius.viewers.StructureViewer

isAminoAcid(String) - Static method in class edu.sdsc.sirius.util.ProteinProperties

isBondOrderImported() - Method in class edu.sdsc.mbt.StructureMap

isBondOrderUserAssigned() - Method in class edu.sdsc.mbt.StructureMap

isChargesUserAssigned() - Method in class edu.sdsc.mbt.StructureMap

isChiral() - Method in class edu.sdsc.sirius.io.StructureEntry

isDNABackbone(Atom) - Static method in class edu.sdsc.sirius.util.DNAProperties

isDividerBorderVisible() - Method in class com.jgoodies.uif_lite.component.UIFSplitPane

Checks and answers whether the divider border shall be visible or invisible.

isElement(short) - Static method in class edu.sdsc.mbt.util.PeriodicTable

isElementSymbol(String) - Static method in class edu.sdsc.mbt.util.PeriodicTable

isLeftExtended() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

Set a flag that the fragment has been extended to the left to fill a gap

isLoaded() - Method in class edu.sdsc.sirius.workbench.WBEntry

Indicates whether the item corresponding to this WBEntry has actually been loaded in SiriusWB

isNucleicAcid(String) - Static method in class edu.sdsc.sirius.util.DNAProperties

isPlasticHighContrastFocusEnabled() - Method in class com.jgoodies.looks.demo.Settings

isPopupDropShadowEnabled() - Method in class com.jgoodies.looks.demo.Settings

isProteinBackbone(Atom) - Static method in class edu.sdsc.sirius.util.ProteinProperties

isRelated(StructureComponent, StructureComponent) - Method in class edu.sdsc.mbt.StructureComponentRelation

Tests to see if one StructureComponent instance is related to another.

isResetView() - Method in class Viewer

isResetView() - Method in interface edu.sdsc.sirius.util.Manager

isRibbonVisible(Chain) - Method in class edu.sdsc.mbt.viewables.StructureStyles

isRibbonsAreSmoothed() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ChainGeometry

isRightExtended() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

Set a flag that the fragment has been extended to the right to fill a gap

isSelected() - Method in class com.jgoodies.uif_lite.panel.SimpleInternalFrame

Answers if the panel is currently selected (or in other words active) or not.

isSelected(StructureComponent) - Method in class edu.sdsc.mbt.viewables.StructureStyles

Get the selection state for the given structure component.

isSelected(Sequence) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

isSelected(Cell) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles

isSequenceSelected() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles

isSingleLetterAminoAcid(String) - Static method in class edu.sdsc.sirius.util.ProteinProperties

isStructure(Sequence) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

isTabIconsEnabled() - Method in class com.jgoodies.looks.demo.Settings

isTerminalBond(Bond) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometryUtils

isTrackBumps() - Method in class edu.sdsc.sirius.export.StateObject

isTrackBumps() - Method in class edu.sdsc.sirius.viewers.StructureViewer

isUseNarrowButtons() - Method in class com.jgoodies.looks.demo.Settings

isUseSystemFonts() - Method in class com.jgoodies.looks.demo.Settings

isVisible() - Method in class edu.sdsc.mbt.Atom

isVisible() - Method in class edu.sdsc.mbt.Bond

isVisible() - Method in class edu.sdsc.mbt.Chain

isVisible() - Method in class edu.sdsc.mbt.Coil

isVisible() - Method in class edu.sdsc.mbt.Fragment

isVisible() - Method in class edu.sdsc.mbt.Helix

isVisible() - Method in class edu.sdsc.mbt.Residue

isVisible() - Method in class edu.sdsc.mbt.Strand

isVisible() - Method in class edu.sdsc.mbt.StructureComponent

isVisible() - Method in class edu.sdsc.mbt.StructureInfo

isVisible() - Method in class edu.sdsc.mbt.Symmetry

isVisible() - Method in class edu.sdsc.mbt.Turn

isWindowsPlatform() - Static method in class edu.sdsc.sirius.util.BrowserControl

Try to determine whether this application is running under Windows or some other platform by examing the "os.name" property.