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S

S - Static variable in class edu.sdsc.mbt.util.Element
SAVE_ENTRY - Static variable in class edu.sdsc.sirius.dialogs.EntryListerDialog
SDFEntryLoader - class edu.sdsc.sirius.io.SDFEntryLoader.
SDFEntryLoader() - Constructor for class edu.sdsc.sirius.io.SDFEntryLoader
SEARCH_TABLE - Static variable in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel
SEARCH_TABLE - Static variable in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel
SELECTED_IGNORE - Static variable in class edu.sdsc.sirius.dialogs.DialogConstants: Loading option: ignore sequence selection in the SequenceViewer.
SELECTED_OMIT - Static variable in class edu.sdsc.sirius.dialogs.DialogConstants: Loading option: omit selected sequences in the SequenceViewer.
SELECTED_USE - Static variable in class edu.sdsc.sirius.dialogs.DialogConstants: Loading option: use selected sequences in the SequenceViewer.
SELECTION_ATOM - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences: Constants that define selection modes.
SELECTION_FRAGMENT - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
SELECTION_RESIDUE - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
SELECTION_STRUCTURE - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
SELECT_ATOM - Static variable in class edu.sdsc.sirius.dialogs.StructureEventRegistry
SEQUENCE_ENTRY - Static variable in class edu.sdsc.sirius.io.Entry
SEQUENCE_VIEWER - Static variable in class edu.sdsc.mbt.util.FrameRegistry
SIMPLE - Static variable in interface edu.sdsc.mbt.viewables.BondForm
SINGLE_FACE - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Standard - Styles: Plane Double Face
SMALL_FONT - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.LabelGeometry
SMOOTH_LAF - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
SOLID_COLOR - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager
SP - Static variable in class edu.sdsc.mbt.Atom
SP2 - Static variable in class edu.sdsc.mbt.Atom
SP3 - Static variable in class edu.sdsc.mbt.Atom
SPLIT - Static variable in interface edu.sdsc.mbt.viewables.BondForm
STRAND_COLOR - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
STRUCTURE_ENTRY - Static variable in class edu.sdsc.sirius.io.Entry
STRUCTURE_VIEWER - Static variable in class edu.sdsc.mbt.util.FrameRegistry
SURFACE_DOT - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
SURFACE_MESH - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
SURFACE_QUALITY_HIGH - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
SURFACE_QUALITY_LOW - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
SURFACE_QUALITY_MEDIUM - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
SURFACE_QUALITY_ULTRA - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
SURFACE_SOLID - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
SaveFragmentDialog - class edu.sdsc.sirius.builder.SaveFragmentDialog.
SaveFragmentDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.builder.SaveFragmentDialog
Se - Static variable in class edu.sdsc.mbt.util.Element
SelectListDialog - class edu.sdsc.sirius.dialogs.SelectListDialog.
SelectListDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.SelectListDialog
Selection - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Selection.
Selection() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Selection
SelectionAreaDialog - class edu.sdsc.sirius.dialogs.SelectionAreaDialog.
SelectionAreaDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.SelectionAreaDialog
SelectionOfAtoms - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.SelectionOfAtoms.
SelectionOfAtoms(PdbWrapper) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.SelectionOfAtoms
SelectionOfResidues - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.SelectionOfResidues.
SelectionOfResidues(PdbWrapper) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.SelectionOfResidues
Sequence - class edu.sdsc.mbt.Sequence.
Sequence(String, String) - Constructor for class edu.sdsc.mbt.Sequence
SequenceComparator - class edu.sdsc.sirius.viewers.SequenceComparator.
SequenceComparator(boolean) - Constructor for class edu.sdsc.sirius.viewers.SequenceComparator
SequenceEntry - class edu.sdsc.sirius.io.SequenceEntry.: This class is a container for any information that may be associated with a database entry, such as sequence, structure, organism, annotations, etc.
SequenceEntry() - Constructor for class edu.sdsc.sirius.io.SequenceEntry
SequencePanel - class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel.: This class is the sequence rendering area of the SequenceViewer and is intended to display sequences in response to the changes in the data model and/or styles in the parent sequence viewer
SequencePanel(SequenceViewer, int, Vector, Vector) - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
SequenceRenameDialog - class edu.sdsc.sirius.dialogs.SequenceRenameDialog.
SequenceRenameDialog(JFrame) - Constructor for class edu.sdsc.sirius.dialogs.SequenceRenameDialog
SequenceScalePanel - class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel.: This class impements a panel displayed on top of the stack of sequence panels and shows residue numbers.
SequenceScalePanel(SequenceViewer, int) - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel: Construct a SequenceScalePanel object.
SequenceStyles - class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles.
SequenceStyles(Sequence) - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles: Primary constructor.
SequenceStylesEvent - class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEvent.
SequenceStylesEvent() - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEvent
SequenceStylesEventListener - interface edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEventListener.: Properties, data, or the organizational structure of data changed.
SequenceViewer - class edu.sdsc.sirius.viewers.SequenceViewer.: The SequenceViewer is a panel that contains a scale area and the sequence display area The display area is painted as a separate component
SequenceViewer(Manager) - Constructor for class edu.sdsc.sirius.viewers.SequenceViewer
Settable - interface edu.sdsc.mbt.util.Settable.: Interface that specifies methods impemented by panels whose dimensions can be set from outside.
Settings - class com.jgoodies.looks.demo.Settings.: Describes most of the optional settings of the JGoodies Looks.
Si - Static variable in class edu.sdsc.mbt.util.Element
SideChain - class edu.sdsc.sirius.io.SideChain.: This class serves as a container for Atoms and Bonds being added to a residue.
SideChain() - Constructor for class edu.sdsc.sirius.io.SideChain
SimpleInternalFrame - class com.jgoodies.uif_lite.panel.SimpleInternalFrame.: A JPanel subclass that has a drop shadow border and that provides a header with icon, title and tool bar.
SimpleInternalFrame(String) - Constructor for class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Constructs a SimpleInternalFrame with the specified title.
SimpleInternalFrame(Icon, String) - Constructor for class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Constructs a SimpleInternalFrame with the specified icon, and title.
SimpleInternalFrame(String, JToolBar, JComponent) - Constructor for class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Constructs a SimpleInternalFrame with the specified title, tool bar, and content panel.
SimpleInternalFrame(Icon, String, JToolBar, JComponent) - Constructor for class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Constructs a SimpleInternalFrame with the specified icon, title, tool bar, and content panel.
SiriusAppletLauncher - class SiriusAppletLauncher.: This class enables deployment of high-end applets which use OpenGL for 3D graphics via JOGL and (optionally) OpenAL for spatialized audio via JOAL.
SiriusAppletLauncher() - Constructor for class SiriusAppletLauncher
Sn - Static variable in class edu.sdsc.mbt.util.Element
SplashWindow - class edu.sdsc.sirius.util.SplashWindow.
SplashWindow(Frame, int) - Constructor for class edu.sdsc.sirius.util.SplashWindow
SsGeometry - class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry.: SsGeometry is the base class for the geometry of all Secondary Structure objects.
SsGeometry() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry
StateHandler - class edu.sdsc.sirius.export.StateHandler.: This class is intended as a utility to save state of the current display to an external file.
StateHandler() - Constructor for class edu.sdsc.sirius.export.StateHandler
StateObject - class edu.sdsc.sirius.export.StateObject.: This is a wrapper class to export the current state of the structure viewer
StateObject(Vector, Vector, Vector, ViewerParameters, float[][][], Vector) - Constructor for class edu.sdsc.sirius.export.StateObject
Status - class edu.sdsc.mbt.util.Status.: Provides a toolkit-wide static status message output mechanism.
Status() - Constructor for class edu.sdsc.mbt.util.Status
StatusEvent - class edu.sdsc.mbt.util.StatusEvent.: A status message container used by the Status class.
StatusEvent() - Constructor for class edu.sdsc.mbt.util.StatusEvent
StatusListener - interface edu.sdsc.mbt.util.StatusListener.: The interface used by the Status class to send StatusEvent events.
StatusPanel - class edu.sdsc.sirius.viewers.StatusPanel.: Provides a GUI component to display toolkit-wide Status messages.
StatusPanel() - Constructor for class edu.sdsc.sirius.viewers.StatusPanel
StericBumpComponent - class edu.sdsc.mbt.StericBumpComponent.
StericBumpComponent(Atom, Atom, String) - Constructor for class edu.sdsc.mbt.StericBumpComponent
StericEvent - class edu.sdsc.sirius.dialogs.StericEvent.
StericEvent(DisplayDialog) - Constructor for class edu.sdsc.sirius.dialogs.StericEvent
Strain - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Strain.
Strain() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Strain
Strand - class edu.sdsc.mbt.Strand.: Implements a StructureComponent container for Strand conformation (secondary structure) data.
Strand() - Constructor for class edu.sdsc.mbt.Strand: Creates a new Strand object.
StrandGeometry - class edu.sdsc.mbt.viewers.GLViewerImpl.StrandGeometry.: StrandGeometry is an SsGeometry container which, primarily, manages the geometry associated with a strand.
StrandGeometry() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.StrandGeometry: Constructs a StrandGeometry objects with default values for the number of facets, segments, and cross section style.
StringLib - class edu.sdsc.mbt.viewers.StructureViewerImpl.util.StringLib.
StringLib() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.util.StringLib
StringUtils - class edu.sdsc.sirius.util.StringUtils.: This class provides static methods to modify Strings by padding them on desired side with any given characters up to the specified total length/
StringUtils() - Constructor for class edu.sdsc.sirius.util.StringUtils
Structure - class edu.sdsc.mbt.Structure.: This class provides the primary interface for a molecular structure object.
Structure() - Constructor for class edu.sdsc.mbt.Structure
StructureAlignmentDialog - class edu.sdsc.sirius.dialogs.StructureAlignmentDialog.
StructureAlignmentDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.StructureAlignmentDialog
StructureBrowser - class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser.
StructureBrowser(Manager) - Constructor for class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser
StructureColorScheme - class edu.sdsc.sirius.rasmol.StructureColorScheme.
StructureColorScheme() - Constructor for class edu.sdsc.sirius.rasmol.StructureColorScheme
StructureComponent - class edu.sdsc.mbt.StructureComponent.: Defines the abstract base class for a StructureComponent data container.
StructureComponent() - Constructor for class edu.sdsc.mbt.StructureComponent
StructureComponentEvent - class edu.sdsc.mbt.StructureComponentEvent.: Properties, data, or the organizational structure of data changed.
StructureComponentEvent() - Constructor for class edu.sdsc.mbt.StructureComponentEvent
StructureComponentEventListener - interface edu.sdsc.mbt.StructureComponentEventListener.: Properties, data, or the organizational structure of data changed.
StructureComponentFilter - interface edu.sdsc.mbt.filters.StructureComponentFilter.: Defines a standard interface to describe a filter implementation class.
StructureComponentIterator - class edu.sdsc.mbt.StructureComponentIterator.: Defines a standard interface to describe a filter implementation class.
StructureComponentIterator(Structure, StructureComponentFilter) - Constructor for class edu.sdsc.mbt.StructureComponentIterator: Construct a StructureComponentIterator for the given structure using the given filter to describe the desired subset.
StructureComponentRegistry - class edu.sdsc.mbt.StructureComponentRegistry.: A class used to register StructureComponent types and their relationships (much like a database schema defines tables and their relational links).
StructureComponentRegistry() - Constructor for class edu.sdsc.mbt.StructureComponentRegistry
StructureComponentRelation - class edu.sdsc.mbt.StructureComponentRelation.: A class used to store a single relationship description between two StructureComponent types (much like a relational link between tables in a database).
StructureComponentRelation(String, String, String) - Constructor for class edu.sdsc.mbt.StructureComponentRelation: Constructor.
StructureDocument - class edu.sdsc.mbt.viewables.StructureDocument.: This class implements the top-level container document for one or more Structure objects.
StructureDocument(Manager) - Constructor for class edu.sdsc.mbt.viewables.StructureDocument: Constructs a StructureDocument object with no initial Structure objects.
StructureDocumentEvent - class edu.sdsc.mbt.viewables.StructureDocumentEvent.: An event generated when structural changes are made to a StructureDocument.
StructureDocumentEvent() - Constructor for class edu.sdsc.mbt.viewables.StructureDocumentEvent
StructureEditDialog - class edu.sdsc.sirius.dialogs.StructureEditDialog.
StructureEditDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.StructureEditDialog
StructureEntry - class edu.sdsc.sirius.io.StructureEntry.: This class is a container for any information that may be associated with a database entry, such as sequence, structure, organism, annotations, etc.
StructureEntry() - Constructor for class edu.sdsc.sirius.io.StructureEntry
StructureEvent - class edu.sdsc.sirius.dialogs.StructureEvent.
StructureEvent(DisplayDialog) - Constructor for class edu.sdsc.sirius.dialogs.StructureEvent
StructureEventRegistry - class edu.sdsc.sirius.dialogs.StructureEventRegistry.
StructureEventRegistry() - Constructor for class edu.sdsc.sirius.dialogs.StructureEventRegistry
StructureInfo - class edu.sdsc.mbt.StructureInfo.: Implements a StructureComponent container for Structure information data.
StructureInfo() - Constructor for class edu.sdsc.mbt.StructureInfo: Creates a new StructureInfo object and initializes the StructureComponent "structure" field.
StructureItem - class edu.sdsc.sirius.util.StructureItem.: This class is an element given to RequestSet and holds the id of the requested Entry along with any flags
StructureItem(String) - Constructor for class edu.sdsc.sirius.util.StructureItem: Simplified constructor.
StructureItem(String, String, String, String, String) - Constructor for class edu.sdsc.sirius.util.StructureItem
StructureMap - class edu.sdsc.mbt.StructureMap.: This class implements a derived data map for a Structure object.
StructureMap(Structure) - Constructor for class edu.sdsc.mbt.StructureMap: Constructs a StructureMap object for a given Structure.
StructureMath - class edu.sdsc.sirius.util.StructureMath.: This class contains all the math necessary to transform atomic coordinates and drive rotation and translation when building structures
StructureMath() - Constructor for class edu.sdsc.sirius.util.StructureMath
StructureRenameDialog - class edu.sdsc.sirius.dialogs.StructureRenameDialog.
StructureRenameDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.StructureRenameDialog
StructureSelectionDialog - class edu.sdsc.sirius.dialogs.StructureSelectionDialog.
StructureSelectionDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.StructureSelectionDialog
StructureSetDialog - class edu.sdsc.sirius.dialogs.StructureSetDialog.
StructureSetDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.StructureSetDialog
StructureStyles - class edu.sdsc.mbt.viewables.StructureStyles.: Stores and retrieves styles associated with viewable objects of a Structure (typically one StructureStyle object is assocated with each Structure by a StructureDocument class).
StructureStyles(StructureMap) - Constructor for class edu.sdsc.mbt.viewables.StructureStyles: Primary constructor.
StructureStylesEvent - class edu.sdsc.mbt.viewables.StructureStylesEvent.: An event generated when changes are made to a StructureStyles object.
StructureStylesEvent() - Constructor for class edu.sdsc.mbt.viewables.StructureStylesEvent
StructureStylesEventListener - interface edu.sdsc.mbt.viewables.StructureStylesEventListener.: Properties, data, or the organizational structure of data changed.
StructureSuperpositionAlignDialog - class edu.sdsc.sirius.dialogs.StructureSuperpositionAlignDialog.
StructureSuperpositionAlignDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.StructureSuperpositionAlignDialog
StructureViewer - class edu.sdsc.sirius.viewers.StructureViewer.: This class impements a 3D structure viewer.
StructureViewer() - Constructor for class edu.sdsc.sirius.viewers.StructureViewer: Construct a StructureViewer object.
StyleManager - class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager.
StyleManager(SequenceViewer) - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager
StyleMap - class edu.sdsc.sirius.export.StyleMap.: This is a holder class to store all arrays that contain styling details based on indices of atoms, bonds, etc.
StyleMap() - Constructor for class edu.sdsc.sirius.export.StyleMap
StylesPreferences - class edu.sdsc.mbt.viewables.StylesPreferences.: This class is a storage and manipulation utility to handle viewing options set through PreferencesDialog.
StylesPreferences(String) - Constructor for class edu.sdsc.mbt.viewables.StylesPreferences
SuperimposeDialog - class edu.sdsc.sirius.dialogs.SuperimposeDialog.: This class impements a dialog box used to color the currently displayed structures.
SuperimposeDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.SuperimposeDialog: Constructor that builds the dialog.
Symmetry - class edu.sdsc.mbt.Symmetry.: Implements a StructureComponent container for Symmetry data.
Symmetry() - Constructor for class edu.sdsc.mbt.Symmetry: Creates a new Symmetry object.
sample(float, Vec3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
save(BufferedImage) - Method in class edu.sdsc.sirius.dialogs.ImageExportDialog: Prompt the user to save the given BufferedImage object, and, if the user approves, save the file to the user-specified file.
save(BufferedImage) - Method in class edu.sdsc.sirius.dialogs.ImageFileChooser: Prompt the user to save the given BufferedImage object, and, if the user approves, save the file to the user-specified file.
saveAlignment(Vector, Manager) - Static method in class edu.sdsc.sirius.util.IOHandler: sequences is a Vector of Sequence objects that need to be saved
saveCustomFragment(StructureComponent, String, StructureComponent[]) - Method in class edu.sdsc.sirius.viewers.StructureViewer: Creates a new fragment record for a user-defined structure.
saveFile(Manager, String, String, String) - Static method in class edu.sdsc.sirius.util.IOHandler
saveImage(Manager, BufferedImage) - Static method in class edu.sdsc.mbt.image.ImageHandler
saveImage(BufferedImage, String) - Static method in class edu.sdsc.mbt.image.ImageHandler
saveImage() - Method in class edu.sdsc.sirius.dialogs.DistributionViewer
saveImage(int, int, int, int, int) - Method in class edu.sdsc.sirius.viewers.StructureViewer
saveInitialCoordinates(Structure) - Method in class edu.sdsc.sirius.viewers.StructureViewer
savePdb(Structure, String, Manager, HashMap) - Static method in class edu.sdsc.sirius.util.IOHandler
savePrint(BufferedImage, String) - Static method in class edu.sdsc.mbt.image.ImageHandler
saveStateForUndo() - Method in class edu.sdsc.sirius.viewers.StructureViewer: Save current state of the display for future undo
saveStructureFile(Structure, Manager) - Static method in class edu.sdsc.sirius.util.IOHandler
saveTable(String) - Method in class edu.sdsc.sirius.dialogs.DistributionViewer
saveTextFile(String, Manager, String) - Static method in class edu.sdsc.sirius.util.IOHandler
saveTextFile(String, String) - Static method in class edu.sdsc.sirius.util.IOHandler: This method saves the provided content to a text file with the given path
saveWBData(int, String, Entry, String, String, String) - Method in class edu.sdsc.sirius.workbench.WBManager: This method saves a new data item to the workbench database.
scalarMultiply(float[], float) - Static method in class edu.sdsc.mbt.util.Algebra: Multiply a vector times a scalar.
scalarMultiply(double[], double) - Static method in class edu.sdsc.mbt.util.Algebra: Multiply a vector times a scalar.
scale(double[], double) - Method in class edu.sdsc.mbt.util.Octree: ???
scale(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AffineCrossSection
scale(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
scale(float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f
scaleAdd(float, Vector3f, Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f
score - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentSettings
selectAll() - Method in class edu.sdsc.mbt.viewables.StructureStyles: Set the selection state for the entire structure to true and then fire an event to all listeners.
selectAll() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles
selectAtomLabel - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
selectAtomSet(String) - Method in class edu.sdsc.sirius.viewers.StructureViewer
selectAtomSet() - Method in class edu.sdsc.sirius.viewers.StructureViewer
selectBackbone() - Method in class edu.sdsc.sirius.viewers.StructureViewer
selectByElement(String) - Method in class edu.sdsc.sirius.viewers.StructureViewer
selectByRadius(Atom, float, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer
selectByResidue(String) - Method in class edu.sdsc.sirius.viewers.StructureViewer
selectByVisibility(boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer
selectCell(Cell, Sequence, boolean, boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer: This method speeds up selection, since it narrows down the search for the Cell to the supplied Sequence object
selectCells(Sequence, Vector) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
selectColumn(int, boolean, boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
selectNone(boolean, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles: Set the selection state for the entire structure to false and then fire an event to all listeners.
selectNone(boolean, boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles
selectResidue(String) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
selectResidues(Vector, int) - Method in class edu.sdsc.sirius.viewers.StructureViewer: Select a group of residues, not necessarily from the same structure
selected - Variable in class edu.sdsc.sirius.dialogs.TableImpl.LineData
selected - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell
selectedAtoms - Variable in class edu.sdsc.mbt.viewables.StructureStyles
selectedResidues - Variable in class edu.sdsc.mbt.viewables.StructureStyles
selectedResidues - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles
selection - Variable in class edu.sdsc.sirius.dialogs.ReplaceResidueDialog
selection - Variable in class edu.sdsc.sirius.dialogs.SelectListDialog
selection - Static variable in class edu.sdsc.sirius.util.IOHandler
selectionColor - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
selectionColor - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
selectionMode - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences: The variable that sets selection level between atom and residue
selectionMode - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
sensitivity - Static variable in class edu.sdsc.sirius.util.BlastSettings
sequence - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell
sequenceAdded(Sequence) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser
sequenceRemoved(Sequence) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
sequenceRemoved(Sequence, boolean) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser
sequenceResidueColor - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
sequenceStyles - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEvent
sequenceViewerFont - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
sequenceViewerFont - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
servletHost - Static variable in class edu.sdsc.sirius.util.DataService
set(Vec3f, Vec3f, Vec3f, Vec3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
set(Vec3f, Vec3f, Vector3f, Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
set(Vector3f, Vector3f, Vector3f, Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
set(float[], float[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Trihedron: Set the tangent and normal vectors.
set(Color) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Color3f
set(float, float, float, float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Color3f
set(float, float, float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Point3f
set(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Point3f
set(float, float, float, float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Quat4f
set(Quat4f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Quat4f
set(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f
set(float[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f
set(float, float, float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f
set(String[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path: Sets the value of this Path.
setAcc(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
setAccession(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
setAlgorithm(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Interpolator: Set the interpolation algorithm.
setAlphaAtom(Atom) - Method in class edu.sdsc.mbt.Residue
setAlphaAtomIndex(int) - Method in class edu.sdsc.mbt.Residue: Set the alpha (backbone) Atom index for this amino acid or nucleic acid residue.
setAltLoc(char) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the "alternate location indicator".
setAngle(double) - Method in class edu.sdsc.sirius.dialogs.AngleMonitorDialog
setAnnotationVisibility(boolean, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setAnnotationVisibility(AnnotationComponent, boolean, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setApplication(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
setAtomColor(Atom, float[]) - Method in class edu.sdsc.mbt.viewables.AtomColorUniform
setAtomColor(StructureComponent, AtomColor, boolean, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setAtomColors(float[][]) - Method in class edu.sdsc.sirius.export.StyleMap
setAtomRadius(int, double) - Static method in class edu.sdsc.mbt.util.ElementProperties: Set the radius of the given element number.
setAtomRadius(String, double) - Static method in class edu.sdsc.mbt.util.ElementProperties: Set the radius of the given element name.
setAtomRadius(StructureComponent, AtomRadius) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setAtomRenderingQuality(short[]) - Method in class edu.sdsc.sirius.export.StyleMap
setAtomRenderingStyle(short[]) - Method in class edu.sdsc.sirius.export.StyleMap
setAtomSelection(boolean[]) - Method in class edu.sdsc.sirius.export.StyleMap
setAtomSetAssignment(int[]) - Method in class edu.sdsc.sirius.export.StyleMap
setAtomSetNames(Vector) - Method in class edu.sdsc.sirius.export.StateObject
setAtomSetNames(Vector) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setAtomSets(HashMap) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setAtomVisibility(boolean[]) - Method in class edu.sdsc.sirius.export.StyleMap
setAttachmentAtom(int) - Method in class edu.sdsc.sirius.builder.FragmentRecord
setAuthor(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
setAuthors(String) - Method in class edu.sdsc.mbt.StructureInfo: Set the authors of this entry.
setBFactor(float) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the temperature factor.
setBackground(float[]) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setBackgroundColor(float[]) - Method in class Viewer
setBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByCharge
setBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity
setBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByType
setBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorDefault
setBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorScaled
setBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorUniform
setBackgroundColor(float[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
setBackgroundColor(float[]) - Method in interface edu.sdsc.sirius.util.Manager: Sets background of the 3D display area.
setBackgroundColor(float[]) - Method in class edu.sdsc.sirius.viewers.StructureViewer: Sets background color.
setBinormal(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
setBondColor(StructureComponent, BondColor) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setBondRadius(StructureComponent, BondRadius) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setBuilderPanel(BuilderPanel) - Method in class edu.sdsc.sirius.builder.CustomFragmentPanel
setBuilderPanel(BuilderPanel) - Method in interface edu.sdsc.sirius.builder.FragmentGroupPanel
setBuilderPanel(BuilderPanel) - Method in class edu.sdsc.sirius.builder.GeneralFragmentPanel
setBuilderPanel(BuilderPanel) - Method in class edu.sdsc.sirius.builder.ProteinFragmentPanel
setBumps(int[][]) - Method in class edu.sdsc.sirius.export.StateObject
setCallable(ResultPanelCallable) - Method in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel
setCellBackgroundDefault(String) - Static method in class edu.sdsc.mbt.viewables.ResidueColorRegistry
setCellColor(Cell, Color, boolean, boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles
setCellColors(float[][][]) - Method in class edu.sdsc.sirius.export.StateObject
setCellColors(float[][][]) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setCellDimensions(Dimension) - Method in interface edu.sdsc.mbt.util.Settable: Sets dimensions of a cell in the sequence viewer.
setCells(Cell[]) - Method in class edu.sdsc.mbt.Sequence
setCells(Cell[]) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles
setCenter(double[]) - Method in class edu.sdsc.mbt.StructureMap
setCenter(double[]) - Method in class edu.sdsc.sirius.io.FragmentEntry
setChain(Path) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByChain
setChainId(String) - Method in class edu.sdsc.mbt.Residue
setChainId(char) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the identifier for chain to which this atom belongs.
setChainId(char) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Chain: Set the chain identifier.
setChainId(char) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Set the chain identifier for this residue.
setChainId(char) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNumAndCh
setCharge(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the electrical charge on this atom.
setChildId(int) - Method in class edu.sdsc.mbt.util.Octree: ???
setChiral(boolean) - Method in class edu.sdsc.sirius.io.StructureEntry
setCircle(int, int, int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.VirtualSphere2: Set the parameters for the screen-space constraining 2D circle.
setCircle(int[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.VirtualSphere2: Set the parameters for the screen-space constraining 2D circle as {x,y,r}.
setClassification(String) - Method in class edu.sdsc.mbt.Residue
setClosedFlag(boolean) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Set the closed/open Polygon flag
setCode(String) - Method in class edu.sdsc.sirius.builder.FragmentRecord
setCollapseOn(boolean) - Method in class edu.sdsc.mbt.util.RangeMap: Set flag to enable/disable collapse feature.
setColorMap(ColorMap) - Method in class edu.sdsc.mbt.viewables.AtomColorByCharge: Set the ColorMap used to color by charge.
setColorMap(ColorMap) - Method in class edu.sdsc.mbt.viewables.ChainColorById: Set the ColorMap used to color by Id.
setColorMap(ColorMap) - Method in class edu.sdsc.mbt.viewables.ResidueColorByCharge: Set the ColorMap used to color by hydrophobicity.
setColorMap(ColorMap) - Method in class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity: Set the ColorMap used to color by hydrophobicity.
setColorMap(Color[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Sets the color map from a given set of colors Deprecated
setColors(Color[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.BackboneLine
setColors(Color[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Extrusion
setColors(Color3f[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
setCommonMotion(boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setCompoundCode(String) - Method in class edu.sdsc.mbt.Residue: Set the 3-letter compound code for this residue.
setCompoundName(String) - Method in class edu.sdsc.mbt.StructureInfo: Set the name of this macromolecular structure.
setConformationType(String) - Method in class edu.sdsc.mbt.Fragment: Set the Conformation type for this Fragment.
setConformationType(String) - Method in class edu.sdsc.mbt.Residue: Set the secondary structure conformation type that should be assigned to this residue.
setConformationType(Vector) - Method in class edu.sdsc.mbt.util.DerivedInformation: Given a RangeMap object, it sets its Value according to the set of Secondary Structures as derived via the Kabsch-Sander algorithm.
setContent(Component) - Method in class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Sets a new panel content; replaces any existing content, if existing.
setContent(Vector) - Method in class edu.sdsc.sirius.util.VectorSet: This method creates a copy of the data instead of referencing the original to avoid multiple consecutive modifications to the same reference vector set
setContents(Vector) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Sets the contents of this PdbWrapper.
setCoordinate(Vec3f) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the three-dimensional coordinate for this atom.
setCoordinates(Vec3f[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
setCoordinates(Vec3f[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Sets the coordinates along which to draw the spine.
setCoordinates(float[][]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Sets the coordinates along which to draw the spine.
setCrossSectionStyle(CrossSectionStyle) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Sets the cross section style
setCrossSectionType(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Sets the cross section type
setData(OctreeDataItem[]) - Method in class edu.sdsc.mbt.util.Octree: ???
setData(DataSet) - Method in class edu.sdsc.sirius.dialogs.DataListerDialog: Sets the display to the given DataSet.
setData(DataSet) - Method in class edu.sdsc.sirius.dialogs.DataWBListerDialog: Sets the display to the given DataSet.
setData(DataSet) - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanelFrame: Sets display to the given DataSet.
setDatabaseID(String) - Method in class edu.sdsc.sirius.io.Entry
setDatabaseSource(String) - Method in class edu.sdsc.sirius.io.Entry
setDefaultBkgColor(float[]) - Static method in class edu.sdsc.mbt.viewables.ResidueColorUniform
setDefaultElementColors() - Static method in class edu.sdsc.mbt.util.ElementProperties: Sets element colors to their default values
setDefaultResidueColors() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setDefaultTab(int) - Method in class edu.sdsc.sirius.util.TabListCellRenderer
setDefaultValue(Object) - Method in class edu.sdsc.mbt.util.RangeMap: Set the default value to a new value.
setDescription(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock: Sets entry description.
setDescription(String) - Method in class edu.sdsc.sirius.io.Entry
setDeterminationMethod(String) - Method in class edu.sdsc.mbt.StructureInfo: Set the exerimental method used to determine this compound.
setDialog(RamachandranViewerDialog) - Method in class edu.sdsc.sirius.viewers.RamachandranViewer
setDiameter(float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CoilGeometry: Sets the coil diameter.
setDiameters(float[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Set the number of vertices
setDirty() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlAxesRenderable
setDirty() - Method in interface edu.sdsc.mbt.viewers.GLViewerImpl.GlRenderable
setDirty() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.MbtRenderable: An event sent to us when one or more style properties have changed.
setDirty() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorRenderable
setDirty() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Renderable: Set the dirty state to true (generally called by an application to indicate that the display list should be re-generated).
setDirty() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.TransformGroupRenderable
setDisplayDialogStatus(boolean) - Method in class Viewer
setDisplayDialogStatus(boolean, DisplayDialog) - Method in class Viewer
setDisplayDialogStatus(boolean) - Method in interface edu.sdsc.sirius.util.Manager: Sets a flag that indicates whether there are any dialogs open.
setDisplayDialogStatus(boolean, DisplayDialog) - Method in interface edu.sdsc.sirius.util.Manager: Sets a flag indicating whether a dialog is open, and sets the reference to the currently open dialog.
setDisplayParameters(DisplayParameters) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setDistanceMonitors(int[][]) - Method in class edu.sdsc.sirius.export.StateObject
setDivider(int) - Method in class edu.sdsc.sirius.util.DialogLayout
setDividerBorderVisible(boolean) - Method in class com.jgoodies.uif_lite.component.UIFSplitPane: Makes the divider border visible or invisible.
setDrawArrow(boolean) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.StrandGeometry: Sets the tangents along the spine.
setElement(String) - Method in class Viewer: This method is called by element palette to set element selection
setElement(String) - Method in class edu.sdsc.mbt.Atom
setElement(String) - Method in interface edu.sdsc.mbt.util.ElementSettable
setElement(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the chemical element of this atom.
setElement(String) - Method in class edu.sdsc.sirius.dialogs.ElementSelectionDialog
setElement(String) - Method in class edu.sdsc.sirius.dialogs.ReplaceAtomDialog
setElementColor(int, float, float, float) - Static method in class edu.sdsc.mbt.util.ElementProperties: Set the RGB color of the given element number.
setElementColor(String, float, float, float) - Static method in class edu.sdsc.mbt.util.ElementProperties: Set the RGB color of the given element name.
setEnd(double) - Method in class edu.sdsc.mbt.util.DoubleRange: Sets end double value.
setEnd(int) - Method in class edu.sdsc.mbt.util.IntRange: Sets end int value.
setEnd(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
setEndNormals(Vector3f, Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
setEndResNumbers(int, int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNum
setEndResNumbers(int, int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNumAndCh
setEndResidueIndex(int) - Method in class edu.sdsc.mbt.Fragment: Set the end Reisude index for this Fragment.
setEntryId(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock: Sets entry database id.
setEv(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
setEvalue(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
setF1 - Static variable in class edu.sdsc.sirius.dialogs.BumpDialog
setF1 - Static variable in class edu.sdsc.sirius.dialogs.HBDialog
setF1 - Static variable in class edu.sdsc.sirius.dialogs.StructureEditDialog
setF2 - Static variable in class edu.sdsc.sirius.dialogs.BumpDialog
setF2 - Static variable in class edu.sdsc.sirius.dialogs.HBDialog
setF2 - Static variable in class edu.sdsc.sirius.dialogs.StructureEditDialog
setFacetCount(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CoilGeometry: Sets facets count.
setFillDisorderedGaps(boolean) - Method in class edu.sdsc.mbt.StructureMap: Should we "fill in" the disordered residue gaps with random coil when we load fragments?
setFilter(Filter) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Selection
setFlag - Static variable in class edu.sdsc.sirius.dialogs.ColorDialog: Static variable that determines what level of coloring is used.
setFlag - Variable in class edu.sdsc.sirius.dialogs.ColorEvent: Variable that denotes the set of atoms/bonds to be colored.
setFlag - Static variable in class edu.sdsc.sirius.dialogs.HydrogenDialog
setFlag - Variable in class edu.sdsc.sirius.dialogs.HydrogenEvent
setFlag - Variable in class edu.sdsc.sirius.dialogs.LabelDialog
setFlag - Variable in class edu.sdsc.sirius.dialogs.LabelEvent
setFlag - Static variable in class edu.sdsc.sirius.dialogs.MotionDialog
setFlag - Static variable in class edu.sdsc.sirius.dialogs.RenderingDialog
setFlag - Variable in class edu.sdsc.sirius.dialogs.RenderingEvent
setFlag - Variable in class edu.sdsc.sirius.dialogs.ResidueLabelDialog
setFlag - Static variable in class edu.sdsc.sirius.dialogs.RibbonColorDialog: Static variable that determines what level of coloring is used.
setFlag - Variable in class edu.sdsc.sirius.dialogs.RibbonColorEvent
setFlag - Variable in class edu.sdsc.sirius.dialogs.RibbonEvent
setFlag - Variable in class edu.sdsc.sirius.dialogs.ViewEvent
setFlag - Variable in class edu.sdsc.sirius.dialogs.VisibilityDialog
setFlag - Variable in class edu.sdsc.sirius.dialogs.VisibilityEvent
setFlag - Static variable in class edu.sdsc.sirius.dialogs.WeightDialog
setFlag - Variable in class edu.sdsc.sirius.dialogs.WeightEvent
setFlags - Variable in class edu.sdsc.sirius.dialogs.StericEvent
setFog(boolean, float, float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
setFolder(String) - Method in class edu.sdsc.sirius.workbench.WBEntry: Sets label of the folder where this item is located
setFont(int) - Method in class edu.sdsc.mbt.LabelComponent
setFont(int) - Method in class edu.sdsc.mbt.ResidueLabelComponent
setFont(Font) - Method in class edu.sdsc.sirius.dialogs.JFontPreviewPanel: Sets the font used to render the preview text.
setFontSizeHints(FontSizeHints) - Method in class com.jgoodies.looks.demo.Settings
setForm(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry: Sets the basic geometric representation used to render the primitive.
setFormalCharge(StructureComponent, String, short) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setFormat(String) - Method in class edu.sdsc.sirius.workbench.WBEntry: Sets format of the data item that corresponds to this WBEntry
setFragment(int, int, String) - Method in class edu.sdsc.mbt.Chain: Set a range of residues in this chain's fragment map to the specified Conformation type.
setFragmentId(String) - Method in class edu.sdsc.sirius.io.FragmentEntry
setFrameIcon(Icon) - Method in class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Sets a new frame icon.
setGeometricalCenter() - Method in class edu.sdsc.mbt.util.Octree: ???
setHBonds(int[][]) - Method in class edu.sdsc.sirius.export.StateObject
setHiddenSequences(Vector) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setId(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
setId(String) - Method in class edu.sdsc.sirius.io.Entry
setId(String) - Method in class edu.sdsc.sirius.workbench.WBEntry: Sets id to this WBEntry object
setIdCode(String) - Method in class edu.sdsc.mbt.StructureInfo: Set the PDB-ID code by which this entry is registered.
setImageBuffer(int, int, Buffer) - Method in class edu.sdsc.mbt.image.TileRenderer: Sets the buffer in which to store the final image
setImageSize(int, int) - Method in class edu.sdsc.mbt.image.TileRenderer: Sets the desired size of the final image
setIndependentAtoms(int[]) - Method in class edu.sdsc.sirius.export.StateObject
setIndependentComponents(Vector) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setIndependentMotion(boolean, double[], double) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
setIndependentMotion(Vector, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setIndependentResidues(int[]) - Method in class edu.sdsc.sirius.export.StateObject
setIndependentStructure(Structure) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setIndependentStructureIndex(int) - Method in class edu.sdsc.sirius.export.StateObject
setInsCode(char) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the insertion code for this atom.
setIonRadius(String, double) - Static method in class edu.sdsc.mbt.util.ElementProperties
setIonRadius(int, double) - Static method in class edu.sdsc.mbt.util.ElementProperties
setJournal(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
setKnotColor(int, float[]) - Method in class edu.sdsc.mbt.viewables.InterpolatedColorMap: Set the color at the specified knot index.
setKnotLocation(int, float) - Method in class edu.sdsc.mbt.viewables.InterpolatedColorMap: Set the location value of the specified knot.
setKnotWeight(float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
setKnots(float[][]) - Method in class edu.sdsc.mbt.viewables.InterpolatedColorMap: Set the knots used by the color map.
setLabel(String) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ArrowGeometry
setLabelColor(float[][]) - Method in class edu.sdsc.sirius.export.StyleMap
setLabelSelection(boolean[]) - Method in class edu.sdsc.sirius.export.StyleMap
setLabelSize(int[]) - Method in class edu.sdsc.sirius.export.StyleMap
setLabelText(String[]) - Method in class edu.sdsc.sirius.export.StyleMap
setLabeledResidueIndices(int[]) - Method in class edu.sdsc.sirius.export.StyleMap
setLabels(int[]) - Method in class edu.sdsc.sirius.export.StyleMap
setLastUsedDirectory(String) - Method in class Viewer
setLastUsedDirectory(String) - Method in interface edu.sdsc.sirius.util.Manager
setLeafCutOffCriterion(int) - Method in class edu.sdsc.mbt.util.Octree: ???
setLeafFlag(boolean) - Method in class edu.sdsc.mbt.util.Octree: ???
setLeftExtended(boolean) - 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
setLevel(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.util.Debug: Sets the current debugging level.
setLoaded(boolean) - Method in class Viewer
setLoaded(boolean) - Method in class edu.sdsc.sirius.workbench.WBEntry: Sets the flag upon loading or removal of an Entry from the SiriusWB workspace
setLookAt(double[]) - Method in class edu.sdsc.sirius.io.FragmentEntry
setMatchedSequences(Vector) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
setMenuBar3DHint(Boolean) - Method in class com.jgoodies.looks.demo.Settings
setMenuBarHeaderStyle(HeaderStyle) - Method in class com.jgoodies.looks.demo.Settings
setMenuBarPlasticBorderStyle(BorderStyle) - Method in class com.jgoodies.looks.demo.Settings
setMenuBarWindowsBorderStyle(BorderStyle) - Method in class com.jgoodies.looks.demo.Settings
setMessage(String, Color) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setMetadata(MetaData) - Method in class edu.sdsc.sirius.io.Entry
setMinimumWidth(int) - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultTable: Sets minimum width of the table.
setModelNum(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the number of the model to which this atom belongs.
setModelNum(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Chain: Set the number of the model to which this chain belongs.
setModelNum(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Model: Set the number of this model.
setModelNum(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Set the model number for this residue.
setMotionCenter(double[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
setName(String) - Method in class edu.sdsc.mbt.Sequence
setName(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the name of this atom.
setName(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock: Sets entry name.
setName(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
setName(String) - Method in class edu.sdsc.sirius.io.Entry
setName(String) - Method in class edu.sdsc.sirius.util.FileCloseListener
setName(String) - Method in class edu.sdsc.sirius.workbench.WBEntry: Assigns label variable of this WBEntry
setNameMenu(boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel
setNextCaCoord(Vec3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Set Next Ca atom coordinate Deprecated
setNextCaCoord(float[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Set Next Ca atom coordinate
setNextSs(SsGeometry) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Sets the next Secondary Structure geometry (in a chain for instance)
setNormal(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
setNormals(Vector3f[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CoilGeometry: Sets the normals along the spine.
setNormals(Vector3f[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.HelixGeometry: Sets the normals along the spine.
setNormals(Vector3f[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.StrandGeometry: Sets the normals along the spine.
setNormalsByVector(Vec3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
setNormalsByVector(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
setNumber(int) - Method in class edu.sdsc.mbt.Residue
setNumberOfHits(int) - Method in class edu.sdsc.sirius.dialogs.DataListerDialog
setNumberOfHits(int) - Method in class edu.sdsc.sirius.dialogs.DataWBListerDialog
setNumberOfHits(int) - Method in class edu.sdsc.sirius.dialogs.EntryListerDialog
setNumberOfHits(int) - Method in interface edu.sdsc.sirius.dialogs.TableImpl.ResultPanelCallable
setNumberOfHits(int) - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanelFrame
setOcc(float) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the occupancy of this atom.
setOrder(float) - Method in class edu.sdsc.mbt.Bond: Set the bond order (the number of covalently shared electron pairs).
setOrderOnly(float) - Method in class edu.sdsc.mbt.Bond: This method sets order without editing atoms' hybridization states it is used in the loading of data with predefined bonding to avoid overwriting of hybridization data in subsequent passes over atoms that participate in bonds of different orders
setOrganism(String) - Method in class edu.sdsc.sirius.io.Entry
setOrigin(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
setOriginOnly(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
setOutputLevel(int) - Static method in class edu.sdsc.mbt.util.Status: Set the output level for subsequent calls to the output method.
setOutputLevel(String) - Static method in class edu.sdsc.mbt.util.Status: Set the output level for subsequent calls to the output method.
setPanelSize(Dimension) - Method in class edu.sdsc.sirius.viewers.TreeViewer.InfoViewer
setPanelVisibility(Sequence, boolean, boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setParent(Octree) - Method in class edu.sdsc.mbt.util.Octree: ???
setParentApplication(Manager) - Method in class edu.sdsc.sirius.builder.CustomFragmentPanel
setParentApplication(Manager) - Method in interface edu.sdsc.sirius.builder.FragmentGroupPanel
setParentApplication(Manager) - Method in class edu.sdsc.sirius.builder.GeneralFragmentPanel
setParentApplication(Manager) - Method in class edu.sdsc.sirius.builder.ProteinFragmentPanel
setPattern(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomAll
setPattern(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByName
setPattern(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNum
setPattern(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNumAndCh
setPercent(float) - Method in class edu.sdsc.sirius.viewers.ProgressPanel
setPickLevel(int) - Static method in class edu.sdsc.mbt.util.PickUtils: Set the structure component pick level.
setPlasticHighContrastFocusEnabled(boolean) - Method in class com.jgoodies.looks.demo.Settings
setPlasticTabStyle(String) - Method in class com.jgoodies.looks.demo.Settings
setPopupDropShadowEnabled(Boolean) - Method in class com.jgoodies.looks.demo.Settings
setPosition(int) - Method in class edu.sdsc.mbt.Residue
setPressed(boolean) - Method in class edu.sdsc.sirius.builder.FragmentButton
setPreviousCaCoord(Vec3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Set Previous Ca atom coordinate.
setPreviousCaCoord(float[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Set Previous Ca atom coordinate.
setPreviousNormal(Vector3f) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
setPreviousSs(SsGeometry) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Sets the previous Secondary Structure geometry (in a chain for instance)
setPriestleSteps(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Set the number of steps done in smoothing coordinates
setPrimaryReference(String) - Method in class edu.sdsc.mbt.StructureInfo: Set the primary citation reference for this entry.
setQuality(float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry: Sets the rendering quality level (0.0 meaning lowest quality but faster rendering, and 1.0 meaning highest quality but slower rendering).
setQuality(float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GeometryEntity: Set the quality parameter.
setRadius(double) - Method in class edu.sdsc.mbt.viewables.AtomRadiusByConstant: Set the constant radius.
setRamaViewers(int[]) - Method in class edu.sdsc.sirius.export.StateObject
setRange(int, int, Object) - Method in class edu.sdsc.mbt.util.RangeMap: Assign an object value to the specified range.
setRangeValue(int, Object) - Method in class edu.sdsc.mbt.util.RangeMap: Set the value currently associated with the given rangeIndex.
setReferenceAtom(int) - Method in class edu.sdsc.mbt.Bond
setReferenceAtom(Atom) - Method in class edu.sdsc.mbt.Bond
setReleaseDate(int[]) - Method in class edu.sdsc.mbt.StructureInfo: Set the date on which this entry was released.
setRenderables(Vector) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer: Set the renderable object vector used to render the scene.
setRenderables(HashMap) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setRenderables(Structure, Vector) - Method in class edu.sdsc.sirius.viewers.StructureViewer: Sets list of renderables for a specific structure
setRenderingStyle(StructureComponent, short, short, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles: Set the style for the given structure component and then fire an event to all listeners.
setRenderingStyle(short, short) - Method in class edu.sdsc.mbt.viewables.StructureStyles: Applies the requested rendering style to the entire structure
setRenderingStyle(Enumeration, short, short, boolean, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setResName(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the name of the residue to which this atom belongs.
setResName(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Set the name of this residue.
setResNum(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the number of the residue to which this atom belongs.
setResNum(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Set the residue number.
setResidue(FragmentButton, String) - Method in class edu.sdsc.sirius.dialogs.ReplaceResidueDialog
setResidueColor(Residue, float[]) - Method in interface edu.sdsc.mbt.viewables.ResidueColor: Sets color assigned to the residues in the future.
setResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByCharge
setResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByElement
setResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity
setResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByType
setResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorDefault
setResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorScaled
setResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorUniform
setResidueColor(StructureComponent, ResidueColor, boolean, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles: 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
setResidueColor(int) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setResidueColors(float[][]) - Method in class edu.sdsc.sirius.export.StyleMap
setResidueCount(int) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel: Sets the value of total residue count in the displayed alignment.
setResidueId(int) - Method in class edu.sdsc.mbt.Residue
setResidueId(Residue, int) - Method in class edu.sdsc.mbt.StructureMap
setResidueLabelColor(float[][]) - Method in class edu.sdsc.sirius.export.StyleMap
setResidueLabelSelection(boolean[]) - Method in class edu.sdsc.sirius.export.StyleMap
setResidueLabelSize(int[]) - Method in class edu.sdsc.sirius.export.StyleMap
setResidueLabelText(String[]) - Method in class edu.sdsc.sirius.export.StyleMap
setResidueLabels(int[]) - Method in class edu.sdsc.sirius.export.StyleMap
setResidueSetAssignment(int[]) - Method in class edu.sdsc.sirius.export.StyleMap
setResidues(Vector) - Method in class edu.sdsc.mbt.Fragment
setRibbonColor(Residue, float[]) - Method in interface edu.sdsc.mbt.viewables.RibbonColor: Sets color assigned to the residues in the future.
setRibbonColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.RibbonColorDefault
setRibbonColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.RibbonColorUniform
setRibbonColor(StructureComponent, RibbonColor, boolean, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setRibbonColor(StructureComponent, ResidueColor, boolean, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setRibbonColors(float[][]) - Method in class edu.sdsc.sirius.export.StyleMap
setRibbonDiameter(Chain, float) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setRibbonForm(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ChainGeometry
setRibbonInSelection(boolean, int, float, float) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setRibbonInVisible(boolean, int, float, float) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setRibbonQuality(Chain, float) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setRibbonQuality(float[]) - Method in class edu.sdsc.sirius.export.StyleMap
setRibbonType(Chain, int) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setRibbonVis(boolean[]) - Method in class edu.sdsc.sirius.export.StyleMap
setRibbonVisible(Chain, boolean, boolean, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setRibbons(int[]) - Method in class edu.sdsc.sirius.export.StyleMap
setRibbonsAreSmoothed(boolean) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ChainGeometry
setRightExtended(boolean) - 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
setRoot(Octree) - Method in class edu.sdsc.mbt.util.Octree: ???
setRotationMode(boolean) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
setRoundedShape(boolean) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Whether the shape should be rounded or not
setRowOrder(int) - Method in class edu.sdsc.mbt.image.TileRenderer: Sets the order of row traversal
setScale(double) - Method in class edu.sdsc.mbt.viewables.AtomRadiusByScaledCpk: Set the CPK radius scale factor.
setScalePanel(SequenceScalePanel) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setScrollToSelection(boolean) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser
setSegId(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the segment identifier for this atom.
setSegmentCount(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Set number of segments to be drawn between any two consecutive CA positions.
setSelected(boolean) - Method in class com.jgoodies.uif_lite.panel.SimpleInternalFrame: This panel draws its title bar differently if it is selected, which may be used to indicate to the user that this panel has the focus, or should get more attention than other simple internal frames.
setSelected(boolean) - Method in class edu.sdsc.mbt.AnnotationComponent
setSelected(boolean) - Method in class edu.sdsc.mbt.ArrowComponent
setSelected(boolean) - Method in class edu.sdsc.mbt.HydrogenBondComponent
setSelected(boolean) - Method in class edu.sdsc.mbt.LabelComponent
setSelected(boolean) - Method in class edu.sdsc.mbt.MonitorComponent
setSelected(boolean) - Method in class edu.sdsc.mbt.ResidueLabelComponent
setSelected(boolean) - Method in class edu.sdsc.mbt.StericBumpComponent
setSelected(StructureComponent, boolean, boolean, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles: Set the selection state for the given structure component and then fire an event to all listeners.
setSelected(boolean) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
setSelected(Sequence, boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setSelected(Cell, boolean, boolean, boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles
setSelectedCells(Vector) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setSelectedChain(Chain) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setSelectedChains(Vector) - Method in class edu.sdsc.mbt.viewables.StructureStyles
setSelectedChains(Vector) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setSelectedColumns(Vector) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel: Enables selection of the specified columns by repainting them so that the column headers appear pushed.
setSelectedIndices(Vector) - Method in class edu.sdsc.sirius.dialogs.DataListerDialog
setSelectedIndices(Vector) - Method in class edu.sdsc.sirius.dialogs.DataWBListerDialog
setSelectedIndices(Vector) - Method in class edu.sdsc.sirius.dialogs.EntryListerDialog
setSelectedIndices(Vector) - Method in interface edu.sdsc.sirius.dialogs.TableImpl.ResultPanelCallable
setSelectedIndices(Vector) - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanelFrame
setSelectedLookAndFeel(LookAndFeel) - Method in class com.jgoodies.looks.demo.Settings
setSelectedSequence(Sequence, Cell[]) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel: Sets selected sequence that is used as the reference to draw residue numbers.
setSelectedTheme(PlasticTheme) - Method in class com.jgoodies.looks.demo.Settings
setSelection(boolean, int) - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel
setSelection(boolean, int) - Method in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel
setSelection(AnnotationComponent, boolean) - Method in class edu.sdsc.sirius.monitors.MonitorDialog
setSelection(AnnotationComponent, boolean) - Method in class edu.sdsc.sirius.monitors.MonitorPanel
setSelectionArea(Residue, double, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setSelectionMode(int) - Method in class Viewer
setSelectionMode(int) - Method in interface edu.sdsc.sirius.util.Manager: Sets selection mode to either atom or residue level
setSeparateMotion(boolean) - Method in class Viewer
setSeparateMotion(boolean) - Method in interface edu.sdsc.sirius.util.Manager: Sets mode of inndependent motion
setSequence(String) - Method in class edu.sdsc.mbt.Sequence
setSequence(Sequence) - Method in class edu.sdsc.sirius.io.SequenceEntry: Sets a Structure object created to represent the 3D structural information
setSequenceColor(Color, boolean, boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles
setSequenceDefault(String) - Static method in class edu.sdsc.mbt.viewables.ResidueColorRegistry
setSequenceIndex(int) - Method in class edu.sdsc.sirius.export.StyleMap
setSequenceSelected(boolean) - Method in class edu.sdsc.sirius.export.StyleMap
setSequences(Vector) - Method in class edu.sdsc.sirius.export.StateObject
setSequences(HashMap, Vector) - Method in class edu.sdsc.sirius.viewers.SequenceViewer: This method matches the entry to those currently loaded and replaces the sequences in the viewer The method is used to update view in the event of an externally derived sequence alignment, such as during the structure alignment.
setSerialNumber(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the atom number.
setShowOrder(boolean) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometry: Set the state of showing/hiding a representation of bond order.
setSideColor(Color3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
setSourceSpecies(String) - Method in class edu.sdsc.mbt.StructureInfo: Set the source species of this compound.
setSourceUrl(URL) - Method in class edu.sdsc.sirius.io.Entry
setSsExtendedFlags() - Method in class edu.sdsc.mbt.util.DerivedInformation
setSsShape(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.HelixGeometry: Sets the general appearance of the helix shape, i.e.
setStart(double) - Method in class edu.sdsc.mbt.util.DoubleRange: Sets start value.
setStart(int) - Method in class edu.sdsc.mbt.util.IntRange: Sets start int value.
setStart(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
setStartResidue(int) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
setStartResidue(int) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel: Sets the residue index from which to begin display.
setStartResidueIndex(int) - Method in class edu.sdsc.mbt.Fragment: Set the start Reisude index for this Fragment.
setStartSequence(int) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
setStereoEnable(boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer: Turn stereo rendering on or off (if supported by the hardware).
setStructure(Structure) - Method in class edu.sdsc.mbt.StructureComponent: Set the Structure to which a StructureComponent instance belongs.
setStructure(Structure) - Method in class edu.sdsc.sirius.io.StructureEntry: Sets a Structure object created to represent the 3D structural information
setStructure(Structure) - Method in class edu.sdsc.sirius.rasmol.RasmolReader
setStructureColor(ResidueColor, AtomColor) - Method in class edu.sdsc.mbt.viewables.StructureStyles: This method sets all bookkeeping values for colors for atoms and residues in the given structure and fires one structure-wide event to the viewers.
setStructureId(String) - Method in class edu.sdsc.sirius.io.StructureEntry
setStructures(Vector) - Method in class edu.sdsc.sirius.export.StateObject
setStyleMap(Vector) - Method in class edu.sdsc.sirius.export.StateObject
setStyleName(String) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Set the Style Name
setSuperimpose(boolean) - Method in class Viewer
setSuperimpose(boolean) - Method in interface edu.sdsc.sirius.util.Manager
setTabIconsEnabled(boolean) - Method in class com.jgoodies.looks.demo.Settings
setTabs(int[]) - Method in class edu.sdsc.sirius.util.TabListCellRenderer
setTangent(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
setTangents(Vector3f[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.HelixGeometry: Sets the tangents along the spine.
setTangents(Vector3f[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.StrandGeometry: Sets the tangents along the spine.
setTileBuffer(int, int, Buffer) - Method in class edu.sdsc.mbt.image.TileRenderer: Specify a buffer the tiles to be copied to.
setTileSize(int, int, int) - Method in class edu.sdsc.mbt.image.TileRenderer: Sets the size of the tiles to use in rendering.
setTitle(String) - Method in class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Sets a new title text.
setTitle(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
setToolBar(JToolBar) - Method in class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Sets a new tool bar in the header.
setToolBar3DHint(Boolean) - Method in class com.jgoodies.looks.demo.Settings
setToolBarHeaderStyle(HeaderStyle) - Method in class com.jgoodies.looks.demo.Settings
setToolBarPlasticBorderStyle(BorderStyle) - Method in class com.jgoodies.looks.demo.Settings
setToolBarWindowsBorderStyle(BorderStyle) - Method in class com.jgoodies.looks.demo.Settings
setTorsion(double[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Extrusion
setTrackBumps(boolean) - Method in class edu.sdsc.sirius.export.StateObject
setTrackBumps(boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setTransform(double[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.TransformGroupRenderable: xxx.
setTransformedCoordinates(HashMap) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setType(int) - Method in class edu.sdsc.sirius.workbench.WBEntry: Sets the type of this WBEntry at the time of its creation
setTypeColor(String, float[]) - Method in class edu.sdsc.mbt.viewables.FragmentColorByType: Set the color used for the given conformation type.
setUndo(boolean) - Method in class Viewer
setUndo(boolean) - Method in interface edu.sdsc.sirius.util.Manager: Sets undo mode
setUndo(boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setUndo(boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
setUndoMode(boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
setUp(double[]) - Method in class edu.sdsc.sirius.io.FragmentEntry
setUseNarrowButtons(boolean) - Method in class com.jgoodies.looks.demo.Settings
setUseSystemFonts(Boolean) - Method in class com.jgoodies.looks.demo.Settings
setUserData(Object) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Sets information (annotation) provided by the user
setValue(int, Object) - Method in class edu.sdsc.mbt.util.RangeMap: Assign an object value to the specified index.
setValueMap(HashMap) - Method in class edu.sdsc.mbt.viewables.AtomColorByCharge
setValueMap(HashMap) - Method in interface edu.sdsc.mbt.viewables.ResidueColor: Sets value map for those implementations that rely on residue position to assign color.
setValueMap(HashMap) - Method in class edu.sdsc.mbt.viewables.ResidueColorByCharge
setValueMap(HashMap) - Method in class edu.sdsc.mbt.viewables.ResidueColorByElement
setValueMap(HashMap) - Method in class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity
setValueMap(HashMap) - Method in class edu.sdsc.mbt.viewables.ResidueColorByType
setValueMap(HashMap) - Method in class edu.sdsc.mbt.viewables.ResidueColorDefault
setValueMap(HashMap) - Method in class edu.sdsc.mbt.viewables.ResidueColorScaled
setValueMap(HashMap) - Method in class edu.sdsc.mbt.viewables.ResidueColorUniform
setValueMap(HashMap) - Method in interface edu.sdsc.mbt.viewables.RibbonColor: Sets value map for those implementations that rely on residue position to assign color.
setValueMap(HashMap) - Method in class edu.sdsc.mbt.viewables.RibbonColorDefault
setValueMap(HashMap) - Method in class edu.sdsc.mbt.viewables.RibbonColorUniform
setVectorLength(double[], double) - Static method in class edu.sdsc.mbt.util.Algebra
setVertexColors(Color3f[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Set the vertex colors
setVertexCount(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Set the number of vertices
setView(ViewerParameters) - Method in class edu.sdsc.sirius.export.StateObject
setViewerParameters(ViewerParameters) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
setVisibility(AnnotationComponent, boolean, boolean) - Method in class edu.sdsc.sirius.monitors.MonitorDialog
setVisibility(AnnotationComponent, boolean, boolean) - Method in class edu.sdsc.sirius.monitors.MonitorPanel
setVisibilityInSelection(int) - Method in class edu.sdsc.sirius.viewers.StructureViewer
setVisibilityMap(boolean[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry
setVisible(boolean) - Method in class edu.sdsc.mbt.AnnotationComponent
setVisible(boolean) - Method in class edu.sdsc.mbt.ArrowComponent
setVisible(boolean) - Method in class edu.sdsc.mbt.HydrogenBondComponent
setVisible(boolean) - Method in class edu.sdsc.mbt.LabelComponent
setVisible(boolean) - Method in class edu.sdsc.mbt.MonitorComponent
setVisible(boolean) - Method in class edu.sdsc.mbt.ResidueLabelComponent
setVisible(boolean) - Method in class edu.sdsc.mbt.StericBumpComponent
setVisible(StructureComponent, boolean, boolean, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles: Set the visibility state for the given structure component and then fire an event to all listeners.
setWeight(int) - Method in class edu.sdsc.mbt.util.Octree: ???
setX(float) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the X-coordinate of this atom.
setY(float) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the Y-coordinate of this atom.
setYear(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
setZ(float) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Set the Z-coordinate of this atom.
shininessTemp - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.CoilGeometry
shininessTemp - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.HelixGeometry
shininessTemp - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.StrandGeometry
showAll(boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles: Set the visibility state for the entire structure to true and then fire an event to all listeners.
showBondOrder - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
showBoundWaters - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
showBoundWaters - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
showCellGrid - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
showCellGrid - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
showDialog(boolean) - Method in class edu.sdsc.sirius.dialogs.AngleMonitorDialog
showDialog(JFrame, Atom) - Static method in class edu.sdsc.sirius.dialogs.AtomRenameDialog
showDialog(Component, String) - Method in class edu.sdsc.sirius.dialogs.JFontChooser: Pops up a Font chooser dialog with the supplied title, centered about the component parent.
showDialog(JFrame, Residue) - Static method in class edu.sdsc.sirius.dialogs.ResidueRenameDialog
showDialog(JFrame, Sequence) - Static method in class edu.sdsc.sirius.dialogs.SequenceRenameDialog
showLastLine() - Method in class edu.sdsc.sirius.viewers.StatusPanel: Cause at least the last line of the text area to scroll into view.
showResidueTips - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
showResidueTips - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
showSelected() - Method in class edu.sdsc.sirius.monitors.MonitorPanel
showSs - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
showSs - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
showSs - Variable in class edu.sdsc.sirius.viewers.SequenceViewer
showStatus() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.util.Debug: Prints the status of the debugging object, including the current level if debugging is active.
showTT(boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
showToolbarTips - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
size() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataSet: Returns the number of DataBlocks included in this DataSet
size() - Method in class edu.sdsc.sirius.util.VectorSet
smooth(Vec3f[], int) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.Priestle
smooth(Vector3f[], int) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.Priestle
smoothRibbon - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
solveSystemOfEquations(double[]) - Static method in class edu.sdsc.mbt.util.Algebra: This method solves a system of three equations with three unknowns and returns an array of x,y,z values
sort(String[]) - Static method in class edu.sdsc.mbt.viewers.StructureViewerImpl.util.StringLib: Sort the supplied array of strings in lexicographic order.
sort - Static variable in class edu.sdsc.sirius.util.BlastSettings
sphereRadius - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
split(String, String) - Static method in class edu.sdsc.mbt.viewers.StructureViewerImpl.util.StringLib: Split the supplied string in two, returning the resulting strings as elements of an array.
ssHeight - Static variable in class edu.sdsc.sirius.viewers.SequenceViewer
start() - Method in class AppletLauncher3D: start asynchroneous loading of libraries if needed
start() - Method in class SiriusAppletLauncher: start asynchroneous loading of libraries if needed
start() - Method in class Viewer
start - Variable in class edu.sdsc.mbt.ArrowComponent
start - Variable in class edu.sdsc.mbt.MonitorComponent
start - Variable in class edu.sdsc.mbt.StericBumpComponent
start_chain - Variable in class edu.sdsc.mbt.Conformation: This value corresponds to the start Atom.chain_id value.
start_compound - Variable in class edu.sdsc.mbt.Conformation: For example, "ALA", "GLU", "LYS", etc.
start_residue - Variable in class edu.sdsc.mbt.Conformation: This value corresponds to the Atom.residue_id value.
startupMagnificationMode - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
startupRenderingQuality - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
startupRenderingQuality - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
state() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.util.Debug: Returns current debugging state: true if debugging is active, false if not.
state(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.util.Debug: Returns true if the current debugging level is higher than the specified level.
stateChanged(ChangeEvent) - Method in class edu.sdsc.sirius.dialogs.PreferencesDialog
stats - Static variable in class edu.sdsc.sirius.util.BlastSettings
status - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.MbtRenderable
status - Variable in class edu.sdsc.sirius.dialogs.RibbonEvent
stickSize - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
stop() - Method in class AppletLauncher3D
stop() - Method in class SiriusAppletLauncher
stop() - Method in class Viewer
store(PdbWrapper) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FileLoader: Write the PDB entry that's encapsulated in the given PdbWrapper to the file.
store(PdbWrapper, File) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FileLoader: Write the PDB entry that's encapsulated in the given PdbWrapper to the given File.
store(PdbWrapper) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.Loader
store(PdbWrapper) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlLoader: Write the PDB entry that's encapsulated in the given PdbWrapper to the file.
store(PdbWrapper, File) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlLoader: Write the PDB entry that's encapsulated in the given PdbWrapper to the given File.
store(PdbWrapper, URL) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlLoader: Write the PDB entry that's encapsulated in the given PdbWrapper to the given {$link URL URL}.
strandColor - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
structure - Variable in class edu.sdsc.mbt.StructureComponent: The Structure to which a StructureComponent instance belongs.
structureColor - Static variable in class edu.sdsc.sirius.dialogs.ColorDialog: Default structure color when the dialog is open.
structureColor - Variable in class edu.sdsc.sirius.dialogs.ColorEvent: The actual value of the chosen color.
structureColor - Static variable in class edu.sdsc.sirius.dialogs.ComponentColorDialog: Default structure color when the dialog is open.
structureColor - Static variable in class edu.sdsc.sirius.dialogs.RibbonColorDialog: Default structure color when the dialog is open.
structureColorIndex - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
structureColorSequence - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
structureColorSequence - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
structureColors - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
structureColors - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
structureComponent - Variable in class edu.sdsc.mbt.StructureComponentEvent
structureComponent - Variable in class edu.sdsc.mbt.viewables.StructureStylesEvent: The StructureComponent for which style changed.
structureComponent - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.MbtRenderable
structureComponent - Variable in class edu.sdsc.sirius.dialogs.ColorEvent
structureComponent - Variable in class edu.sdsc.sirius.dialogs.HydrogenEvent
structureComponent - Variable in class edu.sdsc.sirius.dialogs.LabelEvent
structureComponent - Variable in class edu.sdsc.sirius.dialogs.RenderingEvent
structureComponent - Variable in class edu.sdsc.sirius.dialogs.RibbonColorEvent
structureComponent - Variable in class edu.sdsc.sirius.dialogs.RibbonEvent
structureComponent - Variable in class edu.sdsc.sirius.dialogs.ViewEvent
structureComponent - Variable in class edu.sdsc.sirius.dialogs.VisibilityEvent
structureComponent - Variable in class edu.sdsc.sirius.dialogs.WeightEvent
structureDocument - Variable in class edu.sdsc.mbt.viewables.StructureDocumentEvent: The StructureDocument object for which the state changed (once a Viewer is added to a StructureDocument this value shouldn't change since each Viewer instance only views one document at a time).
structureDocument - Variable in class edu.sdsc.sirius.viewers.SequenceViewer
structureId - Variable in class edu.sdsc.sirius.util.StructureItem
structureMap - Variable in class edu.sdsc.mbt.StructureComponentEvent
structureStyles - Variable in class edu.sdsc.mbt.viewables.StructureStylesEvent: The StructureStyles in which the style changed.
structureStyles - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.MbtRenderable
structureStyles - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorRenderable
structureView - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences
structureView - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache
styleFlag - Static variable in class edu.sdsc.sirius.dialogs.ComponentRenderingDialog
styleFlag - Static variable in class edu.sdsc.sirius.dialogs.RenderingDialog
styleFlag - Variable in class edu.sdsc.sirius.dialogs.RenderingEvent
sub(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f
sub(Vector3f, Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f
subtractVectors(double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra: Subtract one vector from another.
subtractVectors(float[], float[]) - Static method in class edu.sdsc.mbt.util.Algebra: Subtract one vector from another.
superimpose(Structure, Vector, Structure, Vector) - Static method in class edu.sdsc.sirius.util.StructureMath: This method performs RMSD minimization structure superposition.
superimpose(StructureComponent[], StructureComponent[]) - Method in class edu.sdsc.sirius.viewers.StructureViewer
superimposeStructures(Structure, Structure, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer: This method transforms coordinates of the second structure to be as close in 3D as possible to the first structure.
symbol - Variable in class edu.sdsc.mbt.util.Element
symbol - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell

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