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

T

TETRAHEDRAL - Static variable in class edu.sdsc.mbt.util.ElementProperties

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

TREE_VIEWER - Static variable in class edu.sdsc.mbt.util.FrameRegistry

TRIGONAL - Static variable in class edu.sdsc.mbt.util.ElementProperties

TRIGONAL_BIPYRAMIDAL - Static variable in class edu.sdsc.mbt.util.ElementProperties

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

TYPE - Variable in class edu.sdsc.sirius.io.Entry

TYPE_ACTIVE_SITE - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_ADD - Static variable in class edu.sdsc.mbt.StructureComponentEvent

TYPE_ANGLE_MONITOR - Static variable in class edu.sdsc.mbt.AnnotationComponentRegistry

TYPE_ARROW - Static variable in class edu.sdsc.mbt.AnnotationComponentRegistry

TYPE_ATOM - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_BOND - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_BOND_ROTATION - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.MoveEvent

TYPE_CHAIN - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_CHARGE - Static variable in class edu.sdsc.sirius.dialogs.LabelDialog

TYPE_COIL - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

Secondary structure conformation for a Coil.

TYPE_COLOR - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager

TYPE_COVALENT - Static variable in class edu.sdsc.mbt.Bond

Type for a covalent bond (bonding interaction due to electron sharing).

TYPE_CUSTOM - Static variable in class edu.sdsc.sirius.dialogs.LabelDialog

TYPE_DATA - Static variable in class edu.sdsc.mbt.viewables.StructureDocumentEvent

A Structure object was added/removed in the StructureDocument.

TYPE_DIHEDRAL_ANGLE_MONITOR - Static variable in class edu.sdsc.mbt.AnnotationComponentRegistry

TYPE_DISULPHIDE - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_ELEMENT - Static variable in class edu.sdsc.sirius.dialogs.LabelDialog

TYPE_FRAGMENT - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_GEOMETRY_CHANGE - Static variable in class edu.sdsc.mbt.StructureComponentEvent

TYPE_GLOBAL - Static variable in class edu.sdsc.mbt.viewables.StructureDocumentEvent

TYPE_HELIX - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

Secondary structure conformation for a Helix.

TYPE_HYBRIDIZATION - Static variable in class edu.sdsc.sirius.dialogs.LabelDialog

TYPE_HYDROGEN - Static variable in class edu.sdsc.mbt.Bond

Type for a hydrogen bond (bonding interaction due to partial charges).

TYPE_HYDROGEN_BOND - Static variable in class edu.sdsc.mbt.AnnotationComponentRegistry

TYPE_INDEPENDENT_MOTION - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.MoveEvent

TYPE_IONIC - Static variable in class edu.sdsc.mbt.Bond

Type for an ionic bond (bonding interaction due to electrostatic attraction between cations and anions).

TYPE_LABEL - Static variable in class edu.sdsc.mbt.AnnotationComponentRegistry

TYPE_MODEL - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_MODIFY - Static variable in class edu.sdsc.mbt.StructureComponentEvent

TYPE_MONITOR - Static variable in class edu.sdsc.mbt.AnnotationComponentRegistry

TYPE_NAME - Static variable in class edu.sdsc.sirius.dialogs.LabelDialog

TYPE_NONPOLYMER - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_OUTPUT - Static variable in class edu.sdsc.mbt.util.StatusEvent

An output message type of event.

TYPE_POLYMER - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_PROGRESS - Static variable in class edu.sdsc.mbt.util.StatusEvent

A progress type of event.

TYPE_RELOAD_CONTENT - Static variable in class edu.sdsc.mbt.StructureComponentEvent

TYPE_REMOVE - Static variable in class edu.sdsc.mbt.StructureComponentEvent

TYPE_REPLACE - Static variable in class edu.sdsc.mbt.StructureComponentEvent

TYPE_RESIDUE - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_RESIDUE_LABEL - Static variable in class edu.sdsc.mbt.AnnotationComponentRegistry

TYPE_RIBBON - Static variable in class edu.sdsc.sirius.dialogs.VisibilityDialog

TYPE_SALT_BRIDGE - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_STERIC_BUMP - Static variable in class edu.sdsc.mbt.AnnotationComponentRegistry

TYPE_STRAND - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

Secondary structure conformation for a Strand.

TYPE_STRUCTURE - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached type.

TYPE_STRUCTURE - Static variable in class edu.sdsc.sirius.dialogs.VisibilityDialog

TYPE_TURN - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

Secondary structure conformation for a Turn.

TYPE_UNDEFINED - Static variable in class edu.sdsc.mbt.Conformation

If a residue conformation / chain fragment type is not defined, use this value.

TYPE_UNDO_REPLACE - Static variable in class edu.sdsc.mbt.StructureComponentEvent

TYPE_VIEWER - Static variable in class edu.sdsc.mbt.viewables.StructureDocumentEvent

A Viewer object was added/removed in the StructureDocument.

TabListCellRenderer - class edu.sdsc.sirius.util.TabListCellRenderer.

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

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

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

TableViewPanel(JPanel, DataSet, Manager, Vector) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

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

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

TileRenderer - class edu.sdsc.mbt.image.TileRenderer.

A fairly direct port of Brian Paul's tile rendering library, found at http://www.mesa3d.org/brianp/TR.html.

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

Creates a new TileRender object

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

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

Provides a renderable object which contains all properties needed to regenerate geometry for a visible representation of some data.

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

Constructor with basic initialization (empty display list and dirty).

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

Holds a moving trihedron normalized three-tuple of vectors that represents the basis vectors that define a coordinate system.

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

Primary Constructor.

Trihedron(float[], float[]) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.Trihedron

Primary Constructor.

Turn - class edu.sdsc.mbt.Turn.

Implements a StructureComponent container for Turn conformation (secondary structure) data.

Turn() - Constructor for class edu.sdsc.mbt.Turn

Creates a new Conformation object.

text - Variable in class edu.sdsc.sirius.dialogs.LabelEvent

text - Variable in class edu.sdsc.sirius.dialogs.StericEvent

tileClicked(Element, JButton) - Method in class edu.sdsc.sirius.dialogs.ElementSelectionPanel

Called in response to a click on an element tile.

tileClicked(Element, JButton) - Method in class edu.sdsc.sirius.dialogs.ElementStylesEditor

Called in response to a click on an element tile.

title - Variable in class edu.sdsc.sirius.dialogs.TableImpl.PubmedLineData

toString() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron

toString() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path

Convenience method to return this Path as a plain String.

toString() - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock

toString() - Method in class edu.sdsc.sirius.util.DialogLayout

toString() - Method in class edu.sdsc.sirius.util.ExtensionLayout

toString() - Method in class edu.sdsc.sirius.util.FileNameFilter

toString() - Method in class edu.sdsc.sirius.util.Location

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

toVec3d() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.vec.Vec3f

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

toolbarHeight - Static variable in class edu.sdsc.sirius.dialogs.DialogConstants

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

toolbarWidth - Static variable in class edu.sdsc.sirius.dialogs.DialogConstants

topcombon - Static variable in class edu.sdsc.sirius.util.BlastSettings

tossgaps - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentSettings

trFrustum(double, double, double, double, double, double) - Method in class edu.sdsc.mbt.image.TileRenderer

Sets the perspective projection frustrum.

trOrtho(double, double, double, double, double, double) - Method in class edu.sdsc.mbt.image.TileRenderer

Sets the context to use an orthographic projection.

trPerspective(double, double, double, double) - Method in class edu.sdsc.mbt.image.TileRenderer

Convenient way to specify a perspective projection

trRasterPos3f(float, float, float, GL, GLU) - Method in class edu.sdsc.mbt.image.TileRenderer

Tile rendering causes problems with using glRasterPos3f, so you should use this replacement instead

transformAtomSet(Location, Location, Vector) - Static method in class edu.sdsc.sirius.util.StructureMath

transformCoordinates(double[], double[][]) - Static method in class edu.sdsc.sirius.util.StructureMath

This method returns the new x,y,z coordinates for a point given the corresponding rotation matrix

transformCoordinates(double[], double[]) - Static method in class edu.sdsc.sirius.util.StructureMath

transformPoint(Location, Location, double[]) - Static method in class edu.sdsc.sirius.util.StructureMath

transformStructure(Location, Location, Structure) - Static method in class edu.sdsc.sirius.util.StructureMath

transformVector(Location, Location, double[], double[]) - Static method in class edu.sdsc.sirius.util.StructureMath

transformVectorSet(double[], double[], double[]) - Method in class edu.sdsc.sirius.util.VectorSet

VectorSet is transformed into a different coordinate system, where the origin is defined by the given point

transformVectors(double[], double[], Vector) - Static method in class edu.sdsc.sirius.util.StructureMath

translate(int, int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

truncate() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path

Truncates this path by one level.

truncate(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path

Truncates this path to the specified level.

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

type() - Method in class edu.sdsc.mbt.filters.AtomFilter

Return the StructureComponentRegistry type for the Atom object.

type() - Method in class edu.sdsc.mbt.filters.RelationFilter

Return the StructureComponentRegistry type for returned object types.

type() - Method in interface edu.sdsc.mbt.filters.StructureComponentFilter

Return the StructureComponent type that this filter will match and return.

type - Variable in class edu.sdsc.mbt.util.StatusEvent

The message type.

type - Variable in class edu.sdsc.mbt.viewables.StructureDocumentEvent

The type of object that was added/removed in the StructureDocument.

type - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.MoveEvent

type - Variable in class edu.sdsc.sirius.dialogs.StericEvent

type - Variable in class edu.sdsc.sirius.dialogs.StructureEditDialog

typeFlag - Variable in class edu.sdsc.sirius.dialogs.LabelDialog

typeFlag - Variable in class edu.sdsc.sirius.dialogs.LabelEvent

typeFlag - Variable in class edu.sdsc.sirius.dialogs.ResidueLabelDialog

typeFlag - Variable in class edu.sdsc.sirius.dialogs.VisibilityDialog

typeFlag - Variable in class edu.sdsc.sirius.dialogs.VisibilityEvent