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

A

ACCEPT_OPTION - Static variable in class edu.sdsc.sirius.dialogs.JFontChooser

Value returned by showDialog upon a selected font.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

ATTRIBUTE_NAME - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles

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

ATTRIBUTE_QUALITY - Static variable in class edu.sdsc.mbt.viewables.StructureStyles

ATTRIBUTE_RIBBON_VISIBILITY - Static variable in class edu.sdsc.mbt.viewables.StructureStyles

ATTRIBUTE_SELECTION - Static variable in class edu.sdsc.mbt.viewables.StructureStyles

ATTRIBUTE_SELECTION - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles

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

ATTRIBUTE_STYLE - Static variable in class edu.sdsc.mbt.viewables.StructureStyles

ATTRIBUTE_STYLE - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles

ATTRIBUTE_VISIBILITY - Static variable in class edu.sdsc.mbt.viewables.StructureStyles

AboutDialog - class edu.sdsc.sirius.dialogs.AboutDialog.

AboutDialog(JFrame, String) - Constructor for class edu.sdsc.sirius.dialogs.AboutDialog

AboutDialog(JDialog, String) - Constructor for class edu.sdsc.sirius.dialogs.AboutDialog

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

AffineCrossSection is the representation of a CrossSection objects tied to a given point in space.

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

Build an AffineCrossSection from a given intrinsic CrossSection and a given FrenetTrihedron.

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

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

Algebra - class edu.sdsc.mbt.util.Algebra.

This class provides a number of algebreic methods for computing various distances and angles between 3D virtex coordinates (double[3]).

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

AlignmentService - class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentService.

AlignmentService() - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentService

AlignmentSettings - class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentSettings.

AlignmentSettings() - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentSettings

AlignmentSettingsDialog - class edu.sdsc.sirius.dialogs.AlignmentSettingsDialog.

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

AlnEntryLoader - class edu.sdsc.sirius.io.AlnEntryLoader.

This class loads Entries from a file in CLUSTALW alignment format.

AlnEntryLoader() - Constructor for class edu.sdsc.sirius.io.AlnEntryLoader

AminoAcidInfo - class edu.sdsc.mbt.util.AminoAcidInfo.

Provides static information about Amino Acids such as character codes, 3-letter codes, and full names.

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

AminoColorScheme - class edu.sdsc.sirius.rasmol.AminoColorScheme.

AminoColorScheme() - Constructor for class edu.sdsc.sirius.rasmol.AminoColorScheme

AngleDialog - class edu.sdsc.sirius.dialogs.AngleDialog.

This class impements a dialog box used to input the three atoms required to calculate a bond angle.

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

This method creates an instance of the AngleDialog class.

AngleMonitorDialog - class edu.sdsc.sirius.dialogs.AngleMonitorDialog.

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

AnnotationComponent - class edu.sdsc.mbt.AnnotationComponent.

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

AnnotationComponentRegistry - class edu.sdsc.mbt.AnnotationComponentRegistry.

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

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

This class provides the base functionality for geometry factory objects.

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

AppletLauncher3D - class AppletLauncher3D.

Basic JOGL installer for Applets.

AppletLauncher3D() - Constructor for class AppletLauncher3D

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

ArrowComponent - class edu.sdsc.mbt.ArrowComponent.

ArrowComponent(double[], double[], double, float[]) - Constructor for class edu.sdsc.mbt.ArrowComponent

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

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

Construct a new MonitorGeometry object.

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

Atom - class edu.sdsc.mbt.Atom.

Implements a StructureComponent container for atom data.

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

Creates a new Atom object and initializes the StructureComponent "structure" field.

Atom - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom.

A simple holder for atomic data from a PDB entry.

Atom(int, String, char, String, char, int, int, char, Vec3f, float, float, String, String, String) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom

Supply all the fields necessary to define an atom.

AtomColor - interface edu.sdsc.mbt.viewables.AtomColor.

This interface defines how all AtomColor implementation classes should generate a color for a given atomIndex+Atom.

AtomColorByCharge - class edu.sdsc.mbt.viewables.AtomColorByCharge.

AtomColorByElement - class edu.sdsc.mbt.viewables.AtomColorByElement.

This class implements the AtomColor interface by applying a color to the given atomIndex+Atom by using the ElementColor class.

AtomColorFactory - class edu.sdsc.mbt.viewables.AtomColorFactory.

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

AtomColorRegistry - class edu.sdsc.mbt.viewables.AtomColorRegistry.

A class used to register AtomColor implementation objects.

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

AtomColorUniform - class edu.sdsc.mbt.viewables.AtomColorUniform.

AtomDialog - class edu.sdsc.sirius.dialogs.AtomDialog.

This class serves two purposes: specify an atom to delete or get a name of the atom(s) to be selected.

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

AtomFilter - class edu.sdsc.mbt.filters.AtomFilter.

Defines a StructureComponentFilter sub-class which handles Atom type StructureComponent objects.

AtomFilter() - Constructor for class edu.sdsc.mbt.filters.AtomFilter

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

AtomGeometry.java
Please complete these missing tags

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

Construct a new AtomGeometry object.

AtomLabel - interface edu.sdsc.mbt.viewables.AtomLabel.

This interface defines how all AtomLabel implementation classes should generate a String label for a given Atom.

AtomLabelByAtomCompound - class edu.sdsc.mbt.viewables.AtomLabelByAtomCompound.

This class implements the AtomLabel interface by producing a string label from the Atom record's compound.

AtomLabelByAtomElement - class edu.sdsc.mbt.viewables.AtomLabelByAtomElement.

This class implements the AtomLabel interface by producing a string label from the Atom record's element.

AtomLabelByAtomName - class edu.sdsc.mbt.viewables.AtomLabelByAtomName.

This class implements the AtomLabel interface by producing a string label from the Atom record's name.

AtomLabelByChainId - class edu.sdsc.mbt.viewables.AtomLabelByChainId.

This class implements the AtomLabel interface by producing a string label from the Atom record's chain_id.

AtomLabelNone - class edu.sdsc.mbt.viewables.AtomLabelNone.

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

AtomLabelRegistry - class edu.sdsc.mbt.viewables.AtomLabelRegistry.

A class used to register AtomLabel implementation objects.

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

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

Construct a new object for generating bond geometry using default

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

Construct a new BondGeometry object.

AtomRadius - interface edu.sdsc.mbt.viewables.AtomRadius.

This interface defines how all AtomRadius implementation classes should generate a radius for a given atomIndex+Atom.

AtomRadiusByConstant - class edu.sdsc.mbt.viewables.AtomRadiusByConstant.

This class implements the AtomRadius interface by applying a radius to the given an Atom by using the radius of the bond.

AtomRadiusByCpk - class edu.sdsc.mbt.viewables.AtomRadiusByCpk.

This class implements the AtomRadius interface by applying a radius to the given an Atom by using the ElementRadius class.

AtomRadiusByScaledCpk - class edu.sdsc.mbt.viewables.AtomRadiusByScaledCpk.

This class implements the AtomRadius interface by applying a radius to the given an Atom by using the ElementRadius class.

AtomRadiusRegistry - class edu.sdsc.mbt.viewables.AtomRadiusRegistry.

A class used to register AtomRadius implementation objects.

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

AtomRenameDialog - class edu.sdsc.sirius.dialogs.AtomRenameDialog.

AtomRenameDialog(JFrame) - Constructor for class edu.sdsc.sirius.dialogs.AtomRenameDialog

AtomStats - class edu.sdsc.mbt.util.AtomStats.

The AtomStats class provides a number of static methods for computing useful information about a collection of Atom objects.

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

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

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

Accept ALL Atom objects.

accept(StructureComponent) - Method in class edu.sdsc.mbt.filters.CAlphaAtomFilter

Accept only C-Alpha Atom objects.

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

Ask the relation object if the object should be accepted or not.

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

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

accept(Path[], boolean[]) - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Filter

accept(Path) - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Filter

accept(Path[], boolean[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtom

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

accept(Path[], boolean[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomAll

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

accept(Path[], boolean[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByChain

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

accept(Path[], boolean[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByName

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

accept(Path[], boolean[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByType

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

accept(Path[], boolean[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNum

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

accept(Path[], boolean[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNumAndCh

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

accept(Path[], boolean[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterResidue

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

accept(Path[], boolean[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterResidueByName

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

accept(Path[], boolean[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.LogicalGroup

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

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

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

acceptSelection() - Method in class edu.sdsc.sirius.dialogs.JFontChooser

This method is called when the user presses the okay button, selecting the currently displayed font.

accession - Variable in class edu.sdsc.sirius.dialogs.TableImpl.BlastLineData

actionPerformed(ActionEvent) - Method in class edu.sdsc.sirius.dialogs.ElementSelectionPanel.PtListener

actionPerformed(ActionEvent) - Method in class edu.sdsc.sirius.dialogs.ElementStylesEditor.PtListener

actionPerformed(ActionEvent) - Method in class edu.sdsc.sirius.dialogs.JFontChooser

Processes action events from the okay and cancel buttons as well as the current size TextField.

actionPerformed(ActionEvent) - Method in class edu.sdsc.sirius.util.FileCloseListener

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

add(double[], double[]) - Method in class edu.sdsc.mbt.util.Octree

???

add(String, AtomColor) - Static method in class edu.sdsc.mbt.viewables.AtomColorRegistry

Add a new AtomColor implementation.

add(String, AtomLabel) - Static method in class edu.sdsc.mbt.viewables.AtomLabelRegistry

Add a new AtomLabel implementation.

add(String, AtomRadius) - Static method in class edu.sdsc.mbt.viewables.AtomRadiusRegistry

Add a new AtomRadius implementation.

add(String, BondColor) - Static method in class edu.sdsc.mbt.viewables.BondColorRegistry

Add a new BondColor implementation.

add(String, BondForm) - Static method in class edu.sdsc.mbt.viewables.BondFormRegistry

Add a new BondForm implementation.

add(String, BondLabel) - Static method in class edu.sdsc.mbt.viewables.BondLabelRegistry

Add a new BondLabel implementation.

add(String, BondRadius) - Static method in class edu.sdsc.mbt.viewables.BondRadiusRegistry

Add a new BondRadius implementation.

add(String, ChainColor) - Static method in class edu.sdsc.mbt.viewables.ChainColorRegistry

Add a new ChainColor implementation.

add(String, FragmentColor) - Static method in class edu.sdsc.mbt.viewables.FragmentColorRegistry

Add a new FragmentColor implementation.

add(String, FragmentForm) - Static method in class edu.sdsc.mbt.viewables.FragmentFormRegistry

Add a new FragmentForm implementation.

add(String, ResidueColor) - Static method in class edu.sdsc.mbt.viewables.ResidueColorRegistry

Add a new ResidueColor implementation.

add(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f

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

addAtom(Atom) - Method in class edu.sdsc.mbt.Residue

Add an Atom record to this Residue.

addAtom(Atom, Residue, boolean) - Method in class edu.sdsc.mbt.StructureMap

addAtom(Atom, Atom, Bond, boolean) - Method in class edu.sdsc.mbt.StructureMap

addAtom(Atom, Residue, String) - Method in class edu.sdsc.mbt.StructureMap

Simply add an atom to the records don't assign bonds (they may be added later), and assign number based on the current numbering in the structure residue is a new Residue object that will be added to the structure (subsequent atoms may be added to the same residue from the calling method)

addAtom(Atom, Residue, int, String) - Method in class edu.sdsc.mbt.StructureMap

Adds a new atom with the specified position of the residue (if new)

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

addAtom(Atom) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue

Add an atom to the residue.

addAtom(Atom, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

This method assumes that the necessary bookkeeping operations on StructureMap have been done, and it figures out what renderables are needed depending on the current display mode of the atom the new one gets connected to

addAtom(Atom) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser

addBond(Bond) - Method in class edu.sdsc.mbt.StructureMap

Add a Bond to the StructureMap.

addBonds(Vector) - Method in class edu.sdsc.mbt.StructureMap

Add a vector of Bond objects to the StructureMap.

addBonds(Vector, boolean, boolean, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

This method takes care of geometry and consistency of representation of the new bonds between structure map and structure styles

addChain(Chain) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Model

Add the given Chain to this Model.

addChild(GlRenderable) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.TransformGroupRenderable

xxx.

addCustomFragment(Structure, String, Vector, double[], double[]) - Static method in class edu.sdsc.sirius.builder.FragmentRegistry

addCustomFragment(Structure, String, Vector, double[], double[]) - Static method in class edu.sdsc.sirius.builder.FragmentUtil

addData(DataBlock) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataSet

Adds a block to this DataSet

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

addEntry(Entry, boolean) - Method in class Viewer

addEntry(Entry) - Method in class edu.sdsc.mbt.viewables.StructureDocument

Add an Entry to the list of managed/viewed structures, then send an event to inform all registered Viewer objects.

addEntry(Entry, boolean) - Method in interface edu.sdsc.sirius.util.Manager

Adds the specified Entry to the application.

addEntryLoader(EntryLoader) - Static method in class edu.sdsc.sirius.io.EntryFactory

Add (register) an EntryLoader object thus enabling the EntryFactory class to load data with it.

addEntryRecord(Entry) - Method in class edu.sdsc.mbt.viewables.StructureDocument

addLayoutComponent(String, Component) - Method in class edu.sdsc.sirius.util.DialogLayout

addLayoutComponent(String, Component) - Method in class edu.sdsc.sirius.util.ExtensionLayout

addModel(Model) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Pdb

Add the given Model to this Pdb.

addMoveEventListener(MoveEventListener) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

addPickEventListener(GvPickEventListener) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

Add a pick event listener.

addRelation(StructureComponentRelation) - Static method in class edu.sdsc.mbt.StructureComponentRegistry

Register a new StructureComponent relation.

addRenderable(Renderable) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

Add a new renderable object to the scene.

addResidue(Residue) - Method in class edu.sdsc.mbt.Chain

Add a Residue record to this Chain.

addResidue(Residue, int) - Method in class edu.sdsc.mbt.Chain

Add a Residue record to this Chain at the specified position.

addResidue(Residue) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Chain

Add the supplied Residue to the list of Residues in this chain.

addRibbon(Chain, int, float, float, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

addSequence(Sequence) - Method in class edu.sdsc.sirius.io.SequenceEntry

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

addServicePanel(FragmentGroupPanel) - Static method in class edu.sdsc.sirius.builder.FragmentRegistry

addStatusListener(StatusListener) - Static method in class edu.sdsc.mbt.util.Status

Add a StatusListener object in order to start recieving StatusEvent messages.

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

This method incorporates a new structure (fragment) into this structure by importing all data structures and updating names

addStructureComponent(StructureComponent, short, short, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles

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

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

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

Please complete the missing tags for main

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

This method imports styles from a different StructureStyles object

addType(String) - Static method in class edu.sdsc.mbt.StructureComponentRegistry

Register a new StructureComponent type.

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

addViewer(Viewer) - Method in class edu.sdsc.mbt.viewables.StructureDocument

Add a Viewer to the list of viewers.

addWBEntry(String, String, int, String, String) - Method in class edu.sdsc.sirius.workbench.WBManager

Register incoming data items from the list retrieved from the workbench server.

adjustHScrollBar(boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

adjustVScrollBar(boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

align(String) - Static method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentService

alignStructures(Structure, int, String, Structure, int, String, StructureAlignmentDialog) - Method in class edu.sdsc.sirius.viewers.StructureViewer

This method uses a local copy of compiled CE executable.

aligned - Variable in class edu.sdsc.sirius.util.StructureItem

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

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

alphabet - Static variable in class edu.sdsc.sirius.util.DataService

aminoacid - Variable in class edu.sdsc.sirius.builder.FragmentRecord

angle(double[], double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra

Calculate the angle formed by three virtex coordinates.

angleAxisRotate(double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra

Rotate the point by the given angle-axis {angle,x,y,z} rotation vector.

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

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

Determines whether any structure styles object has any selection

append(Object) - Method in class edu.sdsc.mbt.util.RangeMap

Append a new value (increasing the range maximum by 1).

appendBonds(OctreeDataItem, double, Vector) - Method in class edu.sdsc.mbt.util.Octree

???

appendHBondInfo(double[], int, double, int, Vector) - Method in class edu.sdsc.mbt.util.Octree

appendHBonds(OctreeDataItem, double, int, Vector) - Method in class edu.sdsc.mbt.util.Octree

???

applyConfiguration() - Method in class edu.sdsc.mbt.viewables.ElementPreferences

Apply currently stored in this instance colors to ElementStyles.

atom - Variable in class edu.sdsc.mbt.LabelComponent

atom1 - Variable in class edu.sdsc.mbt.HydrogenBondComponent

atom1 - Variable in class edu.sdsc.mbt.MonitorComponent

atom1 - Variable in class edu.sdsc.mbt.StericBumpComponent

atom2 - Variable in class edu.sdsc.mbt.HydrogenBondComponent

atom2 - Variable in class edu.sdsc.mbt.MonitorComponent

atom2 - Variable in class edu.sdsc.mbt.StericBumpComponent

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

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

atomLabels - Variable in class edu.sdsc.sirius.dialogs.StructureEvent

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

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

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

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

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

atoms - Variable in class edu.sdsc.sirius.dialogs.StructureEvent

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

attachmentAtom - Variable in class edu.sdsc.sirius.builder.FragmentRecord

attachments - Variable in class edu.sdsc.sirius.builder.FragmentRecord

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

The main attribute that was changed in the StructureStyles object (see StructureStyles for a list of valid states).

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

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

autoCropAndScale(Image, int, int) - Static method in class edu.sdsc.mbt.image.ImageUtils

Find the edges of the input image using the upper left corner pixel color as the background color, automatically crop the image down to eliminate the excess background border, then scale the image (maintaining the correct aspect ratio of the input image) and then center the image with appropriate background padding of the specified output width and height.

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

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

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

averageNormals() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection