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

F

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

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

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

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

FORM_FLAT - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry

Specifies a rendering style of simple flat polygons.

FORM_LINES - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry

Specifies a rendering style of wireframe lines.

FORM_POINTS - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry

Specifies a rendering style of points.

FORM_THICK - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry

Specifies a rendering style of thick shaded polygons.

FRAGMENT_ENTRY - Static variable in class edu.sdsc.sirius.io.Entry

Factory - class com.jgoodies.uif_lite.component.Factory.

A very light version of the JGoodies UIFactory class.

Factory() - Constructor for class com.jgoodies.uif_lite.component.Factory

FastaEntryLoader - class edu.sdsc.sirius.io.FastaEntryLoader.

Implements the EntryLoader interface to enable reading of Fasta files either from local disk or from a URL.

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

FileCloseListener - class edu.sdsc.sirius.util.FileCloseListener.

FileCloseListener(Manager, StructureDocument, Entry, JMenuItem) - Constructor for class edu.sdsc.sirius.util.FileCloseListener

FileEntryLoader - interface edu.sdsc.sirius.io.FileEntryLoader.

Defines the standard interface for classes which know how to load a Structure from a file or url object.

FileLoader - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FileLoader.

FileLoader is a loader class for generating a PdbWrapper that allows an application to access a disk-based PDB file.

FileLoader(File) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FileLoader

Create a new FileLoader with the specified PDB file.

FileNameFilter - class edu.sdsc.sirius.util.FileNameFilter.

FileNameFilter(String, String) - Constructor for class edu.sdsc.sirius.util.FileNameFilter

FilePdbWrapper - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper.

The FilePdbWrapper class provides access to an instance of a PDB entry.

FilePdbWrapper(String, Vector) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper

Creates a FilePdbWrapper from the contents of a PDB entry.

FileTransfer - class edu.sdsc.sirius.io.FileTransfer.

copy or download a file.

FileTransfer(int) - Constructor for class edu.sdsc.sirius.io.FileTransfer

constructor

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

constructor

Filter - interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Filter.

FilterAtom - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtom.

FilterAtom() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtom

FilterAtomAll - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomAll.

FilterAtomAll() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomAll

FilterAtomAll(PdbWrapper) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomAll

FilterAtomByChain - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByChain.

FilterAtomByChain() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByChain

FilterAtomByName - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByName.

FilterAtomByName() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByName

FilterAtomByName(PdbWrapper) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByName

FilterAtomByType - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByType.

FilterAtomByType(PdbWrapper) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByType

FilterCaByResNum - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNum.

FilterCaByResNum() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNum

FilterCaByResNum(PdbWrapper) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNum

FilterCaByResNumAndCh - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNumAndCh.

FilterCaByResNumAndCh() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNumAndCh

FilterCaByResNumAndCh(PdbWrapper) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNumAndCh

FilterResidue - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterResidue.

FilterResidue() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterResidue

FilterResidueByName - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterResidueByName.

FilterResidueByName(PdbWrapper) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterResidueByName

FogDialog - class edu.sdsc.sirius.dialogs.FogDialog.

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

Fragment - class edu.sdsc.mbt.Fragment.

Implements a StructureComponent container for secondary structure fragment information.

Fragment(int, int, String) - Constructor for class edu.sdsc.mbt.Fragment

Construct a Fragment for the given start Residue index, end Residue index, and conformation type.

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

Constructor variant used when there will likely be an atom list.

FragmentButton - class edu.sdsc.sirius.builder.FragmentButton.

FragmentButton(FragmentRecord, FragmentGroupPanel) - Constructor for class edu.sdsc.sirius.builder.FragmentButton

FragmentButton(FragmentRecord, ReplaceResidueDialog) - Constructor for class edu.sdsc.sirius.builder.FragmentButton

FragmentColor - interface edu.sdsc.mbt.viewables.FragmentColor.

This interface defines how all FragmentColor implementation classes should generate a color for a given Fragment.

FragmentColorByType - class edu.sdsc.mbt.viewables.FragmentColorByType.

This class implements the FragmentColor interface by applying a color to the given Fragment by using its Conformation type.

FragmentColorRegistry - class edu.sdsc.mbt.viewables.FragmentColorRegistry.

A class used to register FragmentColor implementation objects.

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

FragmentEntry - class edu.sdsc.sirius.io.FragmentEntry.

This class is a container for any information that may be associated with a database entry, such as sequence, structure, organism, annotations, etc.

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

FragmentForm - interface edu.sdsc.mbt.viewables.FragmentForm.

This interface defines how all FragmentForm implementation classes should generate a style for a given Fragment.

FragmentFormCartoon - class edu.sdsc.mbt.viewables.FragmentFormCartoon.

This class implements the FragmentForm interface by applying a secondary structure cartoon style.

FragmentFormCylinder - class edu.sdsc.mbt.viewables.FragmentFormCylinder.

This class implements the FragmentForm interface by applying a cylinder style.

FragmentFormLadder - class edu.sdsc.mbt.viewables.FragmentFormLadder.

This class implements the FragmentForm interface by applying a secondary structure ladder style.

FragmentFormRegistry - class edu.sdsc.mbt.viewables.FragmentFormRegistry.

A class used to register FragmentForm implementation objects.

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

FragmentFormRibbon - class edu.sdsc.mbt.viewables.FragmentFormRibbon.

This class implements the FragmentForm interface by applying a ribbon style.

FragmentFormTube - class edu.sdsc.mbt.viewables.FragmentFormTube.

This class implements the FragmentForm interface by applying a tube style.

FragmentFormWireframe - class edu.sdsc.mbt.viewables.FragmentFormWireframe.

This class implements the FragmentForm interface by applying a wireframe style.

FragmentGroupPanel - interface edu.sdsc.sirius.builder.FragmentGroupPanel.

This is an interface for all panels that contain input parameters and output display capabilities for web services, e.g.

FragmentLoader - class edu.sdsc.sirius.io.FragmentLoader.

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

FragmentRecord - class edu.sdsc.sirius.builder.FragmentRecord.

FragmentRecord(String, String, String) - Constructor for class edu.sdsc.sirius.builder.FragmentRecord

FragmentRecord(String, String, String, Vector) - Constructor for class edu.sdsc.sirius.builder.FragmentRecord

FragmentRecord() - Constructor for class edu.sdsc.sirius.builder.FragmentRecord

FragmentRegistry - class edu.sdsc.sirius.builder.FragmentRegistry.

FragmentRegistry() - Constructor for class edu.sdsc.sirius.builder.FragmentRegistry

FragmentTooShortException - exception edu.sdsc.mbt.viewers.GLViewerImpl.FragmentTooShortException.

FragmentTooShortException is used to signal a condition in which a geometry representation of a secondary structure element can not be generated due to a too small number of coordinates.

FragmentUtil - class edu.sdsc.sirius.builder.FragmentUtil.

FragmentUtil() - Constructor for class edu.sdsc.sirius.builder.FragmentUtil

FrameRegistry - class edu.sdsc.mbt.util.FrameRegistry.

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

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

FrenetTrihedron encapsulates a LOCAL reference frame on a curve defined by the LOCAL tangent, normal and binormal vectors.

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

FrenetTrihedron(Vector3f, Vector3f, Vector3f) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron

FrenetTrihedron(Vector3f, Vector3f, Vector3f, int) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron

FrenetTrihedron(Vector3f, Vector3f, Vector3f, Vector3f) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron

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

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

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

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

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

findEdges(int[], int, int) - Static method in class edu.sdsc.mbt.image.ImageUtils

Find the edges of the image by finding the min/max x,y coordinate where pixels are a different color than the upper left pixel.

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

fireMoveEvent(MoveEvent) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

Fire a pick event to all listeners.

firePickEvent(GvPickEvent) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

Fire a pick event to all listeners.

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

fitView(double[], double) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

fixTanCoeff() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite

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

The accelerator flag used for visibility and selections that apply to the entire structure (see StructureStyles for a list of valid states).

flag - Variable in class edu.sdsc.sirius.dialogs.ViewEvent

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

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

this method places camera at 15 A from the specified atom and focus view on it

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

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

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

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

font - Variable in class edu.sdsc.mbt.ResidueLabelComponent

font - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.DisplayParameters

fontAscent - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.DisplayParameters

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

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

Force field type indicates the kind of atom depending on the atoms it's bonded to

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

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

freeGlResources(GL) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlAxesRenderable

freeGlResources(GL) - Method in interface edu.sdsc.mbt.viewers.GLViewerImpl.GlRenderable

freeGlResources(GL) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.MbtRenderable

freeGlResources(GL) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorRenderable

freeGlResources(GL) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.TransformGroupRenderable