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

L

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

LARGE_FONT - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.LabelGeometry

LEVEL_DEBUG - Static variable in class edu.sdsc.mbt.util.Status

On a scale of 1 to 5, how important is the message.

LEVEL_DUMP - Static variable in class edu.sdsc.mbt.util.Status

On a scale of 1 to 5, how important is the message.

LEVEL_ERROR - Static variable in class edu.sdsc.mbt.util.Status

On a scale of 1 to 5, how important is the message.

LEVEL_QUIET - Static variable in class edu.sdsc.mbt.util.Status

On a scale of 1 to 5, how important is the message.

LEVEL_REMARK - Static variable in class edu.sdsc.mbt.util.Status

On a scale of 1 to 5, how important is the message.

LEVEL_WARNING - Static variable in class edu.sdsc.mbt.util.Status

On a scale of 1 to 5, how important is the message.

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

LINEAR - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.Interpolator

LOAD_STRUCTURE - Static variable in class edu.sdsc.sirius.dialogs.EntryListerDialog

LabelComponent - class edu.sdsc.mbt.LabelComponent.

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

LabelComponent(Atom, int, int, String, boolean, float[]) - Constructor for class edu.sdsc.mbt.LabelComponent

LabelDialog - class edu.sdsc.sirius.dialogs.LabelDialog.

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

LabelEvent - class edu.sdsc.sirius.dialogs.LabelEvent.

LabelEvent(DisplayDialog) - Constructor for class edu.sdsc.sirius.dialogs.LabelEvent

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

Construct a new object for generating bond geometry using default

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

Construct a new MonitorGeometry object.

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

LimitedLengthDocument - class edu.sdsc.sirius.util.LimitedLengthDocument.

This class implements a field with fixed length.

LimitedLengthDocument(int) - Constructor for class edu.sdsc.sirius.util.LimitedLengthDocument

Contructor that creates a field with the specified maximum length.

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

A container class for data displayed in one row of the table of ResultPanel.

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

LineData(String, String, String, String, boolean) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.LineData

Constructor that initializes values of the fields.

ListerDialog - interface edu.sdsc.sirius.dialogs.ListerDialog.

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

Loader is the parent class for a group of I/O classes that can read and write PDB format files in various ways, such as to file or URL.

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

Location - class edu.sdsc.sirius.util.Location.

This class contains two vectors and a position point that define location and orientation of an object in 3D space

Location(double[], double[], double[]) - Constructor for class edu.sdsc.sirius.util.Location

Location(double[], double[], double[], double[]) - Constructor for class edu.sdsc.sirius.util.Location

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

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

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

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

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

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

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

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

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

Returns structure component identified by the given string

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

lastEntry() - Method in class edu.sdsc.sirius.dialogs.DataWBListerDialog

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

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

leftPadded(String, int, String) - Static method in class edu.sdsc.sirius.util.StringUtils

Pads a String on the left.

leftPadded(String, int, char) - Static method in class edu.sdsc.sirius.util.StringUtils

Pads a String on the left.

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

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

The message level.

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

levels - Variable in class edu.sdsc.mbt.util.Octree

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

load() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FileLoader

Return a PdbWrapper implementation that contains the current PDB file.

load() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.Loader

load() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlLoader

Return a PdbWrapper implementation that contains the current PDB file.

load() - Method in class edu.sdsc.sirius.dialogs.ImageFileChooser

Prompt the user to load an image file using any of the supported Image Format plug-ins.

load(String, int) - Method in class edu.sdsc.sirius.io.AlnEntryLoader

Loads an EntrySet from a file identified by a name

load(File, int) - Method in class edu.sdsc.sirius.io.AlnEntryLoader

Load an EntrySet from a file.

load(URL, int) - Method in class edu.sdsc.sirius.io.AlnEntryLoader

Load an EntrySet from a URL.

load(BufferedInputStream) - Method in class edu.sdsc.sirius.io.AlnEntryLoader

Loads an EntrySet from a BufferedInputStream.

load(File, int) - Static method in class edu.sdsc.sirius.io.EntryFactory

Walk through the set of registered FileEntryLoader implementations and use the first capable loader to load the Structure the file.

load(URL, int) - Static method in class edu.sdsc.sirius.io.EntryFactory

Walk through the set of registered FileEntryLoader implementations and use the first capable loader to load the Entry from the URL.

load(String, int) - Static method in class edu.sdsc.sirius.io.EntryFactory

Walk through all registered EntryLoader implementations and use the first capable loader to load the Entry.

load(String, int) - Method in interface edu.sdsc.sirius.io.EntryLoader

Returns a reference to a named structure as an Entry object.

load(String, int) - Method in class edu.sdsc.sirius.io.FastaEntryLoader

Returns a reference to a named structure as a Entry object.

load(File, int) - Method in class edu.sdsc.sirius.io.FastaEntryLoader

Returns a reference to an Entry read from the given File object.

load(URL, int) - Method in class edu.sdsc.sirius.io.FastaEntryLoader

Returns a reference to an Entry read from the given URL object.

load(File, int) - Method in interface edu.sdsc.sirius.io.FileEntryLoader

Load an entry from a File object.

load(URL, int) - Method in interface edu.sdsc.sirius.io.FileEntryLoader

Load a entry from a URL object.

load(String, int) - Method in class edu.sdsc.sirius.io.Mol2EntryLoader

Loads the Entry by file name.

load(File, int) - Method in class edu.sdsc.sirius.io.Mol2EntryLoader

Loads the Entry from a File object.

load(URL, int) - Method in class edu.sdsc.sirius.io.Mol2EntryLoader

Loads the Entry from a URL object.

load(String, int) - Method in class edu.sdsc.sirius.io.MsfEntryLoader

Loads an EntrySet from a file identified by a name

load(File, int) - Method in class edu.sdsc.sirius.io.MsfEntryLoader

Load an EntrySet from a file.

load(URL, int) - Method in class edu.sdsc.sirius.io.MsfEntryLoader

Load an EntrySet from a URL.

load(BufferedInputStream) - Method in class edu.sdsc.sirius.io.MsfEntryLoader

Loads an EntrySet from a BufferedInputStream.

load(String, int) - Method in class edu.sdsc.sirius.io.PdbEntryLoader

Loads the Entry by file name.

load(File, int) - Method in class edu.sdsc.sirius.io.PdbEntryLoader

Loads the Entry from a File object.

load(URL, int) - Method in class edu.sdsc.sirius.io.PdbEntryLoader

Loads the Entry from a URL object.

load(URL, int) - Method in class edu.sdsc.sirius.io.SDFEntryLoader

load(String, int) - Method in class edu.sdsc.sirius.io.SDFEntryLoader

load(File, int) - Method in class edu.sdsc.sirius.io.SDFEntryLoader

This method returns a Vector of Entry objects from the SDF file it reads

loadAln(String) - Static method in class edu.sdsc.sirius.util.IOHandler

loadFasta(String) - Static method in class edu.sdsc.sirius.util.IOHandler

loadFile(File) - Method in class Viewer

loadFragment(String) - Method in class Viewer

loadFragment(String) - Static method in class edu.sdsc.sirius.io.EntryFactory

loadFragment(String) - Method in class edu.sdsc.sirius.io.FragmentLoader

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

Loads fragment with specified id into the structure viewer.

loadFragmentComponents(String) - Static method in class edu.sdsc.sirius.io.EntryFactory

This method determines whether the fragment is custom or standard, and call the fragment loader accordingly

loadFragmentComponents(String, boolean) - Method in class edu.sdsc.sirius.io.FragmentLoader

loadGenbank(String) - Static method in class edu.sdsc.sirius.util.IOHandler

loadMol2FromString(String) - Static method in class edu.sdsc.sirius.util.IOHandler

loadMsf(String) - Static method in class edu.sdsc.sirius.util.IOHandler

loadPDBFromString(String, int) - Static method in class edu.sdsc.sirius.util.IOHandler

loadSelected() - Method in class edu.sdsc.sirius.workbench.WBListPanel

Loads selected data item into the SiriusWB workspace

loadSelection() - Method in class edu.sdsc.sirius.dialogs.DataListerDialog

loadSelection() - Method in class edu.sdsc.sirius.dialogs.DataWBListerDialog

This method loads the selected model from the entry.

loadStructure(File) - Method in class edu.sdsc.sirius.io.Mol2EntryLoader

Returns a reference to a Structure read from the given File object.

loadStructure(URL) - Method in class edu.sdsc.sirius.io.Mol2EntryLoader

Returns a reference to a Structure read from the given URL object.

loadStructure(BufferedInputStream) - Method in class edu.sdsc.sirius.io.Mol2EntryLoader

Returns a reference to a Structure read from the given (uncompressed) InputStream.

loadStructure(URL, int) - Method in class edu.sdsc.sirius.io.PdbEntryLoader

Returns a reference to a Structure read from the given URL object.

loadStructure(File, int) - Method in class edu.sdsc.sirius.io.PdbEntryLoader

loadStructure(BufferedInputStream, int) - Method in class edu.sdsc.sirius.io.PdbEntryLoader

Returns a reference to a Structure read from the given (uncompressed) InputStream.

loadUniprot(String) - Static method in class edu.sdsc.sirius.util.IOHandler

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

This method loads the specified entry from the workbench server.

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

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

Move the camera to the specified eye point and orient the view toward the specified 3D center point with a given up vector.

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

Rotate and refocus the camera at the specified 3D point, but keep the current eye location and up orientation of the camera.

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

Move the camera to the specified eye point and orient the view toward the specified 3D center point.

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

lookAt - Variable in class edu.sdsc.sirius.util.Location